You might have heard it in the past few months: some areas of the Internet are buzzing with discussions on “generative art”, that is, artwork generated from “AI” models that were fed with an absurdly large amount of images as training as a base. There are supporters, there are critics, and techology advances: among all this, this post offers my humble experience with computer-generated imagery. In this post, you’ll be guided by Yumiko, Satsuki, and Maya: the first two are characters created by someone else I know (who wants to remain anonymous) which I then expanded, cooperating with their creator in a certain project from a few years ago; the latter is… well, a character with an interesting history, which will be explained later.

After quite a long time, I was finally able to take a look at this series: a rather atypical mecha show that despite some bad production, still manages to be interesting.

Header image credit: 1840151sudarshan (Wikimedia Commons, CC BY-SA) A while ago I posted a way to download 実況動画 from Nicovideo. One of my acquaintances publishes videos there, and he wanted to collect the various comments to reply in a follow up video (what the Nico users call the コメント返し). When the comments are more than just a few, it’s hard to find where they refer to without watching them on Nicovideo itself, and its UI is suboptimal.

実況? Is it something edible? In recent times, I’ve been watching a lot of VOICEROID実況 (じっきょう, jikkyou, literally “commentary”) videos from the rather famous (in Japan) video service ニコニコ動画, better known as “Nicovideo”. In this case, the commentary actually refers to games: they’re basically a Japanese version of the Let’s Play videos that are all around other places like YouTube. The difference from “regular” videos lies in the “VOICEROID” term: this is a name of a TTS software developed by AH Software using an engine devised by a company called AI Inc.

Following up on yesterday’s release, I’ve released Danbooru Client 0.3.0. This early new release is mostly due to the fact that the QML view file wasn’t installed (sorry!) so part of the UI would not even load (or even crash). That said, I’ve managed to get some extra features in: Fade-in/out animation when posts are being downloaded Support for tagging is back (EXPERIMENTAL): it is optional, and requires KFileMetaData (not yet a framework, but should be distributed with Plasma 5).

After my previous post, development went quicker than expected, so I’ve actually managed to get a real version out. ;) So without much ado… here’s Danbooru Client 0.2.0! This redesigned C++ version brings a few more features compared to the PyKDE4 version, notably: Infinite scrolling (experimental) - Just scroll down to load the next set of posts QML-based thumbnail view Click on the image below to have a demonstration of what’s in this release (warning: 2M GIF file): [!

I’m a (happy!) owner of a Casio EX-WORD Dataplus 5 XD-A4700, a Japanese electronic dictionary. Recently I looked into updating the Japanese-English dictionary (currently the Shogakukan PROGRESSIVE dictionary) installed, because it’s not good enough: too often when looking up odd sentences (like the ones in Fate/Extra CCC) I do not find any matches. EDICT is adequate, and while I can use it on my phone and tablet, I like the fact that the EX-WORD has a physical keyboard along with the stylus, and a very nice kanji handwriting recognition.

[]({{ site.url }}/images/2013/01/mmBvi.jpg)

A few days ago I finally completed (after about 3 months) 神次元ゲームネプテューヌV, or “Kami Jigen Game Neptune V”, the latest instalment from Compile Heart in the Neptune franchise of PS3 games. It took quite a while (approximately 3 months), and I think it’s about time to wrap things up.

Sometimes Christmas presents are really unexpected, and today I found out I was given one such gift: the limited edition of _THE IDOLM@STER 2, _PS3 version. It was quite a bulky box, showing all the main characters from the game (and from the recently-ended anime) (click to enlarge):  Of course, having such a box means that there’s a lot of stuff inside. In fact, once opened, there are two game BDs (one being the actual game, the second being the first volume of Gravure for you!

By browsing through sites, I noticed that the Spanish site Akihabara Denno Gumi Universe has posted a translation of an interview the webmaster had with me through email. Here it is (Spanish language). It feels nice to recall some memories of the past once in a while, especially since I couldn’t still believe that dennogumi.org had been such a resource back in the days…

Recently I had the opportunity of viewing a DVD that I had bought in 2006 but never had the chance of seeing: it was the third season of Galaxy Angel, of which I had already viewed the first two years before. After viewing it, I realized I could have viewed it sooner, as I liked it quite a bit. Not only that, but I brought myself up to speed by getting what was left in the series, that is the second half of the third season (marketed by Bandai Visual as Galaxy Angel AA) and the fourth and final season (known in the English speaking market as Galaxy Angel X).

Well, I found the whole franchise quite good: and after having explored also other bits of it, including the manga and the games related to it, I thought it’d be nice to have a retrospective with my own views. Which is the point of this post.

Some of the oldest readers of this blog are well aware of [a certain hobby of mine]({{ site.url }}/category/anime). Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on. Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated?

 It’s been a while since I blogged about anything non-FOSS. This time I’ll be sharing some impressions on one of the games I’m playing at the moment, that is,** Ar Tonelico III** (which arrived at my doorstep two days ago). I admit I haven’t been a fan of Gust games (aside from Ar Tonelico, they’re known mostly for the Atelier series), mostly because technically wise they didn’t really perform that well.

Sometimes answering apparently harmless questions on instant messaging can have unexpected results. In particular, I was telling about Danbooru Client to someone and a question popped up “Why don’t you support pages?”. It seemed a nice idea, so I branched off the code (yay for git!) and started working on it. Well, it took me more than a month to get this thing done… I didn’t spend every day coding, but it was a challenge.

A while ago I presented [“danbooru2nepomuk”]({{ site.url }}/2009/10/danbooru2nepomuk-a-nepomuk-tagger-for-danbooru-images), a small program to tag images coming from Danbooru-based image boards. Today I want to present the evolution of that program, that is a PyKDE4 client for those boards.

Today, after some customs delay and courier problems, I finally received the first volume of Tears to Tiara. Having got a PS3, I chose the Blu-Ray version (priced 8,192 yen, quite steep if you hear me): as I preordered it soon enough, I got the first presse edition, which, according to CDJapan, was comprised of a “deluxe outer case”, a “stick poster” and a booklet, in addition to the Blu-ray itself.


So I’ve heard that _Tears to Tiara _is coming in animated form. Being in the middle of playing its PS3 incarnation, Tears to Tiara - Kaikan no Daichi, I decided to take a look at some images that have been recently published on news.dengeki.com. It was already known that the anime would be an adaptation of the PS3 game, which is a good thing (I didn’t like the original character design). Animation is done by _Oriental Light and _Magic (OLM), and the same staff who adapted another Aquaplus game, Utawarerumono (or should I say Underwater Ray Romano ? snicker).

[]({{ site.url }}/images/kurokamititle.jpg)

New season, new anime to see. Since a certain guy kept me telling wonders about Kurokami (黒神), a manga serialized in Young Gangan by Dall-Young Lim and Sung-woo Park, two Korean artists, I decided to give a go to the animated version, produced by Bandai Visual, which has just been out.

It’s been a hot day here in Kyoto. And I don’t mean lame second meanings, just that the temperature was really over the top. As a consequence, we changed our plans: we were supposed to visit the so-called “path of the philosophy” but instead we set for Nijo Castle. Nijo Castle was the Kyoto residence of Ieyasu Tokugawa (I suspect to tell the emperor who was the real person in power) and it can be visited.

I’m aching all over but I managed to write this entry. Today I went to the Ueno area first, hoping to go to the National Museum: however I forgot it was closed on Mondays, so I had to go to the National Science Museum instead. It turned out that it wasn’t a bad choice after all, as the museum is rich with exhibits and has a very good presentation. After that we moved to the Toshogu Shrine in Ueno Park, a shrine that was dedicated to the shogun Ieyasu Tokugawa.

[]({{ site.url }}/images/2008/07/slayers3.jpg)

It’s been a long time since Slayers had aired on TV, basically since Slayers TRY was released, which means more than 10 years ago. Then, this year news told that two new series were planned, and this post is about the first episode (out of 13, aired on July 2nd; the second series will start sometime around January).

Yesterday I got a few novels that I’ve been waiting for a while: _Slayers _(the last two volumes published by Tokyopop, as ) and Shakugan no Shana 2. I bought the latter as a “final warning” because I’m not very sure I’ll ever continue: the first Shana was written poorly and with a plot that didn’t make much sense (but again, I don’t think the animated version was shining in that respect).

[]({{ site.url }}/images/2008/04/ookami_cover.png)

A rather large number of days ago I got the first DVD of Ookami to koshinryo, better known as Spice and Wolf, which I when the first episode was released. I got the limited edition, which came in with a number of extra features (which still don’t justify its ~ ¥6800 price tag, though). The main one is the inclusion of a 300 piece puzzle, illustrated by the artist who works on the original novels.

Interested by some promotional art and by a resemblance of the main female character to my brother’s own Yumiko, I took a look at the first episode of Ookami to Koshinryo, better known as Spice and Wolf. I’m being told it is inspired by a series of novels and that there is also a manga version.

For a change, my brother has found a place (DLsite.com) that sells dojinshi even to non-Japanese people, and also found three non-hentai Final Fantasy XI dojins, which I’m going to cover in this post. For reference, they are available with these prices:

• FFXI-URUSHI-Chaos: 01 - ¥ 735;

• FFXI-URUSHI-Chaos: 02 - ¥ 735;

• FFXI-URUSHI-Chaos:03 - ¥ 945.

When Tokyopop announced _Slayers, Kino no Tabi _and _Scrapped Princess _my interest was piqued: even more when I read about Seikai no Monsho. After getting what was available (three volumes of Scrapped Princess, the whole Seikai no Monsho trilogy and the single volume of Kino no Tabi) I waited for the rest.

[]({{ site.url }}/images/2007/11/patapi.png)

After a long time I’ve finally got hold (thanks, Melissa) of Akihabara Denno Gumi PataPi!, that is the manga version of Akihabara Denno Gumi (or Cyber Team in Akihabara, if you prefer): some of you may even remember a rather sparse description on this very page when it was still devoted to ADG (almost eight years ago, time flies…).

Straight out of my anime backlog, I watched the first episode of Clannad. I don’t know much about the original name (save for the time it took to be released), but I knew that the animation studio who did this series was Kyoto Animation (The Melancholy of Haruhi Suzumiya, Air, Kanon and Lucky Star).

From the already large backlog of new series, I recently watched the first episode of Prism Ark, an anime adaptation of the H-Game _PRISM ARK ~ PRISM HEART II ~ _by Pajamas Soft (I wonder how some Japanese companies get to choose their names…). It is being directed by Masami Obari, who did Dancougar Nova the last season.

I’m back from holidays, and when I got back I found the Saber Revoltech figure I had preordered in May (!) in the mail. This is the package when I pulled it out from the box it came in (apologies for the image quality, I only had my mobile phone to take it):

[]({{ site.url }}/images/2007/07/strikers_dvd_1_cover.png)

Today I got the first Maho Shojo Lyrical Nanoha StrikerS R2 DVD in the mail. Even though I haven’t watched it properly yet (I plan on doing so tomorrow) I can say I’m already impressed. Usually Japanese DVDs are little more than improved video tapes: they provide just the bare minimum (and not for a cheap price). However, this is not the case with Nanoha StrikerS.

According to the Anime News Network, Geneon Entertainment has bought the license for distributing Maho Shojo Lyrical Nanoha and Nanoha A’s in the United States. Fans rejoice? I think not. Being outside of the USA market, I view things with a different approach. The companies here in Italy have all their problems, but to a certain degree they care about delivering to the user something more than just the episodes. Extras that can also be an incentive over downloading (illegally) over the Internet.

Since I’ve been aggregated to the AnimeBlogger.net Antenna I noticed a number of new visitors coming to my blog. I’m taking the opportunity (see post title) to bring the attention on a pet project of mine, which is also quite tied to anime.

477 Yesterday I got the first DVD of Dancougar Nova in the mail. As it’s a first press edition, there were two nice postcards inside (one of the Dancougar itself, one of Aoi) and the cover is reversible, again showing either the mech or Aoi (the one shown in this post, which is also available in the gallery). So what has changed from the TV version? As far as I can tell, not much as the first two episodes were the ones with the best animation (along with episode 12) , though the DVD cover mentions something changed in episode 2.

I’ve seen very little talk about this anime, inspired by a short story by Shotaro Ishinomori, despite its obvious quality. I’ve seen five episodes so far (out of 12) and I can say I’m quite impressed by the results.

As expected, I couldn’t keep up with the backlog, so I’m again posting on two episodes of Nanoha StrikerS at once. The first one is still a training/preparation one, while the second has some action in it. But let’s look at them in the proper order…

It seems I can’t quite keep up with the episodes given my limited spare time (considering also I have the second book of The S.T.E.A.L. Saga to take care of), so here I am with a recap of the last two episodes of Maho Shojo Lyrical Nanoha StrikerS.

Ok, I _so _tried to keep separate posts for each series I watched. But there are so many, it’s impossible to keep up! (including also my limited time to write). I’ll just present them in reduced form here, along with a few comments.

When I first heard that GONZO was going to make an anime out of the work of William Shakespeare, I can say that I was interested, given their past record with Gankutsuô, namely the visionary adaptation of Alexandre Dumas’ The Count of Monte Cristo.

In an effort to clean up my backlog of entries (curse my tendinitis, luckily I’m going to get therapy soon), I’m posting about the series of the new season that I found interesting. I will start this by talking about the most recent Sunrise production, by the same staff of Mai-HiME and Mai-Otome: Idolm@ster XENOGLOSSIA.

The first episode of Maho Shojo Lyrical Nanoha StrikerS was aired in Japan recently, and I got the chance to see it. I admit I was rather interested because I liked both the original Nanoha and its sequel Nanoha A’s. Both redefined the “Magical Girl” genre, that was in my opinion somewhat stale since the end of Sailormoon, with many twists and a lot of added action.

And so again, I watched last week (yes, I am behind) the fourth episode of Dancougar Nova. The title looks promising: Akai Dancougar (The red Dancougar), which implies that there is another Dancougar around, although the opening animation already hinted at that.

Last week (this should show how behind I am in writing things) I watched the third episode of Dancougar Nova. This new episode gives an insight about what the group (nicknamed Team D where D stands for Dangerous - I am getting a deja vu with regards to Tekkaman Blade’s D-Boy…) is supposed to do and more details about the Dancougar itself.

I’ve watched the second episode of Dancougar Nova, titled Choju Gasshin! yesterday. The animation quality is on a good level (after Gravion I wasn’t so sure) throughout the episode, aside a couple of hiccups here and there.

Since almost everyone’s attention is focused on Naruto Shippuden, not many noticed that on Feb 15th a new mecha show was aired. Titled Juso Kiko Dancougar Nova, this anime is a remake/sequel (I need to figure this out) of the 198X series _Choju Kishin Dancougar _(Super Machine Beast God Dancougar), and coincidentally animated by the same studio (Ashi Productions).

By tracking the statistics of my blog, I noticed that many people came here from web pages that linked directly the old multimedia files I had on dennogumi.org when it was still an information page on Akihabara Denno Gumi. However they aren’t here anymore. I also kindly asked to avoid linking them directly when they were up, but I guess some people just don’t read. In short, if you have come here to get movies, or music files, you won’t find them.

Continuing after Mai-Otome, I gave a look to this OAV (first out of four, with the second one coming out in February).


A few days ago I finished watching Mai-Otome. The series itself was somewhat old (started in October 2005 and finished on 30th March 2006), but I got around to watch it only recently. I can say I’m satisfied with the overall result: overall Sunrise managed to create a better series than its sister, Mai-HiME.

Recently I’ve came across a promotional poster for the upcoming Nanoha StrikerS anime. However I think that this highly anticipated third instalment in the series will disappoint a few people, including myself. Why?

I’m adapting this from the infamous Steve Ballmer quote. This is to introduce the novels I bought recently from amazon.com (thanks to NRK for placing the order).

Recently, Galaxy Angel II has gone on air. I was very interested as I found the original series (and its four seasons, plus specials) to be rather entertaining and funny. So, I watched the first episode eagerly when I had a change to see it. I didn’t expect it to turn into a huge disappointment.

While I was viewing [Yamato Video]({{ site.url }}/www.yamatovideo.com)’s latest Samurai Troopers DVD, I noticed that in the trailers section there was a part showing off some footage of Chrno Crusade. As a few may know, it’s written Chrno and not Chrono for some obscure reason. What it matters though is that Planet Manga already edited the relevant manga with the name Chrono Crusade (same as what AD Vision did in the United States).

I’ve already explained in a previous entry that I like to tweak images, extract them from backgrounds and so on. However I didn’t like that I needed Windows to perform my actions, as I want to use that operating system as less as possible. I tried then to use FOSS (Free and Open Source Software) tools available on Linux to see if I could do the same job.

I like to tinker with images. I’ve been doing this since I first started doing amateur web design, back in 1996. At first it was to create images for my own web pages (Sailormoon, ADG) but nowadays it’s like a hobby I do when I have free time. It can be fun.

I got upgrade hardin (my laptop)’s memory at least, bringing it to 1Gb, at last. However I had two 256 Mb modules installed, that means I had to buy two 512 Mb ones. Oh well, I’ll just try to sell those ones. Everything seems snappier now, and even Firefox seems not to clog the CPU when loading pages (I need to experiment more, since I have no clue why that should have changed).

As the terrace in my house has been finally completed after almost a year, I’m writing from there. While I’m relaxing, I’ll write about two items I recently obtained through archonia.com. This time there wasn’t a misunderstanding like with the Tony Taka book I ordered (which the description didn’t claim it was an H book while instead it was), I’m quite satisfied by what I got.

I’ve watched Fate/stay night a couple of days ago and I can say I am quite enjoying this series. The development of the plot is going a little slow so I expect this anime to be 26 episodes long. My only disappointment is that despite Saber is one of the main characters, she hardly gets to do anything at all.

First of all, the strangest oddity ever. On Friday once at the laboratory I was contacted by an Affymetrix representative regarding [this entry ]({{ site.url }}/2006/01/26/badly-written-software-or-policy/). She wanted to know why I wrote it and that it seemed that I “didn’t contact Affymetrix to see if the problem could be solved”. She wasn’t offended or anything (she will even get me in touch with someone from the software department), but nevertheless this is my blog and I’m entitled to my personal opinions.

I got this one last week. Now that I’ve been 20+ hours into it, I guess I’ll write down some impressions. First of all, I’m pleasantly surprised by the quality of the translation. XSeed has done a much better job than Agetec (who did Wild ARMs - Alter Code: F), and they preserved the voices and the opening song (even if redubbed). I like the game system, it’s fst enough and there are platform-like parts that help in breaking up the monotony of dungeon crawling and fighting.

[]({{ site.url }}/images/saber.png) I just got around to see the first two episodes of this anime, which is an animated version of TYPE-MOON’s H game (without the H aspects, luckily). So far I like it. Despite being from Studio DEEN, the animation quality is good (for now) and the story seems intriguing enough to keep on watching. Music is by Kenji Kawai and is also nice.

The few people who know me may have heard of one of my pet projects, [S.T.E.A.L.]({{ site.url }}/interests/), whose draft PDF is available [here]({{ site.url }}/steal/steal.pdf). I’ve been trying for ages to get an illustrator to do some b/w art for it (a la Slayers), but always with bad results. I’ll be trying to commission it, now that I can afford it, let’s hope I can get some results done at least with money…

I recently got myself a couple of new books, thanks to the folks at Archonia: []({{ site.url }}/images/stvbook.jpeg){: .center-image } This is the first one, Sakura Taisen V Original & Format Collection. It’s like a very detailed encyclopedia on the game, including character profiles, sketches, interviews with the staff and the voice actors. It’s quite a thick book: I may think about scanning something in the future, but I’m not sure now.

(Note: I should really start posting more often nowadays) Last monday, for one of my group, I re-did one of the hardest missions of the whole Chains of Promathia expansion: PM6-4, better known as “One to be Feared”. I was looking forward to redoing it, mainly because I wanted to see if the adjustments that came after I finished the expansion (Sentinel modification, shield blocks modification, etc.) made the job easier.

I haven’t posted anything in a month or so. Quite a long time, considering I used to write at least once per week. The reasons are mainly two: first of all, my work schedule has taken a turn for the worse, which means I have to do my job a lot harder than before; secondly, there wasn’t much interesting stuff to report. Let’s resume from the hiatus by writing about my latest Final Fantasy XI session.

For a change, my brother has found a place (DLsite.com) that sells dojinshi even to non-Japanese people, and also found three non-hentai Final Fantasy XI dojins, which I’m going to cover in this post. For reference, they are available with these prices:

• FFXI-URUSHI-Chaos: 01 - ¥ 735;

• FFXI-URUSHI-Chaos: 02 - ¥ 735;

• FFXI-URUSHI-Chaos:03 - ¥ 945.

Despite the utter lack of content in Wings of the Goddess my brother has managed to create a movie clip (inspired by the opening of Wild ARMs The Vth Vanguard). You can view it below (streaming) or obtain a higher quality version. [googlevideo]http://video.google.com/videoplay?docid=8316261647217076877[/googlevideo] (apologies for the lack of updates. I’ve been quite busy. I will probably post more in during the Christmas holidays)

While I’m waiting for KDE 4.0 to compile, I just wanted to share a small clip of my brother’s character doing the Drain Samba animation. A bit of background: he has leveled Dancer up to level 7, and now he stopped because there is no artifact armor available yet (probably out in February) and because he’s also leveling another job, monk. Given how people rushed to get Dancer to 75 in less than a week (comments are left to the reader) it is a nice change.

[]({{ site.url }}/images/2007/11/pol-2007-11-30-14-56-28-86.png)

Finally my copy of Wings of the Goddess has arrived. It was just a matter of putting the DVD in the drive and let install the measly 350+ Mb of update (rather low for a DVD). As usual, Square Enix’s installation program is greedy with regards to information. Once it was installed, I enabled the expansion in PlayOnline and was good to go (save a 20,000+ file check).

With the new version update, these strange portals have been appearing throughout Vana’diel. They’re supposedly the gateways to the past, but since I don’t have Wings of the Goddess yet I can’t really see what will they do. Nevertheless, I was curious and went to take a look at them. They’re **huge. **I estimate at least twice the height of my character. For those curious, here are two photos (one is of my brother’s character, the other is mine):

And so, with yesterday’s update, FFXI has gained a windowed mode. This has been a much-requested feature from the playerbase, especially from people who didn’t want to use the “unofficial” windower.

However, being the first major touch to the rendering engine, I think something got broken along the way. Mainly, I’m talking about a 20% performance drop of the engine (which didn’t shine before, but that’s another matter).

And so I’m reading that the FFXI Fan Festival has kicked off yesterday (I wish I could have been there). Naturally, reports have been flowing. The FFXI Encyclopedia has a good report of what has been said so far. 1up, the online branch of EGM, has also covered the event, but the article is only focusing on the new jobs (talk about explaining something no one else will ask… not to mention the attitude of that “journalist”).

As most people know already, Square Enix has put a new trailer of Wings of the Goddess on their web page, which has been updated as well. Unlike Treasures of Aht Urghan, it looks that story-driven content will be more present. Also, the trailer shows much more of the story than ToAU’s (and apparently, new weapon skills!): I hope it is an indication that Square Enix has learnt from the problems of the previous expansions.

Yesterday I got word that the FFXI Encyclopedia, a wiki that I often go to read up on information and occasionally contribute, had been defaced. Apparently someone named “Taj” had hijacked the administrator account to change the main page to a short, anger-filled post that pointed to a discussion to the web site of Taj’s linkshell, the extremely famous “Urdr of the Blue Gartr”.

At last, I’ve made it!  Last Wednesday my group took on the last mission of this expansion, “Nashmeira’s Plea”. I was expecting something as tough as Dawn from Chains of Promathia, but that wasn’t the case.

It’s been a while since the update hit the servers, but I couldn’t get my static party up and in shape until last Wednesday. We had already done the introductory cutscenes, and we prepared for the fight (a Blue Mage and several Imperial Gears). My party was made up by Eithin (White Mage), Sechs (Puppetmaster), Necronemesi (Ranger), Mitsuashi (Red Mage) and Daman (Black Mage).

The FFXI Encyclopedia has an interview with the Final Fantasy XI developers with regards to the upcoming expansion, Wings of the Goddess. Skimming through the lines, they give a lot of hints but no definitive answers. Sadly, there will be no barriers for missions, and no one asked about their length: Treasures of Aht Urghan had very short missions, often ridicolously easy, so I’d like a better challenge this time.

On Wednesday we tried Mission 35 again and this time was a success. Daman was not present, but we’ll do another run for him on Sunday.

Due to maintenance, we couldn’t do Dynamis on Tuesday. Instead, we settled for the new large-scale battlefield that has been added in the new update: Einherjar.

Yesterday, at an unusual late hour, I and my group attempted the 35th mission in the Treasures of Aht Urghan line. Preparation was the matter of watching a few (very interesting) cutscenes then we were off to a BC to fight a single enemy, a ninja (the name is a spoiler, so keep on reading only if you know what you are doing).

When starting a run in Dynamis-Beaucedine, some person in charge of my brother’s Dynamis linkshell stated that over a whole Dynamis run (approximately four hours) you should not leave or be away. This statement is misguided at best, and personally I found it rather offensive for a series of reasons: Not everyone is in the same timezone: if you have other commitments that force you to stay away for a longer period (such as meals with other people) you should not be blamed for it, after all real life takes serious precedence over gaming;

I did not expect it, but today Square Enix announced a new expansion for Final Fantasy XI, called Wings of the Goddess (but I like the Japanese title - something along the line of The Holy Warriors of Altana - more). There’s also a trailer available on the main PlayOnline page. From what I can see it looks like a time-warp expansion, set back in time in the Crystal War, but the images are scarce.

The behavior of some people in FFXI is certainly excessive to say the list, with many people (especially in the “endgame” linkshells) showing an extremely arrogant and impolite attitude. I had a really nice show of that yesterday, when I went out to get a few merit points with my static group.

On Wednesday 21st I was finally able to undertake the new Treasures of Aht Urghan missions! It felt nice, since I mostly play for merit points and Dynamis now (and occasionally some action in Al’Taieu, though rare and far between).

You usually don’t expect them to actually appear. Today, after a call made by my brother, was different… []({{ site.url }}/images/2007/03/img_0079.png)

A lot of times when doing Dynamis it happens that people lot for a particular piece of relic armor then when asking about the stats I see responses like “It’s crap” or something similar. This brings the question: why do you want it in the first place? To put it on a mannequin to show off? There **is no use_ _**for relic armor unless worn. So, next time you make a lot, do the others a favor, save it for pieces you really want and let people who want to use the blasted things go first.

On the day after Christmas I went to do Dynamis-Beaucedine with United. I had to be the main assist for this run, and surprisingly everything went well. Not only that, the run had really **loads_ _**of drops (including a 100 currency piece), as the relevant thread says. Most importantly, I finally obtained the Valor Breeches. I had never seen them drop in Beaucedine Glacier, and luckily I was the only one lotting (I managed to lot of the ridicolously low amount of 172).

I noticed recently that Square Enix has announced a new event in FFXI, namely Salvage. Apparently this looks like an Assault with other modifications (such as special conditions forced on the players) thrown in. To me, this is a huge disappointment, as I expected more integration in the extremely fragmented ToAU landscape. Everything looks incomplete, and adding another incomplete part will not cut it. Not to mention that the only rewards are items… items that can only be used with the “regular” activities.

The title of the post pretty much says it all. I’ve finally been able to obtain this piece of artifact armor+1 after searching for the last item I needed for about five months.

Last Tuesday I assembled a group and we took on the (only) battle present in the new Treasures of Aht Urhgan update. I had to look for members, but since Besieged was going on I lost a lot of time shouting for members. In the end I managed to get a red mage and a ninja along people I had arranged to meet with.

At least, after six long months of wait, I obtained a new piece of the Paladin relic set.

UPDATED: Now a movie showing the run is hosted at Google Video.

On Tuesday there was my second attempt at doing Dynamis-Buburimu with United Dynamis. My first attempt, months ago, was a sore loss because of lack of people (and lack of experience, in my opinion). This time we had close to the 36 people needed for the area, and we were much better prepared.

I forgot to mention it in the past entries, but my group finally managed to take on the (only) serious fight in the Treasures of Aht Urghan storyline so far. The mission is known as the “Black Coffin” and even if it involves six members it’s not a battlefield (or Burning Circle as they’re also called) but instead is an Assault. Getting to the spot where the Assault takes place was kind of a tricky because we had a couple of deaths on the way: the area is Caedarva Mire on Dvucca Isle and there are a load of undead (Qutrub) and Imps in the way.

Yesterday, my brother managed to do a BCNM40 with Mercredi and Rezo. It is a battlefield in Horlais Peak, in the San d’Oria region, where a group of three people maximum can enter. It is famous because it can drop a very rare item, the Peacock Charm (Accuracy +10, Ranged Accuracy +10 Dark resistance -10). There are three enemies on the field, all of the mind gazer type. Two are rather small, and one is larger.

I’ve recently slowed down my rate of playing at Final Fantasy XI, mostly because the new update is scheduled for the end of the month, and I don’t have much to do nowadays. Besides, part of the people in my group are on holiday or taking breaks so I won’t get to do anything until the 28th of August or so, when I’ll be back from holidays.

Over the course of three days, Heaven’s Inferno has imploded. This all started between disagreements in the leading council, mostly due to immobilism on one of the parts, Grummish. This person had a good and noble attitude towards helping and people behavior, but sadly “real game” scenario proved to be rather different. People that are 30+ act like children, even, which is rather saddening. Anyway, in the end the same person made a long rant after Dynamis-Beaucedine (I wasn’t there, as it was during night time), that caused, like with my previous linkshell Inferno, a huge hemorrage of members.

Things aren’t going in well in Heaven’s Inferno. Not only people have been leaving, but also I’ve been subject to an intense crossfire, more from the leading committee than anyone else. I correct myself, only parts of the leading committee, who seem hell bent in making things unfair for everyone (and flaming with ridicolous arguments). All of this just to get some items, people bitch and moan all the time about those, which is really lame, and childish.

Yesterday I updated my laptop to Kubuntu Dapper RC. Overall the (long) process was quite smooth save a couple of problems (the use of NetworkManager for exaple, that caused me headaches to make wireless work) including the fact that the ATI drivers were looking in the wrong location (/usr/X11/lib/modules/dri instead of /usr/lib/dri) so 3D acceleration wasn’t working. It seems smooth so far, though I think the idea of NetworkManager needs polishing, as some services that are started before it connects will fail (such as autofs).

I’ve been spending a bit of my time last week to do several FFXI-related events. The most important are related to Assault, as me and my group (Eithin, Mercredi, Sechs and Billyism) managed to win all the level 1 Assaults, and therefore we got promoted to Private First Class (PFC), which sounds a little better than the lame Private Second Class. Here are also some random images from the new areas:

Last Monday I got the new expansion pack for FFXI, namely Treasures of Aht Urghan. After installing (and going through the tedious update procedure), I’ve done some exploring. Some remarks: The missions are either well hidden, or not particularly significant at this point: this in my opinion is a regression from Chains of Promathia, which had an extremely nice storyline; The new areas are huge. Yesterday I’ve done some exploring in the Arrapago Reef area with Sechs, Eithin and Mercredi and we took more than two hours to get to our destination (including one death, and several fights inbetween);

I really can’t believe some people on the Internet act all rough when all you ask them is to be more polite when certain people are around. The issue at stake happened in FFXI, when someone went out with a “C****t” curse because of something. Now, Both my brother and me don’t like those kind of things. All my brother did was asking politely to avoid saying such things in public when he was around, and he got flamed by a certain person (who shall remain nameless).

That (which represent a person kneeling in dejection) is my thought after last night’s Final Fantasy XI run. I assembled a group to take on PM8-5, the last mission so far, and I was pretty confident we could win without too many problems. Well, I was wrong. The battle involves two enemies, who I had already seen in Zilart Missions 8 and 16. One likes to spam magic, the other has extremely annoying abilities.

Finally, we have windows in the office. Before that it was just a room with walls, and it looked a little claustrophobic. It took a good deal of time (4 months) to get these works done, but I think the result is worth it. At least the whole room looks a little more human, now. I will be spending tomorrow’s work day analyzing data with an extremely bad piece of software, at least design-wise (the algorithm used inside it’s very solid, instead).

I haven’t been writing on this blog as much as I wanted, partly because of tiredness, partly because of my always-present tiredness. Today I delivered the receipts from the Bertinoro school and also from Trieste: I hope I get a refund fairly quickly (although usually “fairly quickly” means around 3-4 months if I’m lucky). Also, these days I’m working on the DNAcopy package from Bioconductor (a series of add-on packages for R) to see if I can use the data from Affymetrix’s Chromosome Copy Number Analysis Tool to get a genome-wide view on copy number aberrations (CNAT only permits you to see one chromosome at a time).

Earlier today I logged into FFXI to do my usual Tuesday Dynamis run with the United Dynamis linkshell. I was actually quite eager to do the run, since I missed two in a row because of lack of access to the specific areas. I was also hoping to see some relic armor drop at last. While many players want certain “endgame” items, I’m focused on the Paladin relic armor and weapons.

As today was almost completely uneventful (and kept on raining), I’m putting together an all-in-one entry. First of all I played more with the webcam on Linux. The exposure setting and some other gamma corrections can’t be really set in real-time yet, so it tends to get a little dark. Nevertheless I can get some decent results, here’s an example picture of my desk: general/desktop.jpg I also tried to update my old Mandriva 2006.

Yesterday I was feeling bad and had a mild fever, so I didn’t go to work. I took the chance of playing a bit in Final Fantasy XI. First, a bard in our linkshell needed some items for the opo-opo crown and so I and others tried to help him to get an item that drops off Sand Diggers in Quicksand Caves. We spent a good deal of time there, but we didn’t get any.

Finally I got my hands on something I’ve been wanting to get for a long time! Thanks to some of the folks in Heaven’s Inferno, I managed to assemble a party and get to Riverne - Site B#01, where the notorious monster Imdugud was. Assembling took a bit, but since no one is ever there (probably due to the level 50 cap?) it soon appeared after some hyppogriph kills. Things got a little rough during the fight (no referesher) but in the end we won.

I decided to get on FFXI this morning and I got “recruited” again for some Roc camping. Since I haven’t really helped with that thing recently, I decided to join the expedition. Luckily there was no competition, since people went either away or fell asleep (it was the heart of the night in the States, go figure). The nasty beast decided to appear only at the end of the window. It was a fast and rather plain fight, and no great rewards (crimson blade, vile elixir, reraiser) that even got lost because someone was too hasty in warping, bah.

 On Septemer 1st the open beta of Square Enix’s new MMORPG, FINAL FANTASY XIV Online was launched. I’ve been playing its predecessor since December 2003, although nowadays my presence is limited to doing the “missions” (quests that advance the main storyline). Of course I was interested in the “new MMO” in the works at Square since it was mentioned in 2006. When the official release was announced, I preordered the so-called Limited Collector’s Edition (it comes with nice items inside, along with an in-game item).

You might have heard it in the past few months: some areas of the Internet are buzzing with discussions on “generative art”, that is, artwork generated from “AI” models that were fed with an absurdly large amount of images as training as a base. There are supporters, there are critics, and techology advances: among all this, this post offers my humble experience with computer-generated imagery. In this post, you’ll be guided by Yumiko, Satsuki, and Maya: the first two are characters created by someone else I know (who wants to remain anonymous) which I then expanded, cooperating with their creator in a certain project from a few years ago; the latter is… well, a character with an interesting history, which will be explained later.

In the past months I’ve set up LDAP at home, to avoid having different user accounts for the services that I run on my home hardware. Rather than the venerable OpenLDAP I settled for 389 Directory Server, commercially known as Red Hat Directory Server, mainly because I was more familiar with it. Rather than describing how to set that up (Red Hat’s own documentation is excellent on that regard), this post will focus on the steps required to enable encryption using Let’s Encrypt certificates.

Because changes occur when one least expects them. This post is about one such change.

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others) As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in.

Omnia? The Turris Omnia is quite a nice (although a little pricey) OpenWRT-based router from CZ.NIC. It provides a fairly powerful CPU, relatively unconstrained eMMC space, and quite a lot of hackability (some revisions even have GPIO ports to play with). It runs a modified version of OpenWRT, named TurrisOS. The problem A few years ago, I built a custom NAS for my storage needs, using a cheap Intel SoC (J1900 chipset) and a (much pricier) mini-ITX small form factor server tower.

The migration happened and well… it turns out that it was not as smooth as I expected. In particular, comments weren’t working at all due to a filesystem permission on the database (which meant nothing would get written at all). That is now fixed. Sorry for the problems. To add problems over problems, I had a hardware failure (RAID card) last June, which wrecked the root filesystem and I had to reinstall everything from scratch.

You might have noticed that the blog has a markedly different look than before. It has not only changed visually, but also under the hood. This (brief) post summarizes the reasons behind the change. Why? Simply put, the previous solution was unmaintainable. “But,” you might say, “it was a static site generator! How could it become unmaintainable?”. It can. You might recall I moved from Wordpress to Jekyll about six years ago.

Yesterday I finally flipped the switch on the MX record and moved to a new server (still aptly named after another character from アキハバラ電脳組). The machine was found through Hetzner’s server auctions and has quite a good configuration for the price paid: Intel Xeon CPU E31245 @ 3.30GHz 16G ECC RAM (ECC was the deciding factor) LSI Hardware RAID 1 with two 3x2T disks Now, since the old server has been chugging along since 2011, the 5 eurocent question is why did you move at all?

Header image credit: 1840151sudarshan (Wikimedia Commons, CC BY-SA) A while ago I posted a way to download 実況動画 from Nicovideo. One of my acquaintances publishes videos there, and he wanted to collect the various comments to reply in a follow up video (what the Nico users call the コメント返し). When the comments are more than just a few, it’s hard to find where they refer to without watching them on Nicovideo itself, and its UI is suboptimal.

実況? Is it something edible? In recent times, I’ve been watching a lot of VOICEROID実況 (じっきょう, jikkyou, literally “commentary”) videos from the rather famous (in Japan) video service ニコニコ動画, better known as “Nicovideo”. In this case, the commentary actually refers to games: they’re basically a Japanese version of the Let’s Play videos that are all around other places like YouTube. The difference from “regular” videos lies in the “VOICEROID” term: this is a name of a TTS software developed by AH Software using an engine devised by a company called AI Inc.

If you look through this blog’s archives, you may notice that although Free and Open Source Software is what I write most about, it is not the exclusive topic. I’ve written on science (my day job) as well as other interests. And today I’d like to lift the wraps on another project which I take part on, unrelated to the above. Notice for those who read my blog coming from FOSS aggregators like Planet KDE: this is fairly different than most recent topics from me, so be warned before you continue reading.

In the past week, the KDE Community Forums administrators had been discussing how to improve the current forum layout. There are a few reasons in favor of a reorganization. First of all, to reflect better what KDE is (a community that produces software). Secondly, to provide a better organinzation for all kinds of people: those that require support, those that offer support, and those who want to contribute. All of this within a (hopefully) logical structure.

(Inspired by http://viccuad.me/blog/GPG-transition-statement/) This exact same text can be found at this location. -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Sun Jun 7 14:12:39 CEST 2015 For a number of reasons, i've recently set up a new OpenPGP key, and will be transitioning away from my old one. The old key will continue to be valid for some time, but i prefer all future correspondence to come to the new one. I would also like this new key to be re-integrated into the web of trust.

As I said in my latest post, I wasn’t very happy with using Disqus to store my comments, mainly because I do not want my data to be hosted by someone else. Thanks to some commenters, I was made aware of an alternative, called isso. After reading the online documentation, I decided to set it up with dennogumi.org. It was all a matter of creating a new user called isso, setting a virtualenv to its home dir, and then installing isso itself and uWSGI:

Since [26th December 2005]({{ site.url }}/2005/12/up-and-running/), I’ve been runnning this blog with Wordpress. At the time there were little alternatives and finally I had got hold of a host (Dreamhost, at the time) that supported PHP and MySQL without being overly restrictive. 10 years later, things have somehow changed. The issue The main reason lies in how Wordpress has evolved over time: no, I’m not speaking about the subjective “bloat”, but the fact that it’s been moving towards a full-blown CMS, which is not what I have in mind to run my blog.

A lot has been happening on the KDE side of openSUSE… this post summarizes what’s been going on so far. Live media for Plasma 5 One of the most-often requested ways to test Plasma 5, given it can’t be coinstalled with the 4.x Workspace, is the availability of live images to test either in VM or bare metal without touching existing systems. Given that other distributions started doing so since a while, naturally openSUSE couldn’t stay still.

After my previous post, development went quicker than expected, so I’ve actually managed to get a real version out. ;) So without much ado… here’s Danbooru Client 0.2.0! This redesigned C++ version brings a few more features compared to the PyKDE4 version, notably: Infinite scrolling (experimental) - Just scroll down to load the next set of posts QML-based thumbnail view Click on the image below to have a demonstration of what’s in this release (warning: 2M GIF file): [!

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too. I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

This was inspired by this forum thread on the Piwigo forums. Set up rewrite rules in nginx where “piwigo” is the path the gallery lies in: location @rewrite { rewrite ^/piwigo/picture((/|$).*)$ /piwigo/picture.php$1 last; rewrite ^/piwigo/index((/|$).*)$ /piwigo/index.php$1 last; # The following is needed for batch operations which use i.php rewrite ^/piwigo/i((/|$).*)$ /piwigo/i.php$1 last; } location /piwigo { index index.php; try_files $uri $uri/ @rewrite; } location ~ ^(?

Requests to unlock KWallet automatically on login (assuming the wallet password and user password are the same), like gnome-keyring can do, have been going on for years: in fact, bug reports requesting this feature are quite old. Recently, thanks to the efforts of Alex Fiestas, a PAM module, which interfaces KWallet to the system authentication methods, has been developed. In parallel, the necessary glue code has been also added to the various parts of the KDE workspace so that it could make use of it.

I’m a (happy!) owner of a Casio EX-WORD Dataplus 5 XD-A4700, a Japanese electronic dictionary. Recently I looked into updating the Japanese-English dictionary (currently the Shogakukan PROGRESSIVE dictionary) installed, because it’s not good enough: too often when looking up odd sentences (like the ones in Fate/Extra CCC) I do not find any matches. EDICT is adequate, and while I can use it on my phone and tablet, I like the fact that the EX-WORD has a physical keyboard along with the stylus, and a very nice kanji handwriting recognition.

Following up on my previous post, a different type of image has been made by the openSUSE KDE community members. In particular, alin has created images sporting the same software from KDE (4.10 RC2) but using the upcoming openSUSE 12.3 as base. Download links: 32 bit version 64 bit version Release directory (in case the above links go 404; the files are named KDE4-.4.10.RC2-Live) These images are provided not only to test 4.

[]({{ site.url }}/images/2013/01/mmBvi.jpg)

A few days ago I finally completed (after about 3 months) 神次元ゲームネプテューヌV, or “Kami Jigen Game Neptune V”, the latest instalment from Compile Heart in the Neptune franchise of PS3 games. It took quite a while (approximately 3 months), and I think it’s about time to wrap things up.

When I’m not on forum duty or handling openSUSE-related contributions, I try to improve my code contributions to KDE, even though I’m by no means an experienced programmer (I program all day long in Python, but I’m still a biologist after all). For the upcoming 4.10 release I’ve been polishing up Python 3 support. As you may know, Python 3 isn’t the standard in many distributions (Arch Linux excluded), but despite the slow start, it is slowly gaining steam.

Like everything, openSUSE is not perfect. Bugs crop here and there, or there is missing / quirky functionality that users may run into. Being a distribution of heterogeneous software, this means that bugs fall into these categories: Upstream bugs in the software shipped by openSUSE Bugs in the packaging Bugs in distribution-specific setups or that derive from interactions with these setups (e.g. kernel, low level software stack, etc.

Although the release of openSUSE 12.3 is yet to come, the people of the openSUSE community contributing to KDE are already at work to bring the best possible KDE experience for the new release.

Many of you know that KDE Brainstorm ideas aren’t posted straight away: they are always pre-screened to avoid repetitions, features that cannot be implemented technically, violations of the Code of Conduct, and so on. This is possible thanks to the work of the Idea Moderators, that patrol Brainstorm and evaluate the new ideas being posted. Recently, a few of them got too busy and thus we’re experiencing a backlog of ideas staying in the Vault (the staging area for evaluation) for longer times than usual.

The recent post by Dario on the KDE Workspace Vision raised some concerns on why Brainstorm was not used.One commenter even said _Right now it feels like “Throw an idea over a wall for no-one but end users to discuss until it bitrot’s”. _ _ _ The Brainstorm section is indeed in need of help. To make it more useful, a couple of things are needed: Statistics to evaluate which ideas are best representative: it can’t be just the number of votes per se as there are things like confirmation bias or controversies that may inflate the numbers Integration with Bugzilla: a way to automatically (using XML-RPC) send the ideas flagged as representative to a bug report filed under “wishlist”.

Sometimes Christmas presents are really unexpected, and today I found out I was given one such gift: the limited edition of _THE IDOLM@STER 2, _PS3 version. It was quite a bulky box, showing all the main characters from the game (and from the recently-ended anime) (click to enlarge):  Of course, having such a box means that there’s a lot of stuff inside. In fact, once opened, there are two game BDs (one being the actual game, the second being the first volume of Gravure for you!

By browsing through sites, I noticed that the Spanish site Akihabara Denno Gumi Universe has posted a translation of an interview the webmaster had with me through email. Here it is (Spanish language). It feels nice to recall some memories of the past once in a while, especially since I couldn’t still believe that dennogumi.org had been such a resource back in the days…

After many years of (good) service, I’m in the process of moving from Dreamhost web hosting to a Virtual Private Server (VPS) service hosted by the folks at Linode. It’s definitely more pricey but I like the control and freedom that I have at my disposal. Thanks to a number of guides and some help, I was able to set up lighttpd and php-fpm to serve web pages, and Postfix+dovecot+amavisd-new for email.

Like every year, it’s finally time for me to go away and enjoy some hard-earned holidays. I’ll be spending next week traveling around France, then going to the sea. As such, my online presence will be reduced to the minimum: reports from the trip and some photos when I’m in France. See you on August 30th!

Yesterday I’ve been in Camogli and Portofino, two small towns in the eastern part of Liguria. The weather was nice and warm, and I took the opportunity of taking a few photos: [singlepic id=328 w=320 h=240 float=] [singlepic id=331 w=320 h=240 float=] Those are samples, the rest are available [in the gallery.]({{ site.url }}/nggallery/page-494/album-1/gallery-9)

Some say that all good things must come to an end. I’m not entirely sure that this is a universal truth, but I can say that at some point in life there are decisions that need to be taken. In this case I made my own: today was the last day inDr.Cristina Battaglia’s laboratory, a place where I spent my three-year Ph.D. course and one year as a post-doc research fellow.

As you have noticed, I have upgraded FailWordpress to version 2.7, getting also a new theme in the process. The header image is temporary, until I or someone else gets it fixed. The gallery has also changed: I ditched WPG2 and Gallery 2 because they kept on breaking every time I upgraded Wordpress (of course it’s probably Wordpress’s API and schema instability to blame). Therefore, the gallery had been organized and most likely older posts won’t show images anymore (I’ll get to fix those eventually).

Ok, ok… my definition of “tomorrow” is not like what most people use, apparently. Although I took quite a while, now [there is a static page on DataMatrix]({{ site.url }}/projects-2/datamatrix). There you will find a summary of wht I wrote in my other blog posts regarding this module. Of course, it will be kept up-to-date should I release a new version. Aside that, I put a contact form on this blog.

Following the instruction from Mike Arthur’s post on planetkde, I tried posting on dennogumi.org from KOrganizer (KDE 4.1.1). Lo and behold, it works! It’s always better to use an application rather than a clunky web user interface…

At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax. In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).

All right, it didn’t quite turn out as I had expected. This post wasn’t “soon"as I predicted originally. The reason? The fact that the video card I bought died after three days of usage, and getting a replacement took a while. Finally though, I have a functional system. It’s a Core 2 Duo CPU (7200) with 2 Gb of RAM and an ATI Radeon 3870 HD video card. I installed Linux on it, of course, but instead of Kubuntu I gave openSUSE a try.

Sadly (for me) I’m back from the holidays. For those of you who wondered why the updates on Japan stopped: when I got back to Tokyo I didn’t have an Internet connection, so I had no means to update. The whole holiday was a blast, though, and we’re considering getting back in two years. Aside from that, work has picked up a really fast pace immediately (why on Earth journals don’t accept LaTeX-produced PDFs?

Today we went to Nar, site of the first capital of Japan, especially to see the Todaiji Temple, designated as a World Heritage site by UNESCO. We used an express train to get to Nara and then a bus to get to the Todaiji itself (actually it’s a quick walk, I just didn’t know the distance was so short). The temple lies inside the Nara-koen, or Nara park, which is famous for its 1200 tame sacred deers.

It’s been a hot day here in Kyoto. And I don’t mean lame second meanings, just that the temperature was really over the top. As a consequence, we changed our plans: we were supposed to visit the so-called “path of the philosophy” but instead we set for Nijo Castle. Nijo Castle was the Kyoto residence of Ieyasu Tokugawa (I suspect to tell the emperor who was the real person in power) and it can be visited.

I was too tired to write an entry yesterday, so I’ll just sum things up here. Yesterday we went to Nikko, home of the Rinnoji Temple, the Toshogu Shrine and the Futarasan Shrine. We decided to visit it to see the tomb of Ieyasu Tokugawa. We took the Tobu Railways SPACIA train to Nikko then used a special pass I had bought beforehand online (the World Heritage Pass) to see the places.

I’m aching all over but I managed to write this entry. Today I went to the Ueno area first, hoping to go to the National Museum: however I forgot it was closed on Mondays, so I had to go to the National Science Museum instead. It turned out that it wasn’t a bad choice after all, as the museum is rich with exhibits and has a very good presentation. After that we moved to the Toshogu Shrine in Ueno Park, a shrine that was dedicated to the shogun Ieyasu Tokugawa.

I didn’t get time to write before about it, but I and my brother went to Japan for a 10-day holiday there, starting on yesterday. After a 12 hour trip, we arrived in Narita Airport and I took the chance of getting an IC card (prepaid subway/bus card) plus a shinkansen reservation I could only make in Japan (and that cost me “just” 27,000 yen). Once that was settled, we boarded the Japan Rail (JR) Narita Express and arrived in Tokyo.

In preparation for my trip to Japan (I really need to write about it), I have spent a few euro on a digital camera, a Canon Powershot A590. It looks like a decent camera, has a viewfinder (essential for me), some manual customization and of course it works with Linux (using digikam). Here are two examples, depicting no less than my two felines: []({{ site.url }}/images/2008/07/img_0004.jpg)[]({{ site.

After almost a month of wait (Dynamism.com doesn’t like simple order procedures), I finally got hold of an Asus Eee PC 900 (obviously - for the readers of this blog - the 20 Gb Linux version). Read more for some quick impressions and pictures.

Yesterday I updated _The S.T.E.A.L. Saga _to Wordpress 2.5.1. I thought the upgrade would be painless, but I was wrong. First of all, the auto plugin updater kind of confused between the various plugins, so it marked some as updateable although they weren’t. Then, some plugins (albeit incompatible), disappeared from the plugin list (the fix was downloading a more recent version). The biggest issue was, however, the mangling of my .

Since my work schedule is bordering on the hectic, I was thinking on buying something to get me more organized. Rather than a PDA, I’ve been rather interested in the Asus Eee PC: small form factor, SSDs and Linux preinstalled are definitely pluses. It’s too bad that at least in Italy Asus sells only the 512M RAM version (when there are more powerful options available elsewhere). I’d like to get impressions on the Asus Eee, before considering a purchase (€ 300 are still a lot): did you try it?

I have upgraded this blog to Wordpress 2.5. As a result, there are some functions, such as the image gallery, that have been disabled due to the annoying habit of the Wordpress developers of making core changes in very little time. Please report any problems you find, and notice that although the thumbnails look truncated in the new gallery, the full images are actually displayed correctly. I had to fiddle a bit wit the “new media manager”, not only because it’s in Flash, but because at least on Linux it gives odd results (apparently no one from the WP team bothered to check past Win and OSX?

I haven’t posted anything in a month or so. Quite a long time, considering I used to write at least once per week. The reasons are mainly two: first of all, my work schedule has taken a turn for the worse, which means I have to do my job a lot harder than before; secondly, there wasn’t much interesting stuff to report. Let’s resume from the hiatus by writing about my latest Final Fantasy XI session.

From today on I’ll try to write posts without a browser, since I’m not that fond of such an approach. As a matter of fact, I’m using kblogger now, a blogging application for KDE 4 (I didn’t mention that I switched to that full time, more on that when I get time). If you notice something odd in the way the posts are written, please let me know. Thanks.

The title clearly shows what I think about the aforementioned company. The reason surfaced a few days ago, when I tried to see if they would ship Wings of the Goddess to Italy. I had ordered from them a few times before, and although their customer service left a lot to be desired, I couldn’t complain much. Two days ago I found that they will no longer ship anything to Italy.

The other day I was thinking about how to make screencaps for the anime I watch. Windows users often use Media Player Classic, which can create a video contact sheet (i.e., a series of captures) out of a movie file. I had two problems with this: The biggest is that it runs on Windows, and I don’t use Windows; The frames needed to be manually cropped every time, which was slow.

I just read from Weblog Tools Collection that CollegeScholarships.org is hosting a vote for a round of $10,000 blogging scholarships. Now, I may be a little out of the “Web 2.0” trend (actually for me “2.0” does not relate to Tim O’Reilly’s buzzword, but to real and interesting technologies like the Semantic Web), but I find this absurd. I mean, I have no doubts that the people listed there have made interesting blogs.

After some thoughts, I switched dennogumi.org to the dKret theme. Please report any errors you may find. The header is the default image, but it will be changed soon (hint: Melissa, you already know what to do…).

I’ve recently upgraded this blog to Wordpress 2.3. While I’m interested in the new changes this release brings (like tagging support) I question the way the transition to the new version was handled. In particular, I am referring to the (questionable) idea of breaking the database schema three weeks before the release. Given the amount of breakage that brought upon plugins, it should have been announced at the start of the 2.

I was thinking about writing something on the line of what I announced in the past entry, but what has happened recently surrounding the artist who does the work for The S.T.E.A.L. Saga, that is Too, made me change my mind.

Recently I haven’t had the time to write any decent entries. That is due to the fact that my Ph.D. thesis needs to be completed by Oct 18th, and while I’m (hopefully) on track I still have to finish correcting the Introduction and completing the Discussion section (lots of scientific literature to study…). As I’m working on that even on weekends, it means I really have little free time. Not all’s lost.

After little more than a year, I’ve been moved to a new office, because new people needed to be put in the room I was in. The new place is slightly bigger (four desks instead of six) and for now quieter. I spent most of the morning fixing things and setting up network connections. This is how it looks now: []({{ site.url }}/images/2007/09/016.JPG) [![A closer look]({{ site.

I haven’t been able to post much recently, mostly because I’ve been quite busy regarding my thesis and work and because I’m preparing everything for the holidays. I’ll be leaving on August 3rd for Rome, and after a week’s stay, I’ll go to the sea until August 26th. Unfortunately I’ll have to bring my work with me to do something as I’m a little behind in writing the thesis. Due to the holidays, I won’t be able to update here regularly (if any), however I’ll try to post one last entry before leaving.

Looks like NRK beat me to it, but I’ve seen this film myself yesterday night. To be frank, I wasn’t really expecting a nice result. That is, because most Hollywood “conversions” from other franchises often end up being terrible (Street Fighter, anyone?). Nevertheless, having watched the animated series when I was little (it was good, despite some shortcomings), I was set on seeing Transformers since its original announcement. Despite not being related to the TV series, I found it to be rather good.

Two weeks ago I went to a sea resort in Liguria, called Loano. While plagued by a cold, the hiliday was much needed to relax. Finally I’ve managed to scan the photos (I only had an one-use camera) and so I’ve put them online. Click on the thumbnail to get to the specific album. [  ]({{ site.url }}/v/loano/)

Today I made a simple sed script that converts a tab-delimited text file to a format that can be pasted into a DokuWiki wiki. There is a plugin that permits to read CSV files directly, however: It doesn’t support tab-delimited text files; It’s incompatible with some plugins (one being DokuTexit, which I need). Hence the need for this script. To use it, just copy and paste the code (see below) into a new file, make it executable (chmod +x) and then invoke it with

At work I’ve recently got hold of two nice hardware upgrades: a portable 60 Gb HD (useful for carrying around large data) and an 80 Gb hard disk. The latter was much needed as the 40 Gb HD inside my Acer Veriton 7500G was getting rather small, both on the Windows side (which sadly I still need to use for some things) and on the Linux side (at one point / filled up, resulting in a system that would not log into X at all).

Just something different, for a change. I got up this morning and on one of my windows I saw this: []({{ site.url }}/images/2007/03/026.JPG) (for the record, those are my two cats, Minou on the left and Matisse on the right)

Today I went over my old Python code, back when I first started programming. I’d say that I found what I had written to be largely amusing to say the least. Loads of ugly hacks all over the place, duplicated functions, etc… in short, a real mess. I’m quite happy of the results I achieved in the past month, since I finally learnt how to code properly and started making my own classes (this book was immensely helpful).

I’ve found always hard to express certain types of ideas on the Internet. I probably think that it’s due to the abuse of the anonimity that the net gives to most people (hint: think of the angsty teens on MySpace). The overall result is that some people feel put off in writing anything that is closely related to being emotional (either positive or negative), and on the other hand, other people may be annoyed after reading a lot of emotional things without real content.

Work is getting hectic as we’re finally gathering a lot of data for a new publication. This means reading a lot of literature, choosing the figures and planning results and discussion properly. On top of that, I’m starting to study pathway analysis for my thesis, and of course, seeing how I can use that to study our own data. I also have some other non research duties to attend to, such as being the person repsonsible for data handling of our group in relation to the [server that we bought recently]({{ site.

Yesterday I and another person went to the server room to do the basic configuration of the Apple Xserve we have bought, along with its Xserve RAID unit. Despite the general “idea” that anything Apple does is user-friendly, our experience was plagued by problems.

By tracking the statistics of my blog, I noticed that many people came here from web pages that linked directly the old multimedia files I had on dennogumi.org when it was still an information page on Akihabara Denno Gumi. However they aren’t here anymore. I also kindly asked to avoid linking them directly when they were up, but I guess some people just don’t read. In short, if you have come here to get movies, or music files, you won’t find them.

I’ve upgraded to Wordpress 2.1 yesterday. Aside some minor issues with one of my plugins, that may be resolved in the future, everything went well. If you spot any quirks, let me know here with a comment.

I’m pretty happy. As some of you already know, the book I wrote with my brother is finally out. The preview copies I had ordered arrived yesterday, and I can see it’s pretty impressive to hold the book you have written with your own hands: 470 It only needed a couple of adjustments in the drawings’ captions, so I made it available for everyone last night. All I need to do now is to wait and see the reactions…

That’s right. Thanks to my brother, now I am an owner of this game console (the North American version), along with the game Resistance: Fall of Man. To be precise, I have the 60 Gb version (essential as I can’t use wired connectivity where it is, just wireless)I haven’t had yet the time to play well with this beast, but I managed to take (poor quality) pictures.

I usually manage to write an entry or two during the weekend. This week was (almost) not the case as my computer time was spent editing and correcting the Lost Innocence manuscript. And when that was done, there were some problems with the cover files so I had to fix those, as well. Last but not least, the FAQ section of stealsaga.net needs an overhaul. Yes, plenty of S.T.E.A.L. related work going on.

In the past two days, aside studying the Python basics, I’ve been looking to find a decent GUI toolset to develop user interfaces in Python.

Reading Wesley J. Chun’s excellent Core Python Programming I realized I could definitely improve [my wallpaper checker]({{ site.url }}/2006/12/23/wallpaper-size-checker/), at least internally. That’s what I did today, and aside that, I added an option to view a thumbnail of the images contained in the lists. Note that it is not meant to be an image viewer, just a way to show the images in the list (and I suggest you filter it first if it’s long).

UPDATE: Some stupid bugs had crept in the code, so I updated the archives. Sorry for the inconvenience.

I’ve writtern a small Python script to find wallpapers with right size or aspect ratio I needed, and now I’m releasing it to the public. It may come in handy especially when you download lots of desktop wallpapers (archives, torrents) and you don’t know which ones are suited for your monitor.

I recently completed Final Fantasy XII. Overall it lasted over a month of play (1 hour per day, approximately), so at least I can say that I spent my money decently. The game is **very **reminiscent of FFXI, in some areas even identical. It is also quite big, with many sub-quests and monsters to hunt. Not to mention that it is very impressive from a technical point of view. However, the main plot is awful.

In the past two days I’ve been tackling an annotation problem. I’m trying to provide annotations for genes found in regions that are significantly altered, DNA copy-number wise (thanks to the STAC method). The idea would be to annotate those regions (that span one megabase) using UCSC Table Browser. However, the task was impractical, so I decided to automate it a bit. I converted the data into ranges and then used the KnownGene annotation file (downloaded from UCSC) to obtain which genes were in which reagion.

Two days ago I decided to install Linux on the new computer I had obtained, so I just got a Kubuntu 6.10 alternate CD and went through the steps. THe network card was not detected, but by reading around I found it was just a matter of the r1000 module not being present in the installation kernel. The problems arose when GRUB was installed. Actually, that part of the installation went fine, but once rebooted I got “error 21”, which meant “disk not found”.

A post I wrote ended up on the front page of nodalpoint.org. I liked that, even though it may not seem a lot to many: at least it shows that some of my concerns are shared with other people in the scientific community. Also after viewing some presentations about Web 2.0 at the EMBL, I decided to make a del.icio.us account. I find it quite handy so far to organize bookmarks and such.

As you can see I have a new heading, courtesy of Melissa, featuring Saber from Fate/stay Night. Aside that, updates on this blog will continue to be slow for a little while, as I will try to rush and finish S.T.E.A.L. at last this Sunday.

In the past two days I’ve written a simple annotator program, that given an input list of RefSeq genes, automatically determines the relevant Entrez Gene IDs and annotates them using the flat files provided by the NCBI. A direct conversion was not possible due to limitations in Biopython’s parsers, but I managed to use the GenBank parser to identify and extract the references to the Gene IDs (and putting them in a list).

Since recently (thanks to my brother) I got a new cellular phone with better capabilities, photo-wise, I decided to take a few photos of my workplace. I changed office a while ago, now I’m located on the first floor of the building, sharing the office with 5 other people: Raoul, Michele, Giorgio, Roberta and Alessandro. This photo shows my current computer setup: 429 Quant was running a screensaver when I took this photo: the mouse pad and that other black thing next to the keyboard are gel pads to help me with my tendinitis.

EURASIP Journal on Bioinformatics and Systems Biology is having a special issue on text mining for biology. My boss wants to publish something there, and asked if I and a colleague could work on that. I’ll probably focus on evaluation methods, since I’m not an expert in text mining or language processing. And that’s where the problem comes in: I know almost nothing on text mining. Which means this will add up to the ever growing pile of papers and books I have to study, including but not limited to Python programming, microarray analysis and XML…

After discussing my second PhD year today, and after noticing that not even a single professor from the commitee was there (save my boss and a person that joined later on), I realized that the situation for students like me isn’t really the best. A PhD program is supposed (at least here) to be a cross between a research job and a student’s position, since you should study but at the same time conduct research and (if you’re lucky) also get paid for it.

Wednesday I got around to assemble a replacement for largo, what used to be my old “main” desktop. I also got a new case and power supply for leon, the other desktop I own, but I need to switch things around from the “old” largo to leon and I didn’t have the time yet. Without any more delay, here are the specifications: Pentium Core 2 Duo 6600 NVIDIA GeForce 7950GT

Finally I cleaned up my code enough to post it here. It’s probably still ugly, but not as ugly as when I wrote it down the first time. It’s all about manipulating text files, to be precise tab-delimited files. All the snippets are published under the GNU GPL v2 (not that I think that anyone would use them, but just in case…).

I haven’t had much time to write here as I’ve been busy fixing and arranging things for the web page on S.T.E.A.L. It appears that thanks to Too’s deviation posting and subsequent journal entry, hits have skyrocketed. This makes me happy but it also means more work and need for refinement. As a matter of fact, I wrote a little more yesterday, and today I’ll be aiming to complete chapter 4.

As the title implies, I’ve been over, along with my twin brother to my brother’s house in Leiden last weekend. It was a fun experience overall. My brother has a very nice apartment in Leiden, big although somewhat empty (but that’s the policy of the organization that gave him the place). Aside being extremely sick on the plane, I arrived more or less in time on Friday night. The following day we had a trip around Amsterdam, which honestly disappointed me somehow: while the streets, the canals, the places look nice, it doesn’t seem that it has a thousand years of history.

I recently obtained a copy of Valkyrie Profile Silmeria in a language that I can understand. I’ve been playing it for a while and I can say I like it. 396 The graphics look nice, but I don’t understand why tri-Ace made a fake 2D perspective. In my opinion it makes all that 3D look rather useless, since there’s little you can do depth-wise. The same can be said for the battles: while you can move around in 3D, the perspective shifts in 2D when you attack (in a manner similar to the original Valkyrie Profile).

WARNING: This entry is somewhat political in nature.

Given the recent controversies about the GPL v3 draft, I thought I’d give my insight on the Free Software Foundation and especially its founder, Richard M. Stallman, better known as RMS. I won’t cover the GPL v3 debate as I haven’t read the license draft, though I think that the kernel developers’ standing must be at least given attention.

Jucato has some screenshots of the recently released Kubuntu Edgy Eft Knot 3. I like very much the new artwork, but it doesn’t seem that there’ll be Oxygen icons, at least from what I can gather. In any case I will try to play with it as soon as it hits a beta stage. On unrelated news, I still have got some RSI issues, so I’ll have to slow down posting.

I’m finally back from holidays and since there’s almost no one in the office here I thought I’d write a little mixed entry, while quant is busy compiling a patched 2.6.17 kernel (but quant as an odd overheating problem that I will describe in another entry, so I have to compile it by steps). Work is somewhat slow, as the people I need to contact are still on holiday. In the mean time, I’m reading an interesting paper on some GPLed software for Single Nucleotide Polymorphism analysis, written in Perl and R.

That’s right, I’m going on holiday from today until August 28th. As I don’t have a proper internet connection there, my entries will be few and far in between (not that I’ve been very active recently, I’ve been busy putting the house in order). I’ll be staying in Loano, in Liguria, for about 17 days, and I’ll spend the rest traveling around central Italy (Arezzo, Perugia, Assisi, Todi, Gubbio, Siena).

Two days ago, my younger brother left for The Netherlands, where he’ll stay for two years working for the European Space Agency (ESA). I hope I’ll be able to keep in touch with him. I don’t like emotion-filled entries so I’ll just stop here.

Yes, I’m still alive somewhat. I have a lot to write, but my stupid wrists don’t let me save a few minutes per day. I’ll probably try to wrap things up this weekend with a series of multiple entries.

It was just tendinitis on both hands, thanks to a stupid table that I will have to fix soon. The good news is that I can get back on track soon, using some medicines and the so-called laser therapy to get rid of the inflammation. Also, I will post soon about the next S.T.E.A.L. snapshot and the upcoming FFXI update (scheduled today).

I’ve got RSI (Repetitive Strain Injury) on both my wrists. This means I won’t update in a while, as I’m trying to put my hands to rest. I’ll still try to write some S.T.E.A.L., though.

Yesterday I was trying to adjust some files in order to make a program use Affymetrix SNP arrays data (instead of arrayCGH data like the program was designed for). I had a big (116,000 rows) tab-delimited text file and I needed to use only part of the columns there.

I’ve already explained in a previous entry that I like to tweak images, extract them from backgrounds and so on. However I didn’t like that I needed Windows to perform my actions, as I want to use that operating system as less as possible. I tried then to use FOSS (Free and Open Source Software) tools available on Linux to see if I could do the same job.

As you may have noticed the theme and the layout changed slightly. I updated the [Regulus]({{ site.url }}/www.binarymoon.co.uk/projects/regulus/) theme to the newest version, making it widget-enabled and improving the overall layout. That means I can customize my own sidebar as I please without coding using the so-called Widgets, and that’s why it changed. The only problem is that the gallery now looks a little fuzzy, but it’s ok for my tastes.

I like to tinker with images. I’ve been doing this since I first started doing amateur web design, back in 1996. At first it was to create images for my own web pages (Sailormoon, ADG) but nowadays it’s like a hobby I do when I have free time. It can be fun.

I got upgrade hardin (my laptop)’s memory at least, bringing it to 1Gb, at last. However I had two 256 Mb modules installed, that means I had to buy two 512 Mb ones. Oh well, I’ll just try to sell those ones. Everything seems snappier now, and even Firefox seems not to clog the CPU when loading pages (I need to experiment more, since I have no clue why that should have changed).

I haven’t been writing a lot here mostly because of the rather hectic work schedule I’m having. We’re nearing the completion phase of a paper that includes quite a bit of my work (and also a lot of other people’s contributions), and I’m also swamped with PhD classes (two weeks to go). Also, one of my bosses has assigned me another project which I’ve yet to tackle, and I got to help my colleague with a poster as well.

As the terrace in my house has been finally completed after almost a year, I’m writing from there. While I’m relaxing, I’ll write about two items I recently obtained through archonia.com. This time there wasn’t a misunderstanding like with the Tony Taka book I ordered (which the description didn’t claim it was an H book while instead it was), I’m quite satisfied by what I got.

This week has been absolutely exhausting. I’ve been having PhD classes (statistics, effective writing, and more statistics) almost every day (save tomorrow) and also heaps of work piled up. I’ve got new data to work on, and also I’ve been assigned to do something else along with my current bioinformatics work. I also need to get in touch with the Partek software representative to let him know what I think of their genomics software.

Today I’ve been trying to set up suspend to RAM and suspend to disk (also known as hibernate) on my laptop using Kubuntu 6.06 LTS. Both tries failed miserably, sadly. The machine would suspend and also wake up, but I’d get only a garbled screen. This means that the video driver failed to wake up properly: this is the well known fglrx driver, the binary only driver that ATI made for Linux.

Finally, the new version of Kubuntu 6.06 LTS (Long Term Support) is out! Not that I noticed many differences since I kept it constantly dist-upgraded since I put the beta on the desktop and the RC on the laptop. I really like it so far (save minor nags with 3D acceleration that I solved by issuing a couple of shell commands). Also, KDE 3.5.3 packages are already available from 3rd-party repositories. I will be upgrading them soon.

Yesterday I updated my laptop to Kubuntu Dapper RC. Overall the (long) process was quite smooth save a couple of problems (the use of NetworkManager for exaple, that caused me headaches to make wireless work) including the fact that the ATI drivers were looking in the wrong location (/usr/X11/lib/modules/dri instead of /usr/lib/dri) so 3D acceleration wasn’t working. It seems smooth so far, though I think the idea of NetworkManager needs polishing, as some services that are started before it connects will fail (such as autofs).

Today I obtained a trial license of a data analysis program. I plan on using it for the next two weeks to see if it could improve the analysis workflow in our laboratory. I noticed this software uses the Tk widget set to achieve cross-platform capability (in fact, it can run on Linux, which is a big plus for me). However, in my opinion, Tk widgets look rather ugly. I wonder why the company didn’t consider using Trolltech’s Qt widgets.

Today I found out that my own ISP’s (Fastweb) mailserver got into a spam blacklist. I can understand how it happened, since Fastweb has a limited pool of public IPs and everything is behind a massive NAT. I checked the web page of the organization that blacklisted the IP and noticed they want you to pay a fine of $50 to get removed. I can understand that perhaps this is due to spammers being on a rampage around, but those guys just blacklisted an entire ISP’s mail server because they didn’t bother to check.

This has been a rather stressful period work-wise. Things are looking extremely confusing on the (upcoming) paper we need to write and even a small doubt can cause huge time losses (I spent the whole morning checking to see if my analysis was correct or not while in fact it was correct in the first place). I’ve been shown a new software for microarray analysis, well, at least some brochures. I’m going to inquire about pricing (the most important part) and platform availability (I’d love if it could run on Linux).

Today I found out that a computer running Windows had been “self-writing” words when an Internet Explorer window was open. This obviously led to the conclusion that there was some kind of malware running. I immediately unplugged the network cable but the typing continued - this is a good sign meaning that it was just some random program doing it. It only affected IE, no other programs. I wonder how it got there, I can only suspect the current user, as I never do any network-based activity there, only analysis (and I run a much safer Linux box - no Windows for me).

Last Monday I got the new expansion pack for FFXI, namely Treasures of Aht Urghan. After installing (and going through the tedious update procedure), I’ve done some exploring. Some remarks: The missions are either well hidden, or not particularly significant at this point: this in my opinion is a regression from Chains of Promathia, which had an extremely nice storyline; The new areas are huge. Yesterday I’ve done some exploring in the Arrapago Reef area with Sechs, Eithin and Mercredi and we took more than two hours to get to our destination (including one death, and several fights inbetween);

The main reason my posts here are so scarce recently it’s because of that. Shortly after the Easter outdoor trip I did, I got fever for the rest of the week (and some kickback yesterday since I was foolish enough to go to work), and it was impossible for me to stay in front of a screen for a long time. Luckily there are more holidays on sight so I think I can recover fast.

Today one of our desktops won’t turn on at all. I didn’t even see the POST lights turning on (this is a Dell computer), so I assume that the PSU is dead. I’d have already called for support but since the box has been bought in the USA (part of a bundle of our GeneChip systems) I had to request a warranty transfer (notice that I don’t even know if there’s still a warranty!

Finally, we have windows in the office. Before that it was just a room with walls, and it looked a little claustrophobic. It took a good deal of time (4 months) to get these works done, but I think the result is worth it. At least the whole room looks a little more human, now. I will be spending tomorrow’s work day analyzing data with an extremely bad piece of software, at least design-wise (the algorithm used inside it’s very solid, instead).

I’ve upgraded the theme (now it uses a non-hacked version of Regulus), the image gallery with the new Gallery v2.1, and also the new[ WPG]({{ site.url }}/wpg.galleryembedded.com) 2.0. Everything should work smoothly, according to the tests I made. Also, I added a direct link to the gallery, now that I found out how to do it properly.

I haven’t been writing on this blog as much as I wanted, partly because of tiredness, partly because of my always-present tiredness. Today I delivered the receipts from the Bertinoro school and also from Trieste: I hope I get a refund fairly quickly (although usually “fairly quickly” means around 3-4 months if I’m lucky). Also, these days I’m working on the DNAcopy package from Bioconductor (a series of add-on packages for R) to see if I can use the data from Affymetrix’s Chromosome Copy Number Analysis Tool to get a genome-wide view on copy number aberrations (CNAT only permits you to see one chromosome at a time).

Talks, talks, talks. That’s all about this day. Some were also extremely difficult to understand, and I’m not sure I took good notes. Talks went on from 8.30 to 18.00 (excluding lunch break) and then a workshop until 19.30. I’m really beat. I retired to my room while the others wanted to play karaoke, but I was too tired. Tomorrow is the last day, thank goodness! I’m tired of waking up at 6.

I just came home and I’m terribly tired, so I’ll be rather brief. This morning we had four lectures, including two interesting ones on protein structure prediction, though one speaker was too fast and I almost couldn’t take notes. Then we went in the afternoon to Ravenna. I took some pictures during the sightseeing and I’ll post them when I get home. We visited the “Mausoleo of Teodorico”, the “Basilica di S.

Today was much more tiring than yesterday. It was a full day with courses, and especially the ones in the afternoon were rather heavy on the subjects. First of all there were some talks on networks and promoter site prediction (I liked a lot the second one) , followed by some talks on microarray data analysis (I knew a bit already of this stuff). The afternoon talks featured more statistics for bioinformatics (ugghhhh) followed by a nearly non-understandable talk that lasted for almost two hours and really drained the life out of me.

Finally I got hold of a stable Internet connection so I can post about my experience in Bertinoro di Romagna so far.

I haven’t blogged in a while, mostly because I’m either doing something else, or when I want to, I find out I’m really tired (this and the past week have been very tiring for me). In any case, I’ll make a big, random entry. I’ll start saying that I’m amazed at how badly software can be written. In the life sciences field you see very clear examples. Horrible UIs and poor documentation mostly (while the algorithms and methods implemented are usually very solid).

I’ve been migrating settings and files from the old router to the new one (check my brother’s blog to understand better what I’m talking about). I noticed the free space already dropped significantly, as you can see from this: [code] lb@hari:~$ df -h Filesystem Size Used Avail Use% Mounted on /dev/hda1 9,2G 859M 7,9G 10% / tmpfs 43M 0 43M 0% /dev/shm tmpfs 43M 13M 30M 30% /lib/modules/2.6.12-10-386/volatile /dev/hda6 83G 8,5G 70G 11% /home

After sorting out the bureaucracy, finally I was able to enroll for the 6th Course in Bioinformatics for Molecular Biologists that will take place in Bertinoro di Romagna in three weeks. I’m glad I was able to, the course program looks really interesting and perhaps I’ll be finally able to learn bioinformatics in the right way, since so far I’m entirely self-taught, and sadly, it shows. On another topic, the ceiling is going to be fixed by tomorrow, I hope, so I’ll be able to get back to my old office at last.

Yesterday something happened: while I was working in the office I heard a loud THUD. Then nothing happened. I kept on doing my work till the site manager arrived, asking us to go out of the room. The reason is that the steel cables that were keeping the ceiling up had loosened, and the whole ceiling bent downwards, which was very dangerous. We temporarily moved in an unfinished laboratory, and we’re still there until repairs are done (it will take a few days, I’m being told).

As today was almost completely uneventful (and kept on raining), I’m putting together an all-in-one entry. First of all I played more with the webcam on Linux. The exposure setting and some other gamma corrections can’t be really set in real-time yet, so it tends to get a little dark. Nevertheless I can get some decent results, here’s an example picture of my desk: general/desktop.jpg I also tried to update my old Mandriva 2006.

I’ve just upgraded my blog to WP 2.0.1. Aside a little problem with the gallery images (easily fixed) everything seems to run smooth for now. If you notice any glitches please post a comment and I’ll get it fixed.

general/webcam_work.jpg I have this Trust Mini-Webcam WB-1200p since my younger brother gave it to me as a present for my last birthday. It’s a decent webcam, pity it has a CIF sensor and not a CCD one, but it’s still OK for daily use. Until now there wasn’t a decent Linux driver around, and so I was forced to boot into Windows (which I almost do not use now, save for Final Fantasy XI).

First of all, the strangest oddity ever. On Friday once at the laboratory I was contacted by an Affymetrix representative regarding [this entry ]({{ site.url }}/2006/01/26/badly-written-software-or-policy/). She wanted to know why I wrote it and that it seemed that I “didn’t contact Affymetrix to see if the problem could be solved”. She wasn’t offended or anything (she will even get me in touch with someone from the software department), but nevertheless this is my blog and I’m entitled to my personal opinions.

That was the only noteworthy event of today’s work. I arrived late (took 1 hour and 30 just to get there) and then during lunch break we moved again to the LITA to celebrate. We got a sort of necklace for her which she liked quite a lot, and we got time to have a toast and eat some cake. It took way more than I expected - I was back at the CISI at around 15.

Work is progressing, although at slow rate. I’ve asked the person I wanted to commission the illustration work a sketch of one of the characters and at the same time I forwarded the descriptions of the various scenes. Estimated time frame is a month - which is reasonable for me. He said the sketch will be done by the end of the week: I’m waiting so I can see what kind of style he decided to suse and if I have some corrections to make.

Today while working I got stuck in what probably is an intentional flaw of the software we’re using. When we scan Affymetrix’s GeneChips there are a number of files produced by the GeneChip Operating Software (GCOS in short) including raw acquisition images and various analyses. Now, a certain number of people need to use those data to work (including myself), but I don’t want people to fiddle on the scanner workstation unless they know what they’re doing.

Well, it mostly seems that my cat has reached the end of its life. It’s being slowly consumed (apparently it’s not absorbing much of the food it eats) and it’s way too weak to keep on. Rather than seeing it dying of starvation, we asked the vet to end its life (on Friday, probably). It’s odd… I’ve seen a lot of animals die, many by my own hands (due to my past work - I’ve sworn never to do that again), but when it comes to my pet I can’t help being sad about it.

I finished it two days ago. It’s got to be the shortest RPG I’ve ever played: a week is definitely too little (and I played only in the evenings for a couple hours). The game system is good indeed, but the story sucks completely. I’ve rarely seen characters that are so badly developed, or not developed at all. It’s a shame because the game system is good. Wild ARMs 3 had much better character development and was also longer.

I got this one last week. Now that I’ve been 20+ hours into it, I guess I’ll write down some impressions. First of all, I’m pleasantly surprised by the quality of the translation. XSeed has done a much better job than Agetec (who did Wild ARMs - Alter Code: F), and they preserved the voices and the opening song (even if redubbed). I like the game system, it’s fst enough and there are platform-like parts that help in breaking up the monotony of dungeon crawling and fighting.

Now that the office is more or less in working order (if we exclude the lack of chairs) I thought I’d post something about it. I finally finished setting everything up (including the 250 Gb network drive) today, so I can finally resume my real work next week (that is, bioinformatic analysis). I plan on buying a cheap chair this weekend so I can get at least a place to sit: there are two chairs only for 6 stations.

Finally today there was the (largely) anticipated move from the LITA to the CISI. I actually showed up at the CISI first, to do some research work, then after the lunch break I and a colleague went to the LITA to pack things up. We almost looked like robbers (and for sure got some funny looks from people as we moved to put things in the car): we had four computers, four monitors and keyboards, lots of cables, my notebooks, and more.

I haven’t been able to write because I always end up extremely tired from work. Since I’m moving to the CISI next week, it looks like everyone needs me. I managed to study a bit, then I had to help a couple people with a protocol, then work on the firewall/router migration (we’re restructuring our Intranet once I move a few computers there) then help with a software, etc. And tomorrow looks the same.

Some things strike me as being really odd. Regarding the [commission post]({{ site.url }}/2006/01/05/drawing-commissions/) I made: it’s not the first time I try doing this. After I realized that asking for free was not really going to help (because many people don’t have time, or the will to do such a project) I already tried in the past about offering money. And in the past I didn’t get any responses. Perhaps I chose the wrong channel of communication?

The two items in the title aren’t really related but they sum up today’s entry. My cat had to be visited by the vet, that diagnoesed renal insufficiency and strong dehydration. Something to be worry about, but it will be at lest kept under control soon. The second part of the entry deals with the fact that I’m trying to find a decent finance program that works under Linux (no thanks to any program on Windows, sorry): I tried KMyMoney but aside the fact that it doesn’t have any Italian template, it’s a little confusing.

And so it comes again. I personally didn’t want to celebrate, but I had some people over at home anyway. At least it was more or less calm. There were fireworks in the distance, and some landed up right in my terrace (no damage luckily). More or less, a decent night, though I still personally think that celebrations like that (with the exception being Carnival, which is worse) are more or less pointless.

It’s up at last, though the header image is still missing. I’ll patch it up so I can use one I was provided (but that has text I’d like removed). This marks the return of dennogumi.org, in the form of a (mostly anime-oriented) blog, as there’s really no more demand for web pages that provide information (sadly). UPDATE: Oops, I forgot about link pages. I’ll have to ask Melissa to fix the logo.

As many readers of this blog are aware, openSUSE has been offering packages of git snapshots from KDE since quite a while. They are quite useful for those wiling to test, report bugs, and / or hack on the code, but also for those who want to see what’s brewing in KDE land (without touching their existing systems). However, a major drawback for non English speakers was the lack of translations.

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others) As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in.

The migration happened and well… it turns out that it was not as smooth as I expected. In particular, comments weren’t working at all due to a filesystem permission on the database (which meant nothing would get written at all). That is now fixed. Sorry for the problems. To add problems over problems, I had a hardware failure (RAID card) last June, which wrecked the root filesystem and I had to reinstall everything from scratch.

You might have noticed that the blog has a markedly different look than before. It has not only changed visually, but also under the hood. This (brief) post summarizes the reasons behind the change. Why? Simply put, the previous solution was unmaintainable. “But,” you might say, “it was a static site generator! How could it become unmaintainable?”. It can. You might recall I moved from Wordpress to Jekyll about six years ago.

If I look back at the last post I made on ths blog… let’s say quite a lot of time has passed. The reason? Well, first of all, one would call it a lack of motivation1, and afterwards, the emergence of a small yet quite annoying pathogen which caused a bit of a stir worldwide. But today I’m not going to talk about viruses: perhaps some other time when you can avoid hear about it for breakfast, lunch, and dinner.

Part of this post is about openQA, openSUSE’s automated tool which tests a number of different scenarios, from installation to the behavior of the different desktop environments, plus testing the freshest code from KDE git. Recently, thanks to KDE team member Fabian Vogt, there has been important progress when testing KDE software. Testing the Dolphin file manager Those who use KDE software, either in Plasma or in other desktop environments have at least heard of Dolphin, the powerful file manager part of KDE Applications (by the way, have you checked out the recent beta yet?

As you may already know (if you don’t, please check these older posts) openQA, the automated testing system used by openSUSE runs daily tests on the latest KDE software from git. It works well and uncovered a number of bugs. However, it only tested X11. With Wayland starting to become usable, and some developers even switching to Wayland full time, it was a notable shortcoming. Until now. Why would openQA not run on Wayland?

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highlights of the new version Unbreak konachan.com support (change in URL format) Coming up next HTTPS support!

In the past three weeks, the openSUSE community KDE team has been pretty busy to package the latest release of Applications from KDE, 16.12. It was a pretty large task, due to the number of programs involved, and the fact that several monolithic projects were split (in particular KDE PIM). This post goes through what we did, and how we improved our packaging workflow. Some prerequisites In openSUSE speak, packages are developed in “projects”, which are separate repositories maintained on the OBS.

Admit it: how many times you have seen “software from this branch is completely untested, use it at your own risk” when you checked the latest code from any FOSS project? I bet you have, many times. For any reasonably modern project, this is not entirely true: Continuous Integration and automated testing are a huge help in ensuring that the code builds and at least does what it is supposed to do.

You may be aware that openSUSE Leap 42.2 is now in the release candidate stage, and there’s a lot of activity aimed at squashing those pesky bugs before they hit the final release. One particular bug proved to be quite tough to fix, and it was only solved thanks to the “heroes” mentioned in the title. This is the history of the bug. The report October 6th, 2016 - A bug iss reported against Plasma reporting a hard freeze of Plasma when using the Noveau driver, but not with the closed NVIDIA blob.

As you may know (unless you’ve been living in Alpha Centauri for the past century) the openSUSE community KDE team publishes LiveCD images for those willing to test the latest state of KDE software from the git master branches without having to break machines, causing a zombie apocalypse and so on. This post highlights the most recent developments in the area. Up to now, we had 3 different media, depending on the base distribution (stable Leap, ever-rolling Tumbleweed) and whether you wanted to go with the safe road (X11 session) or the dangerous path (Wayland):

Every day, a sizable number of people posts problems on the KDE Community Forums and the ever-helpful staff does their best to solve whatever issues they’re facing. But what exactly does one do when this happens? This post provides more insights on the process. NOTE: The following applies to my workflow for the Kontact & PIM subforum. Step 1: Someone posts a problem The questions posted are various, and range from simple tasks (“how I do XXX”) to very specific workflows.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version Support for width / height based filtering: now you can exclude posts that are below a specific width or height (or both) New dependency: KTextWidgets Coming up next Sooner or later I’ll get to finish the multiple API support, but given that there’s close to no interest for these programs (people are happy to use a browser) and that I work on this very irregularly (every 6-7 months at best), there’s no ETA at all.

Ever since the launch of Argon and Krypton, the openSUSE community KDE team didn’t really stand still: a number of changes (and potentially nice additions) have been brewing this week. This post recapitulates the most important one. I’d like the most recent Qt, please As pre-announced by a G+ post, the openSUSE repositories bringing KDE software directly from KDE git (KDE:Unstable:Frameworks and KDE:Unstable:Applications) have switched their Qt libraries from Qt 5.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version The image window is shown again with recent Qt and KF5 versions; Remember the last directory saved when saving images; Remove (hopefully) hang when saving images.

In the past week, the KDE Community Forums administrators had been discussing how to improve the current forum layout. There are a few reasons in favor of a reorganization. First of all, to reflect better what KDE is (a community that produces software). Secondly, to provide a better organinzation for all kinds of people: those that require support, those that offer support, and those who want to contribute. All of this within a (hopefully) logical structure.

KDE has recently released the newest Release Candidate of the Applications 15.08 release. Among the new features and changes of this release, there is a technology preview of the new KF5-based KDE PIM suite (including reworked, faster Akonadi internals), new applications ported to KF5 (the most notable ones being Dolphin and Ark). After some consideration and thinking on how to allow users to test this release without affecting their setups too much, the openSUSE community KDE team is happy to bring this latest RC to openSUSE Tumbleweed and openSUSE 13.

Since [26th December 2005]({{ site.url }}/2005/12/up-and-running/), I’ve been runnning this blog with Wordpress. At the time there were little alternatives and finally I had got hold of a host (Dreamhost, at the time) that supported PHP and MySQL without being overly restrictive. 10 years later, things have somehow changed. The issue The main reason lies in how Wordpress has evolved over time: no, I’m not speaking about the subjective “bloat”, but the fact that it’s been moving towards a full-blown CMS, which is not what I have in mind to run my blog.

A lot has been happening on the KDE side of openSUSE… this post summarizes what’s been going on so far. Live media for Plasma 5 One of the most-often requested ways to test Plasma 5, given it can’t be coinstalled with the 4.x Workspace, is the availability of live images to test either in VM or bare metal without touching existing systems. Given that other distributions started doing so since a while, naturally openSUSE couldn’t stay still.

Following up on yesterday’s release, I’ve released Danbooru Client 0.3.0. This early new release is mostly due to the fact that the QML view file wasn’t installed (sorry!) so part of the UI would not even load (or even crash). That said, I’ve managed to get some extra features in: Fade-in/out animation when posts are being downloaded Support for tagging is back (EXPERIMENTAL): it is optional, and requires KFileMetaData (not yet a framework, but should be distributed with Plasma 5).

After my previous post, development went quicker than expected, so I’ve actually managed to get a real version out. ;) So without much ado… here’s Danbooru Client 0.2.0! This redesigned C++ version brings a few more features compared to the PyKDE4 version, notably: Infinite scrolling (experimental) - Just scroll down to load the next set of posts QML-based thumbnail view Click on the image below to have a demonstration of what’s in this release (warning: 2M GIF file): [!

Some of you may remember a semi-complex application I wrote back in the days, namely [Danbooru Client]({{ site.url }}/projects/danbooru-client/). Written in PyKDE4, it provided a semi-decent interface to Danbooru-style boards. It mostly worked and received little maintenance (also because I didn’t have that much time for maintenance). In the mean time, I started learning some C++. No, it’s not that I don’t like Python (in fact I do, I use it a lot in my day job), but I wanted to gain at least some basic skills to be able to contribute directly to KDE software.

The ever-amazing Plasma team from KDEjust put out a new release of Plasma. I won’t spend much describing how big of an improvement it is - the release announcement at KDE has all the details needed to whet your appetite. And of course, now it’s the turn of distributions to get out packages for the users at large. This is also the case for openSUSE. The KDE:Frameworks5 repository hosts the new 5.

Short version: the KDE PIM in openSUSE Tumbleweed is moving from 4.14.x to the KF5 based version. More details below. Some history As you may know, up to now the default PIM suite for Plasma 5 in openSUSE Tumbleweed was the KDE PIM 4.14, based on kdelibs 4.x. While upstream KDE has offered a KF5-based version since Applications 15.08, it has been originally marked as a technology preview, so we (the openSUSE community KDE team) thought it would be more prudent to stick with the 4.

Following up onKDE’s announcement of the latest stable release, we have now packages available for 12.3 and 13.1 (a 13.2 repository will be made available after it is out). You will find them in the KDE:Current repository. Current users of this repository will get the new release automatically once they update. Why you should upgrade? You can take a look at the list of changes to get an idea. These fixes touch many important KDE applications, including KMail, Okular and Dolphin.

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too. I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

Since a couple of weeks the packages offered by openSUSE in the KDE:Unstable:Frameworks repository have undergone a series of changes. In particular, the packages now install to /usr. For the libraries (KDE Frameworks 5) this will mean a transparent change for the userbase as they are expected to be co-installable, but the workspace components (Plasma 5) will confict with the existing Plasma 4.11.x installation. What does this mean in practice? If you want to use Plasma 5 you will not be able to use a 4.

Requests to unlock KWallet automatically on login (assuming the wallet password and user password are the same), like gnome-keyring can do, have been going on for years: in fact, bug reports requesting this feature are quite old. Recently, thanks to the efforts of Alex Fiestas, a PAM module, which interfaces KWallet to the system authentication methods, has been developed. In parallel, the necessary glue code has been also added to the various parts of the KDE workspace so that it could make use of it.

This is a guest post by Raymond “tittiatcoke” Wooninck, with contributions from myself and Hrvoje “shumski” Senjan In the next hours the [KDE:Current]({{ site.url }}/2014/03/being-current/) repository will publish the latest release from KDE (4.13). As that this release comes with a big change (the new semantic search), we would like some simple steps in order to perform the right upgrade. Before the upgrade In order to migrate data automatically from the Nepomuk store to the new format, you will need Nepomuk up and running, and just for the time needed for the migration.

It is not news that openSUSE, through to the effort of the openSUSE community KDE team, offers several third-party repositories for those who want the latest software from KDE. Since a while, stable releases were offered in the KDE:Release:4x repositories, created with every major release of KDE software. These were meant to offer the latest and greatest to the users without having them to track KDE:Distro:Factory, which is instead used to track packaging for the next openSUSE release and is more in a state of flux.

Yesterday KDE released their first beta of the upcoming 4.13 version of Workspaces, Applications and Development platform. As usual with the major releases from KDE, it’s packed with a lot of “good stuff”. Giving a list of all the improvements is daunting, however there are some key points that stand out: Searching: KDE’s next generation semantic search is a prominent feature of this release. It’s several orders of magnitude faster, much leaner on memory and generally is a great improvement from the previous situation (this writer has been testing it for the past months and he’s absolutely delighted about it).

Among the different widgets I use on my desktop, there is a small one which tells me my current public IP address. The reason I’m having it is due to the fact that my own ISP uses a NAT for almost all its customers (don’t ask - long story) and so I need to keep tabs on my current IP, because it may have been blacklisted, and so on. Up to now I was using this plasmoid written in Python, but the code had several issues and used its own way of getting the public IP.

And so, finally openSUSE 13.1 is out of the door (I couldn’t celebrate like I wanted, as I’ve been very busy). This release has lots of improvements, and of course, the latest stable software from KDE. It is time (perhaps?) to look back and see what the team has done during this development cycle. With regards to the KDE software packaging, the past 8 months have seen quite an increase in the involvement of poeple from the community.

In the past few days, the openSUSE KDE team has been working hard, following the footsteps of the nice work done by the Kubuntu and Arch Linux communities, to provide Qt5 packages for the distribution. In fact, work was already done in the past, but the packages were not coinstallable with the existing Qt4 installation. Thanks to a renewed effort, the OBS holds now Qt5 packages that won’t overwrite the existing Qt4 install: they currently live in the KDE:Qt51 repository (Factory and openSUSE 12.

The latest release of the KDE Platform, Workspaces, and Applications (4.11) is around the corner: in fact, the last RC was recently made available. We’re almost there, but it doesn’t mean that testing and reporting should stop: on the contrary, it is needed even more to ensure that no bad bugs crawl up in the final release. As part of this effort, openSUSE packages for RC2 have been released through the OBS, and are available in the KDE:Distro:Factory repository.

The latest release from KDE moved from beta to RC stage, thus finding and reporting bugs is more important that ever. At the same time, the distribution packaging teams are also working in polishing their packages. As far as openSUSE is concerned (not dissing other distros, just mentioning the one I’m involved in ;), you can kill two birds with one stone by installing the packages provided in the KDE:Distro:Factory repository.

KDE released the second beta of the KDE Platform, Workspaces and Applications 4.11, and after the necessary time for the OBS to build packages from the released tarballs, packages are available for openSUSE 12.3 and openSUSE Factory. Like the previous beta, they are available through the KDE:Distro:Factory repository. 4.11.x is is targeted for inclusion in the upcoming openSUSE 13.1. So far 4.11 has been pretty stable for me, but you should never forget these packages are for testing and bug reporting purposes: don’t use them on production systems.

As a consequence of [the recent changes in the repositories]({{ site.url }}/2013/06/upcoming-changes-to-opensuse-kde-repositories), the openSUSE KDE team is happy to announce the availability of packages containing the first beta of the KDE Platform, Workspaces and Applications 4.11. Packages are available in the KDE:Distro:Factory repository. As it is beta software, it may have not-yet-discovered bugs, and its use is recommended only if you are willing to test packaging (reporting bugs to Novell’s bugzilla) or the software (reporting bugs directly to KDE).

Since KDE has released the first beta of Platform, Workspaces, and Applications 4.11, there will be some changes in the packages offered in the openSUSE repositories. In short: KDE:Distro:Factory will now start tracking 4.11 betas and RCs: packages are being worked on. Use this version to test packages and to report bugs upstream. KDE:Release:410 has been decoupled from KDE:Distro:Factory. If you were using 4.10 packages from KDF, you’re highly encouraged to move to this repository.

These posts kind of sound like a broken record, right? ;) Anyway, since KDE has released new versions of Platform, Workspaces and Applications as part of the stable release cycle, thanks to the OBS we have packages available for openSUSE 12.2 and 12.3. The 4.10.4 update will also be released as an official update for 12.3 in due time. Where you can get the packages? Two places, as usual: KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release; KDE:Release:410 (openSUSE 12.

KDE released 4.10.3 versions of the Platform, Workspaces and Applications yesterday, with more than 70 bugs being fixed. Notably: Several fixes in handling encrypted mails in KMail Fixes for KDEPIM syncing and ownCloud A number of improvements in Dolphin, including crash fixes Optimizations in the Plasma Workspaces [The full list](https://bugs.kde.org/buglist.cgi?query_format=advanced&bug_status=RESOLVED&bug_status=VERIFIED&bug_status=CLOSED&bugidtype=include&chfieldfrom=2013-01-01&chfieldto=Now&chfield=cf_versionfixedin&chfieldvalue=4.10.3&order=Bug Number&list_id=638034) has other important changes. As usual, there are two different repositories from which you can get them:

KDE has released its monthly update for the 4.10 release, and after a brief wait while the Open Build Service worked over the released tarballs, the openSUSE KDE team is pleased to announce the availability of the 4.10.2 release packages for openSUSE 12.2 and 12.3. []({{ site.url }}/images/2013/04/757111961.png) Despite being a minor release, more than 100 bugs were fixed, in particular there were many KDEPIM fixes touching both the low level stack and KMail/KAddressbook/Kontact.

Hot on the heels of the announcement from KDE, the openSUSE KDE team is happy to announce the availability of packages for the latest stable release of the KDE Platform, Workspaces, and Applications. Packages are available in the KDE:Distro:Factory repository (which is where the packages to land in 12.3 are tested) for openSUSE Factory (soon to be 12.3) and openSUSE 12.2 and soon (when the Open Build Systen finishes rebuilding a number of packages) in the KDE:Release:410  repository for openSUSE 12.

Following up on the announcement from KDE, the openSUSE KDE team is happy to announce the availability of 4.10 RC3 packages. Remember that they are packages meant for testing and reporting bugs, so that the next release will be as polished as possible. You will find the packages in the KDE:Distro:Factory repository. An updated live media based on the upcoming openSUSE 12.3 ([see previous post]({{ site.url }}/2013/01/test-the-upcoming-opensuse-12-3-and-kde-workspace-applications-and-platform-4-10-rc2)) is also available (files named KDE4-4.

Following up on my previous post, a different type of image has been made by the openSUSE KDE community members. In particular, alin has created images sporting the same software from KDE (4.10 RC2) but using the upcoming openSUSE 12.3 as base. Download links: 32 bit version 64 bit version Release directory (in case the above links go 404; the files are named KDE4-.4.10.RC2-Live) These images are provided not only to test 4.

The 4.10 release for the KDE Development Platform, Workspaces and Applications is drawing nigh… as you may have read, there is now an additional release candidate in order to test some last-minute changes. Of course, the KDE developers can only do so much: it’s impossible to test all possible combinations. That is, unless the community at large helps by finding and reporting issues the developers can fix. But doing so requires a 4.

Yesterday Alex Fiestas showed on his blog a video of a recent development version of the KScreen library, created to handle easily multiple monitor setups in KDE, almost in an “automagic” way. As this is a project where configurations and setups are highly heterogeneous, a lot of testing is required to ensure things work reliably. Of course, you cannot ask a developer to have all sorts of screen combinations, but remember one of the strengths of FOSS: “many eyes make bugs shallow”.

openSUSE is migrating to the use of systemd for the upcoming 12.3 version, given the difficulties that emerged in trying to co-maintain two different init systems (SysV + systemd). While I am not going into the details of this choice (I leave this to more informed people), this has some consequences for software higher in the stack. As ConsoleKit is deprecated, systemd offers its own daemon to keep track of sessions and assigned seats in a system.

The KDE community has just released Beta 2 of the upcoming 4.10 release of the Development Platform, Workspaces, and Applications. Of course, distributions are providing binary packages for the adventurous… and how could the green distro be left out? In fact, it is not. Beta 2 packages were uploaded and built in the KDE:Distro:Factory repository. Updated packages have also been submitted to the development version of openSUSE (Factory) as the ultimate goal is having 4.

When I’m not on forum duty or handling openSUSE-related contributions, I try to improve my code contributions to KDE, even though I’m by no means an experienced programmer (I program all day long in Python, but I’m still a biologist after all). For the upcoming 4.10 release I’ve been polishing up Python 3 support. As you may know, Python 3 isn’t the standard in many distributions (Arch Linux excluded), but despite the slow start, it is slowly gaining steam.

As others, bigger members in the KDE community say, “nobody will do it for you, and therefore they will”. The patch from the title comes from such a story. Let’s give some background first: I’m really a heavy activity user, especially when working. My home PC has about five activities, my work one 3, and I managed to compartimentalize the various “topics” that each activity does pretty well. After an update a couple of weeks ago from the latest code from KDE git, I started noticing weird behavior.

Recently Fedora’s Lukas Tinkl pushed to kdelibs (for the 4.10 release) a patch that enabled Solid to talk to udisks2, which is a replacement for udisks. Fedora already moved to udisks2 (and killed HAL) and future GNOME releases will only use udisks2, so the need for a working backend was a necessity, and at the same time they acted like good open source citizens, and pushed the code both to 4.

Many of you know that KDE Brainstorm ideas aren’t posted straight away: they are always pre-screened to avoid repetitions, features that cannot be implemented technically, violations of the Code of Conduct, and so on. This is possible thanks to the work of the Idea Moderators, that patrol Brainstorm and evaluate the new ideas being posted. Recently, a few of them got too busy and thus we’re experiencing a backlog of ideas staying in the Vault (the staging area for evaluation) for longer times than usual.

The recent post by Dario on the KDE Workspace Vision raised some concerns on why Brainstorm was not used.One commenter even said _Right now it feels like “Throw an idea over a wall for no-one but end users to discuss until it bitrot’s”. _ _ _ The Brainstorm section is indeed in need of help. To make it more useful, a couple of things are needed: Statistics to evaluate which ideas are best representative: it can’t be just the number of votes per se as there are things like confirmation bias or controversies that may inflate the numbers Integration with Bugzilla: a way to automatically (using XML-RPC) send the ideas flagged as representative to a bug report filed under “wishlist”.

Recently we’ve seen several blog posts on Planet KDE related to Nepomuk. Reading those I thought that I could add some (little) semantic features to [Danbooru Client]({{ site.url }}/projects/danbooru-client). Danbooru Client already makes use of Nepomuk: if enabled, tags extracted from Danbooru items are added as Nepomuk tags. But since at least some Danbooru boards are specialized in certain types of images (e.g., wallpapers only, for examples) I found it would be nice to have Nepomuk show me only the images that come from a specific Danbooru board.

Recently in the Plasma mailing list, KDE developers have discussed a new screen-locking implementation that could be added to the upcoming 4.8 release of the KDE Workspaces. The first reason to do so was to solve some security constraints of the existing implementation. As an added bonus, screen locking should be also more aestetically pleasing. There is however a trade-off: such implementation would mean that screensavers that rely on X (also called X screensavers) would not be compatible.

In one of my previous blog posts I dealt with [tagging files and resources with Nepomuk]({{ site.url }}/2010/10/pykde4-tag-and-annotate-files-using-nepomuk). But Nepomuk is not only about storing metadata, it is also about retrieving and _interrogating _data. Normally, this would mean querying the metadata database directly, using queries written in SPARQL. But this is not intuitive, can be inefficient (if you do things the wrong way) and error prone (oops, I messed up a parameter!

Recently, a question came up on the KDE Community Forums regarding the use of multiple Google Calendars with KOrganizer. The preferred access up to now has been with googledata Akonadi resource, however that doesn’t support more than one calendar, and (at least from my unscientific observation) seems to be rather unmaintained these days.

Luckily, not all’s lost. Akonadi recently gained the opportunity of accessing CalDAV resources, and Google Calendar also offers a CalDAV interface, hence this is possible.

This post will briefly describe how (thanks go to PIMster krop, which casually mentioned the possibility on IRC and prompted me to investigate).

Some of the oldest readers of this blog are well aware of [a certain hobby of mine]({{ site.url }}/category/anime). Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on. Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated?

As you may already know, recently the KDE sysadmins completely overhauled the commit hooks used with the Git infrastructure. Written in Python, they have already brought significant improvements to the current workflows. These hooks include keywords that when specified trigger particular actions: the most used are to CC specific email addresses (CCMAIL), to CC bug reports (CCBUG) or to close bug reports (BUG). With the adoption of Review Board to facilitate code reviews, there were also requests for a REVIEW keyword that could close the review requests without asking the submitters to do so manually (which is slow and not always effective).

One of the greatest strengths of KDE is undoubtedly the asynchronous and network-transparent I/O access, employed by the so-called “I/O” slaves, part of the KIO class. If you are developing an application that requires file or network access, those classes make things incredibly simple to do, and they don’t freeze your GUI when you are in the middle of a process. In this post I’ll show how to use KIO to retrieve files from network resources using PyKDE4.

Some time has passed since I last blogged… this was not only due to lack of time but also due to motivation (writing long texts can be discouraging at times). In any case, I’d like to rectify for that. In this post, I’ll talk about Nepomuk, and in particular how to use it to tag and annotate arbitrary files using its API in PyKDE4. Before starting, let me say that creating this tutorial was only possible thanks to the help of Sebastian Trueg, who helped me by pointing out some mistakes I was doing.

The rest is up to you to figure out.

With my last entry, I announced the start of the work for an OCS library for the KDE Community Forums. Today I’d like to blog again about the recent developments. First of all, now there isn’t one, but two Python modules: _ocslib, _ a pure Python module that can be used to interface with OCS-based forum systems; ocslibkde, a PyKDE4 based module that can be used to interface with OCS-based forum system in KDE applications.

For KDE developers, web-based forums are often uncommon workflows. Indeed, for communication among developers mailing lists are much better tools, especially since you can handle everything inside a client (most of the time), compared to forums where you have to use a web browser. The ways of reading, replying and interacting with posters are dramatically different. And that is why some developers find themselves uncomfortable with the KDE Community Forums.

In the past weeks and days, the KDE Community Forums staff has been working to bring new features to improve even more the user experience. A few months ago, the staff was discussing the idea of finding a way to guide users to the most appropriate forum to post their questions or discussions. Now, thanks also to the return in service of one of our admins (welcome back, sayakb!) the feature is now being implemented, as the screenshots below will show.

 My Akademy talk proposal was not accepted, but the organizers were kind enough to offer me the chance to hold a BoF on the same subject. Now I bet you wonder on what I’m going to discuss, and I think the title already gives you an idea: KDE and bioinformatics: the missing link Although in the KDE community we have our fair share of scientists (hey there, Stuart!

Those who use PyQt and PyKDE4 are certainly familiar with the syntax used to connect signals and slots: [python] from PyQt4 import QtCore from PyQt4 import QtGui from PyKDE4 import kdeui class MyGUI(QtGui.QWidget): def __init__(self, parent=None): super(MyGUI, self).__init__(parent) self.pushbutton = kdeui.KPushButton() self.pushbutton.setText("Push me!") QObject.connect(self.pushbutton, QtCore.SIGNAL("clicked()"), self.button_pushed) def button_pushed(self): print "Button clicked" [/python] The main advantage of this syntax is that it’s very close to the C++ equivalent, and so you can translate easily from C++ to Python.

Recently, I investigated how to perform some checks on web addresses using KIO for Danbooru Client. My old code was synchronous, so it blocked the application while checking, thus causing all sort of troubles (UI freezing, etc.). Therefore, making the switch to KIO was the best solution. However, I had one problem: how could I check the HTTP response? I knew already that the various ioslaves can store metadata, consisting of key-value pairs which are specific on the slave used.

With my brand-new SVN account, I just committed some code to kdeexamples, KDE’s example code module. In particular, I committed a simple example which shows how to use KConfigXT via PyKDE4, a simplified version of [what I wrote about here]({{ site.url }}/2009/10/howto-kconfigxt-with-pykde4). As most of KDE is C++, and the Python API docs are translated directly from the C++ API docs, it is essential to have good examples to help newcomers learn faster.

Sometimes answering apparently harmless questions on instant messaging can have unexpected results. In particular, I was telling about Danbooru Client to someone and a question popped up “Why don’t you support pages?”. It seemed a nice idea, so I branched off the code (yay for git!) and started working on it. Well, it took me more than a month to get this thing done… I didn’t spend every day coding, but it was a challenge.

KDE SC 4.4 Beta 1 has been released, and of course I couldn’t stay still. Thanks to the friendly openSUSE Build Service, there were packages available, so I just pointed my zypper sources to KDE:KDE4:UNSTABLE:Desktop repository, adjusted a few other things (mainly other third-party repositories) and updated.

Do you like KDE? Did you ever find yourself in a position of wanting to help, but you didn’t know what to do, or who to talk to? Do you feel you could use help to get started? Today, the KDE Community Forums would like to provide the opportunity to answer those questions by annoucing the continuation of the tutorial courses known as Klassrooms. What are Klassrooms? Klassrooms are tutorial “lessons” held in a specific area of the forum.

Well, there wasn’t a Day 1 for me (I got to the hotel too late to follow the first day of the meeting), so that is why I’m starting on day 2. To start, I need to say that I had never been to a sprint before: I am already accustomed to meeting for real someone from online, but for all the attendants, they had been just names or nicks on IRC.

A while ago I presented [“danbooru2nepomuk”]({{ site.url }}/2009/10/danbooru2nepomuk-a-nepomuk-tagger-for-danbooru-images), a small program to tag images coming from Danbooru-based image boards. Today I want to present the evolution of that program, that is a PyKDE4 client for those boards.

If you read around the KDE Techbase, or if you develop KDE applications, you may have heard about KDE’s KConfigXT. This is an extension of KDE’s KConfig, and can be used to generate nice configure dialogs with multiple pages with minimal effort, also taking care of saving and applying settings. In short, something really neat! But there are problems when using it with interpreted language bindings (such as PyKDE, which is the one I use):

• KConfigXT requires an XML file and an INI-like file to be compiled by kconfig_compiler in order to produce C++ files
• There is no such a tool (at least to my knowledge) that does the same job for bindings

So what to do? Either give up on the niceness of KConfigXT, or work around the issue. I chose the latter.

In line with the project’s committment to openness, the KDE developers and contributors are not a secretive bunch. In fact, the “People Behind KDE” initiative has provided the community with interviews of quite a number of the developers. And by reading those interviews, haven’t you ever felt the need of asking a specific question, outside from those prepared by the interviewer? For example, more details about what the specific developer is doing, or what his/her plans are for the next version of KDE.

While browsing around kde-look.org, I’ve stumbled upon a nice little Plasma scripted widget, and I’m publishing this to have it get more exposure. A good part of the KDE community knows at least little about Nepomuk, and its ability to attach semantic tags to your files - basically words that describe the file, be it an image, a text document, or anything you’d like. For example, you could tag all the photos from your vacation with the name of the place you’ve been.

Hello people! Yes, it’s been a while but I haven’t forgotten about it… with the Brainstorm’s new look and most technical issues resolved, I’m able to make Brainstorm Digests more often (hopefully!) Issue 3 - Special summary issue Since we have skipped a few months, what I’d like to present today (aside the usual data about the past month), is a general overview of the state of Brainstorm since the start of the initiative a while ago.

As you all know, KDE 4.3.0 has been releeased today! Now it’s the time to tell the developers “thanks” for their hard work. Join us in the KDE Community Forums and spread the word!

Up to now, the main language in which KDE applications are developed is C++. This is a perfectly valid choice: however, at least for users that don’t have a computing background (I include myself in the list: I do science) C++ can be a rather steep requirement (although Hans, fellow staff member at the KDE Community forums, is doing a nice job in explaining his learning experience). Scripted language bindings (that have a lower barrier of entry) for KDE exist: on top of my memory I can list Python, Ruby, and C# (and I’ve probably missed a few).

The KDE Brainstorm, where users can post and vote for feature requests for KDE, is the most visited area of the KDE Community Forums. In an effort to improve the experience of both users and developers, the KDE Community Forums staff is proud to present a brand new version of the KDE Brainstorm.  The new interface resembles the IdeaTorrent sites, but it is still powered by the forum software (phpBB), a clear example of the flexibility of the platform.

A few may know that I more or less maintain the Plasma FAQ page on KDE’s UserBase. Given the rapid advance of Plasma between KDE versions, each time a new version is out a new FAQ needs to be made, as the content rapidly becomes obsolete. For 4.3, unfortunately, I’m not sure I’ll be able to put a new version up in time for the 4.3 release. The reason is mostly practical: it takes a bit of work to collect and add information, and currently my free time is limited due to a rather heavy workload and some other commitments.

Today, a major upgrade of the KDE Community Forums took place. The change brings quite a number of changes to the forums themselves, and it’s a further step towards providing a better experience for KDE users (and developers too!).

Hello, and welcome to the second issue of the KDE Brainstorm Digest! This issue comes in slightly late, due to some real time commitments, but I couldn’t leave you without it, could I?

A rather big change has gone into KDE’s SVN recently: Ben Cooksley (bcooksley) and Mathias Soeken (msoeken) have committed a complete rework of System Settings.

Compared to the previous implementation, System Settings now has two operational modes, one being the current icon-based view since KDE 4 (and also seen in Kubuntu prior to KDE 4), and a second view, named “Classic”, which reimplements the old KControl look and feel. The latter change is probably very welcome to anyone who found System Settings less useful than the old KControl. The current view used can be changed in the configuration options. In addition, upon hovering an icon or module that show if there are any sub-modules associated.

Currently, the openSUSE Build Service contains Amarok 2.1 beta packages only for the KDE:KDE4:UNSTABLE repository (i.e. current trunk, soon-to-be 4.3). However, a quick search identified a repository that contains a RPM of current 2.0.90 compiled for the KDE:KDE4:Factory Desktop (which will change to 4.3 with Beta 1) andanother one for the KDE:42 repository. So you can add them using YaST or zypper and download the relevant package. I had to force a repository using zypper, otherwise zypper would complain and try to install amarok 1.

Hello, and welcome to the first “issue” of the KDE Brainstorm monthly digest. First of all, a few words of introduction. There are quite a number of ideas being posted on the KDE Brainstorm, and it would be nice to know how the initiative is faring, and important highlights, like what ideas are more popular, which are more controversial, etc. That is why the idea of a monthly digest was born (in a similar fashion as the fabolous Commit Digest).

Via Harald Hvaal’s blog I learnt that the first non-forum suggestion has been implemented! I think this shows without doubt that initiatives like the KDE Brainstorm are undoubtedly useful to the community at large, both users and developers. Keep on rocking!

In the past months I’ve always wanted to write a small Plasma applet to aid me in some boring tasks as a bioinformatician. One example (for the non-scientific crowd out there) is when I find a specific gene out of my analysis work which I want to take a look at. I am often lazy, so instead of firing up the browser to look at the online resources, I wanted to write something which could access said resources programmatically.

Now that the KDE Brainstorm has been launched, it’s time to take a look at the results so far. Currently, the forum hosts 160 threads, approximately one for each idea, and 441 posts. Not bad for the first two days of operation. At the same time, the staff has been working hard to make sure only appropriate ideas (not bug reports, not duplicates…) are on the forum. People have also begun voting, although slowly: it’s understandable, given the fact that there are so many threads in so little time.

It’s finally there: KDE Brainstorm has been launched today! Like this, it will be possible to propose features and have them voted by the community, and then submit the most voted requests to the developers. Every feature request is screened prior to posting, so duplicates, spam and flames are unlikely to occur. There is no guarantee that the voted upon features will be implemented, but as opposed to individual postings, this approach reduces the noise a lot, and allows a better communication between the “two worlds” (users and developers).

No, it’s not_ _a teen-like “I hate my life, I’m going to die tomorrow” post. I’m actually referring to the comments of a person nicknamed “I Love” that are popping up in almost all blogs that are linked to PlanetKDE which deal with Plasma or KDE4 adoption. The name “I Love” contrasts with an attitude that is unconstructive and rather trollish. This wouldn’t be such a big problem, if not for the fact that posts from said individual have had a rather negative effect: for example Aaron was forced to turn comment moderation on on his blog, Jos’ entry on the new Plasma in the upcoming KDE 4.

Mtux, of choqok fame, along with another person, has written Bilbo Blogger, a blogging utility for Blogger or any blog that supports Blogger1.0, MetaWeblog, and MovableType APIs (EDIT: also GData). It is based on the KDE4 libraries and it includes a WYSIWYG editor, an HTML editor, and a Post Preview function that can even fetch your blog’s CSS to render the entry and see how it looks. It’s not released yet, but for the daring, you can actually try and compile it.

During the course of my research work, I may obtain results that are worthy of publication in scientific journals. Since my master’s thesis I’ve been using LaTeX as my writing platform, mainly because I can concentrate on content rather than presentation (I find it useful also for writing non-scientific stuff as well). Also, I can handle bibliography (essential for a scientific publication) very well without using expensive proprietary applications (such as Endnote).

In my early days I used kLyX first, then LyX, but I found the platform to be too limited for my tastes, and also LaTeX errors were difficult to diagnose. I needed a proper editor, and that’s when I heard of kile, a KDE front-end for LaTeX. Kile is currently at version 2.0.2 and is a KDE 3 application. However, in KDE SVN work is ongoing to produce a KDE4 version (2.1) and that’s what I’ll look at in this entry.

I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

I have been thinking of doing another Kourse at the KDE Forums, similar to the one that has produced three nice screencasts. My idea would be to show very brief and focused screencasts, a sort of “how do I…”. I have a few ideas, but I’d like to ask the KDE community at large. I’m mostly interested in showing single features (short videos), preferably of the “eye-opener” kind. If you have any suggestions, leave a comment.

Yes, I know I’m a bit late to the party (unfortunately today was one of the busiest days ever where I work), but I thought I’d join the other members of the KDE community, because KDE 4.2 has been released today. Take a look at the visual guide, or see if your distribution has already packages for you. For your enquiries, the KDE Forums are at your disposal.

If everything has gone correctly, my blog should be on PlanetKDE now. That means it’s time for an introduction for those readers. My name is Luca Beltrame, I’m a biotechnologist doing bioinformatics in the life sciences areas, and I’m a Free Software user/enthusiast since many years. I’ve been using KDE since 1.0 or so (if memory serves me well), but only recently, with the 4.x line of development, I’ve been trying to actually contribute a bit back to the project.

I just finished writing a new Python tutorial on KDE’s Techbase. This one deals with writing DataEngines in Python (a complement to Simon Edwards’s own Using DataEngines). Let me know what you think. As it’s a wiki, comments and suggestions are welcome.

It turned out I forgot to add the last screencast produced by the students of Kourse 2, so I’ll fix my mistake right now. Here’s Panel settings, by Kourse student TeaAge: [blip.tv ?posts_id=1653914&dest=-1]

Students from Kourse 2 fengshaun and Primoz have prepared two nice screencasts, dealing with the Zooming User Interface (ZUI) and desktop settings respectively. Without further ado, here they are: Zooming User Interface by fengshaun [blip.tv ?posts_id=1648944&dest=-1] Desktop settings by Primoz [blip.tv ?posts_id=1646835&dest=-1] As usual, both Free and non-Free versions are available. The students are also at work on subtitled versions, without the Notes plasmoid. I’ll be sure to post them once they’re done.

As some people already know,I’m mentoring a group of students on KDE Forum to create Plasma screencasts (from the upcoming KDE 4.2 version). After several adjustments back and forth, the first one (made by kourse student Primoz), showing off the various desktop settings, is complete. This version uses the Notes plasmoid to keep track of annotation, but we’re also evaluating subtitle-based versions. In the mean time, enjoy! (and spread the word).

Today I was adjusting a bit the layouts of the Activities (as defined in Plasma) to better suit my workflows. To do so I was using the brand new Activity Bar which is present in KDE 4.2. It’s very neat, but takes up space on the desktop, and while it’s not a big deal on my main PC (1280x1024 resolution), it is an issue on my recently-resuscitated EeePC (1024x600). It was then that it occured to me that such applets are, in Plasma-speak, PopupApplets, which means they adjust their behavior depending if they are in a panel or “free”.

Today I’m in a posting spree…This clip shows how to resize and move Plasma panels around. [youtube]http://www.youtube.com/watch?v=Rmpv-S5JJI4[/youtube]

Following up on my previous post, here is another screencast showing off how to create a sidebar panel and add a few plasmoids to it. As usual, the version on Youtube has annotations. [youtube]http://www.youtube.com/watch?v=WPeFSDdt2PY[/youtube]

I’ve put together a small video that shows what you can do with zooming in and out with Plasma’s Zooming User Interface (ZUI). Enjoy. (note: the version on Youtube has also annotations that explain better what is going on) [youtube]http://www.youtube.com/watch?v=EhODrJkoidA[/youtube] If you can, please spread the link to the video. We need more correct information out there.

Those of you that follow my Linux-related posts know that I work (along with others) on a FAQ trying to explain some magic behind KDE 4.x’s Plasma. Now, especially since on the Internet, there is the need to spread correct information (most of the naysayers are not quite informed). So, if you want to help KDE, please spread the word on the Plasma FAQ! If people have questions on Plasma, just direct them to

Now even the (once respected) Steven J. Vaughan-Nichols is jumping on the bandwagon of Plasma haters. With a rather uninformed and rant-ish entry that just advocates a fork, like some other people said on the kde-devel mailinglist a week or two ago. The entry is rather dismissive of everything in KDE 4 save Plasma (and a mention on Dolphin’s single click icon), and also gets some facts and links wrong (yes, the Plasma web site is outdated, but since the developers are busy coding, someone else should step up and help).

Taking advantage of the holidays, I’ve managed to land a number of fixes in Danbooru Client, and therefore I think it’s time for a new version, 0.4.0! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.

As many readers of this blog are aware, openSUSE has been offering packages of git snapshots from KDE since quite a while. They are quite useful for those wiling to test, report bugs, and / or hack on the code, but also for those who want to see what’s brewing in KDE land (without touching their existing systems). However, a major drawback for non English speakers was the lack of translations.

One thing I always wanted to do when going on holiday is to track where I go, the places I’ve been, and see how much I’ve travelled around. This is true in particular when going to places where I walk around a lot (Japan stays at the top of the list, also for other reasons that are not related to this post). Something like viewing a map showing where you were, and where did you go, with optional export to KML or GPX to import into other programs like Marble.

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others) As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in.

Omnia? The Turris Omnia is quite a nice (although a little pricey) OpenWRT-based router from CZ.NIC. It provides a fairly powerful CPU, relatively unconstrained eMMC space, and quite a lot of hackability (some revisions even have GPIO ports to play with). It runs a modified version of OpenWRT, named TurrisOS. The problem A few years ago, I built a custom NAS for my storage needs, using a cheap Intel SoC (J1900 chipset) and a (much pricier) mini-ITX small form factor server tower.

Part of this post is about openQA, openSUSE’s automated tool which tests a number of different scenarios, from installation to the behavior of the different desktop environments, plus testing the freshest code from KDE git. Recently, thanks to KDE team member Fabian Vogt, there has been important progress when testing KDE software. Testing the Dolphin file manager Those who use KDE software, either in Plasma or in other desktop environments have at least heard of Dolphin, the powerful file manager part of KDE Applications (by the way, have you checked out the recent beta yet?

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highlights of the new version Unbreak konachan.com support (change in URL format) Coming up next HTTPS support!

In the past three weeks, the openSUSE community KDE team has been pretty busy to package the latest release of Applications from KDE, 16.12. It was a pretty large task, due to the number of programs involved, and the fact that several monolithic projects were split (in particular KDE PIM). This post goes through what we did, and how we improved our packaging workflow. Some prerequisites In openSUSE speak, packages are developed in “projects”, which are separate repositories maintained on the OBS.

Admit it: how many times you have seen “software from this branch is completely untested, use it at your own risk” when you checked the latest code from any FOSS project? I bet you have, many times. For any reasonably modern project, this is not entirely true: Continuous Integration and automated testing are a huge help in ensuring that the code builds and at least does what it is supposed to do.

You may be aware that openSUSE Leap 42.2 is now in the release candidate stage, and there’s a lot of activity aimed at squashing those pesky bugs before they hit the final release. One particular bug proved to be quite tough to fix, and it was only solved thanks to the “heroes” mentioned in the title. This is the history of the bug. The report October 6th, 2016 - A bug iss reported against Plasma reporting a hard freeze of Plasma when using the Noveau driver, but not with the closed NVIDIA blob.

As you may know (unless you’ve been living in Alpha Centauri for the past century) the openSUSE community KDE team publishes LiveCD images for those willing to test the latest state of KDE software from the git master branches without having to break machines, causing a zombie apocalypse and so on. This post highlights the most recent developments in the area. Up to now, we had 3 different media, depending on the base distribution (stable Leap, ever-rolling Tumbleweed) and whether you wanted to go with the safe road (X11 session) or the dangerous path (Wayland):

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version Support for width / height based filtering: now you can exclude posts that are below a specific width or height (or both) New dependency: KTextWidgets Coming up next Sooner or later I’ll get to finish the multiple API support, but given that there’s close to no interest for these programs (people are happy to use a browser) and that I work on this very irregularly (every 6-7 months at best), there’s no ETA at all.

Ever since the launch of Argon and Krypton, the openSUSE community KDE team didn’t really stand still: a number of changes (and potentially nice additions) have been brewing this week. This post recapitulates the most important one. I’d like the most recent Qt, please As pre-announced by a G+ post, the openSUSE repositories bringing KDE software directly from KDE git (KDE:Unstable:Frameworks and KDE:Unstable:Applications) have switched their Qt libraries from Qt 5.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

Recently I’ve been setting up LDAP authentication on CentOS servers to give a shared authentication method to all the compute nodes I use for my day job. I use 389-DS as it’s in my opinion much better to administer and configure than openLDAP (plus, it has very good documentation). As I have a self built NAS at home (with openSUSE Tumbleweed), I thought it’d be nice to use LDAP for all the web applications I run there.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version The image window is shown again with recent Qt and KF5 versions; Remember the last directory saved when saving images; Remove (hopefully) hang when saving images.

Recently I’ve been testing out murmur, http://wiki.mumble.info/wiki/Main_Page server component, on my CentOS 7 server. Murmur requires specific ports being open to operate, and when using it I would open them manually, and close them after the session had been completed. I found it pretty tedious: I wanted to wrap it into a single call to the service, so I could enable my user (via sudoers) to be able to start and stop the service without worrying about elevating permissions to start and stop the firewall.

In the past week, the KDE Community Forums administrators had been discussing how to improve the current forum layout. There are a few reasons in favor of a reorganization. First of all, to reflect better what KDE is (a community that produces software). Secondly, to provide a better organinzation for all kinds of people: those that require support, those that offer support, and those who want to contribute. All of this within a (hopefully) logical structure.

KDE has recently released the newest Release Candidate of the Applications 15.08 release. Among the new features and changes of this release, there is a technology preview of the new KF5-based KDE PIM suite (including reworked, faster Akonadi internals), new applications ported to KF5 (the most notable ones being Dolphin and Ark). After some consideration and thinking on how to allow users to test this release without affecting their setups too much, the openSUSE community KDE team is happy to bring this latest RC to openSUSE Tumbleweed and openSUSE 13.

(Inspired by http://viccuad.me/blog/GPG-transition-statement/) This exact same text can be found at this location. -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Sun Jun 7 14:12:39 CEST 2015 For a number of reasons, i've recently set up a new OpenPGP key, and will be transitioning away from my old one. The old key will continue to be valid for some time, but i prefer all future correspondence to come to the new one. I would also like this new key to be re-integrated into the web of trust.

As I said in my latest post, I wasn’t very happy with using Disqus to store my comments, mainly because I do not want my data to be hosted by someone else. Thanks to some commenters, I was made aware of an alternative, called isso. After reading the online documentation, I decided to set it up with dennogumi.org. It was all a matter of creating a new user called isso, setting a virtualenv to its home dir, and then installing isso itself and uWSGI:

Since [26th December 2005]({{ site.url }}/2005/12/up-and-running/), I’ve been runnning this blog with Wordpress. At the time there were little alternatives and finally I had got hold of a host (Dreamhost, at the time) that supported PHP and MySQL without being overly restrictive. 10 years later, things have somehow changed. The issue The main reason lies in how Wordpress has evolved over time: no, I’m not speaking about the subjective “bloat”, but the fact that it’s been moving towards a full-blown CMS, which is not what I have in mind to run my blog.

A lot has been happening on the KDE side of openSUSE… this post summarizes what’s been going on so far. Live media for Plasma 5 One of the most-often requested ways to test Plasma 5, given it can’t be coinstalled with the 4.x Workspace, is the availability of live images to test either in VM or bare metal without touching existing systems. Given that other distributions started doing so since a while, naturally openSUSE couldn’t stay still.

Following up on yesterday’s release, I’ve released Danbooru Client 0.3.0. This early new release is mostly due to the fact that the QML view file wasn’t installed (sorry!) so part of the UI would not even load (or even crash). That said, I’ve managed to get some extra features in: Fade-in/out animation when posts are being downloaded Support for tagging is back (EXPERIMENTAL): it is optional, and requires KFileMetaData (not yet a framework, but should be distributed with Plasma 5).

After my previous post, development went quicker than expected, so I’ve actually managed to get a real version out. ;) So without much ado… here’s Danbooru Client 0.2.0! This redesigned C++ version brings a few more features compared to the PyKDE4 version, notably: Infinite scrolling (experimental) - Just scroll down to load the next set of posts QML-based thumbnail view Click on the image below to have a demonstration of what’s in this release (warning: 2M GIF file): [!

Some of you may remember a semi-complex application I wrote back in the days, namely [Danbooru Client]({{ site.url }}/projects/danbooru-client/). Written in PyKDE4, it provided a semi-decent interface to Danbooru-style boards. It mostly worked and received little maintenance (also because I didn’t have that much time for maintenance). In the mean time, I started learning some C++. No, it’s not that I don’t like Python (in fact I do, I use it a lot in my day job), but I wanted to gain at least some basic skills to be able to contribute directly to KDE software.

The ever-amazing Plasma team from KDEjust put out a new release of Plasma. I won’t spend much describing how big of an improvement it is - the release announcement at KDE has all the details needed to whet your appetite. And of course, now it’s the turn of distributions to get out packages for the users at large. This is also the case for openSUSE. The KDE:Frameworks5 repository hosts the new 5.

Short version: the KDE PIM in openSUSE Tumbleweed is moving from 4.14.x to the KF5 based version. More details below. Some history As you may know, up to now the default PIM suite for Plasma 5 in openSUSE Tumbleweed was the KDE PIM 4.14, based on kdelibs 4.x. While upstream KDE has offered a KF5-based version since Applications 15.08, it has been originally marked as a technology preview, so we (the openSUSE community KDE team) thought it would be more prudent to stick with the 4.

I’ve found myself in a situation where my ISP, notorious for having problems with certain online services (not to mention putting everyone under a permanent NAT) started misbehaving with Sony’s Playstation Network: I was getting timeouts of all sorts with no reason (and reading online you see all sorts of attempts from people to work around the issue). When using my phone as hotspot, everything worked, as I went through my mobile operator’s network.

Following up onKDE’s announcement of the latest stable release, we have now packages available for 12.3 and 13.1 (a 13.2 repository will be made available after it is out). You will find them in the KDE:Current repository. Current users of this repository will get the new release automatically once they update. Why you should upgrade? You can take a look at the list of changes to get an idea. These fixes touch many important KDE applications, including KMail, Okular and Dolphin.

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too. I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

Since a couple of weeks the packages offered by openSUSE in the KDE:Unstable:Frameworks repository have undergone a series of changes. In particular, the packages now install to /usr. For the libraries (KDE Frameworks 5) this will mean a transparent change for the userbase as they are expected to be co-installable, but the workspace components (Plasma 5) will confict with the existing Plasma 4.11.x installation. What does this mean in practice? If you want to use Plasma 5 you will not be able to use a 4.

Recently I was looking for a laptop: the previous one I had (an Asus EeePC 900) was almost dead (the fan broke, and the idea of dismantling everything to get to it wasn’t appealing). When looking around, I had the following requirements: It needed to run on Linux well. No exceptions. _Portable: _ at home and at my workplace I have rather powerful machines, so a desktop replacement was not needed.

This was inspired by this forum thread on the Piwigo forums. Set up rewrite rules in nginx where “piwigo” is the path the gallery lies in: location @rewrite { rewrite ^/piwigo/picture((/|$).*)$ /piwigo/picture.php$1 last; rewrite ^/piwigo/index((/|$).*)$ /piwigo/index.php$1 last; # The following is needed for batch operations which use i.php rewrite ^/piwigo/i((/|$).*)$ /piwigo/i.php$1 last; } location /piwigo { index index.php; try_files $uri $uri/ @rewrite; } location ~ ^(?

Requests to unlock KWallet automatically on login (assuming the wallet password and user password are the same), like gnome-keyring can do, have been going on for years: in fact, bug reports requesting this feature are quite old. Recently, thanks to the efforts of Alex Fiestas, a PAM module, which interfaces KWallet to the system authentication methods, has been developed. In parallel, the necessary glue code has been also added to the various parts of the KDE workspace so that it could make use of it.

This is a guest post by Raymond “tittiatcoke” Wooninck, with contributions from myself and Hrvoje “shumski” Senjan In the next hours the [KDE:Current]({{ site.url }}/2014/03/being-current/) repository will publish the latest release from KDE (4.13). As that this release comes with a big change (the new semantic search), we would like some simple steps in order to perform the right upgrade. Before the upgrade In order to migrate data automatically from the Nepomuk store to the new format, you will need Nepomuk up and running, and just for the time needed for the migration.

Yesterday KDE released their first beta of the upcoming 4.13 version of Workspaces, Applications and Development platform. As usual with the major releases from KDE, it’s packed with a lot of “good stuff”. Giving a list of all the improvements is daunting, however there are some key points that stand out: Searching: KDE’s next generation semantic search is a prominent feature of this release. It’s several orders of magnitude faster, much leaner on memory and generally is a great improvement from the previous situation (this writer has been testing it for the past months and he’s absolutely delighted about it).

Among the different widgets I use on my desktop, there is a small one which tells me my current public IP address. The reason I’m having it is due to the fact that my own ISP uses a NAT for almost all its customers (don’t ask - long story) and so I need to keep tabs on my current IP, because it may have been blacklisted, and so on. Up to now I was using this plasmoid written in Python, but the code had several issues and used its own way of getting the public IP.

And so, finally openSUSE 13.1 is out of the door (I couldn’t celebrate like I wanted, as I’ve been very busy). This release has lots of improvements, and of course, the latest stable software from KDE. It is time (perhaps?) to look back and see what the team has done during this development cycle. With regards to the KDE software packaging, the past 8 months have seen quite an increase in the involvement of poeple from the community.

As you may know, there is an ongoing effort to rearrange and adjust the openSUSE KDE repositories. In line with the previously announced deletions, and more recent adjustments, a number of changes went into the organization and layout of the KDE repositories: KDE:Distro:Factory and KDE:Release:4xy will now hold the “core” KDE packages: this means the base Development Platform, Workspaces and Applications, and additional applications for a basic desktop experience.

Summer is ending soon (at least for those living in the northern hemisphere) and while usually cleaning is done during spring, the KDE team decided to do what I’d call… autumn cleaning of repositories. You may know that the KDE presence in openSUSE, aside being the default desktop, is quite a long one. In the past years different repositories were created by the members of the openSUSE KDE team (at the time mostly made up by KDE people hired by Novell) in order to review and test packages, like newer Qt versions, KDE software, and so on.

In the past few days, the openSUSE KDE team has been working hard, following the footsteps of the nice work done by the Kubuntu and Arch Linux communities, to provide Qt5 packages for the distribution. In fact, work was already done in the past, but the packages were not coinstallable with the existing Qt4 installation. Thanks to a renewed effort, the OBS holds now Qt5 packages that won’t overwrite the existing Qt4 install: they currently live in the KDE:Qt51 repository (Factory and openSUSE 12.

The latest release of the KDE Platform, Workspaces, and Applications (4.11) is around the corner: in fact, the last RC was recently made available. We’re almost there, but it doesn’t mean that testing and reporting should stop: on the contrary, it is needed even more to ensure that no bad bugs crawl up in the final release. As part of this effort, openSUSE packages for RC2 have been released through the OBS, and are available in the KDE:Distro:Factory repository.

The latest release from KDE moved from beta to RC stage, thus finding and reporting bugs is more important that ever. At the same time, the distribution packaging teams are also working in polishing their packages. As far as openSUSE is concerned (not dissing other distros, just mentioning the one I’m involved in ;), you can kill two birds with one stone by installing the packages provided in the KDE:Distro:Factory repository.

KDE released the second beta of the KDE Platform, Workspaces and Applications 4.11, and after the necessary time for the OBS to build packages from the released tarballs, packages are available for openSUSE 12.3 and openSUSE Factory. Like the previous beta, they are available through the KDE:Distro:Factory repository. 4.11.x is is targeted for inclusion in the upcoming openSUSE 13.1. So far 4.11 has been pretty stable for me, but you should never forget these packages are for testing and bug reporting purposes: don’t use them on production systems.

As a consequence of [the recent changes in the repositories]({{ site.url }}/2013/06/upcoming-changes-to-opensuse-kde-repositories), the openSUSE KDE team is happy to announce the availability of packages containing the first beta of the KDE Platform, Workspaces and Applications 4.11. Packages are available in the KDE:Distro:Factory repository. As it is beta software, it may have not-yet-discovered bugs, and its use is recommended only if you are willing to test packaging (reporting bugs to Novell’s bugzilla) or the software (reporting bugs directly to KDE).

Since KDE has released the first beta of Platform, Workspaces, and Applications 4.11, there will be some changes in the packages offered in the openSUSE repositories. In short: KDE:Distro:Factory will now start tracking 4.11 betas and RCs: packages are being worked on. Use this version to test packages and to report bugs upstream. KDE:Release:410 has been decoupled from KDE:Distro:Factory. If you were using 4.10 packages from KDF, you’re highly encouraged to move to this repository.

These posts kind of sound like a broken record, right? ;) Anyway, since KDE has released new versions of Platform, Workspaces and Applications as part of the stable release cycle, thanks to the OBS we have packages available for openSUSE 12.2 and 12.3. The 4.10.4 update will also be released as an official update for 12.3 in due time. Where you can get the packages? Two places, as usual: KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release; KDE:Release:410 (openSUSE 12.

KDE released 4.10.3 versions of the Platform, Workspaces and Applications yesterday, with more than 70 bugs being fixed. Notably: Several fixes in handling encrypted mails in KMail Fixes for KDEPIM syncing and ownCloud A number of improvements in Dolphin, including crash fixes Optimizations in the Plasma Workspaces [The full list](https://bugs.kde.org/buglist.cgi?query_format=advanced&bug_status=RESOLVED&bug_status=VERIFIED&bug_status=CLOSED&bugidtype=include&chfieldfrom=2013-01-01&chfieldto=Now&chfield=cf_versionfixedin&chfieldvalue=4.10.3&order=Bug Number&list_id=638034) has other important changes. As usual, there are two different repositories from which you can get them:

I’m a (happy!) owner of a Casio EX-WORD Dataplus 5 XD-A4700, a Japanese electronic dictionary. Recently I looked into updating the Japanese-English dictionary (currently the Shogakukan PROGRESSIVE dictionary) installed, because it’s not good enough: too often when looking up odd sentences (like the ones in Fate/Extra CCC) I do not find any matches. EDICT is adequate, and while I can use it on my phone and tablet, I like the fact that the EX-WORD has a physical keyboard along with the stylus, and a very nice kanji handwriting recognition.

During the discussions for the release of openSUSE 12.3, the topic of update notifications and applets was brought up again. Originally openSUSE shipped with a custom update applet, but since it was basically unmaintained, the decision was made to switch to Apper for openSUSE 12.2 The original Apper used in that version had a number of issues, which the upstream developer (Daniel Nicoletti) fixed in a newer version, which also had a lot of other improvments.

The 4.10 release for the KDE Development Platform, Workspaces and Applications is drawing nigh… as you may have read, there is now an additional release candidate in order to test some last-minute changes. Of course, the KDE developers can only do so much: it’s impossible to test all possible combinations. That is, unless the community at large helps by finding and reporting issues the developers can fix. But doing so requires a 4.

Yesterday Alex Fiestas showed on his blog a video of a recent development version of the KScreen library, created to handle easily multiple monitor setups in KDE, almost in an “automagic” way. As this is a project where configurations and setups are highly heterogeneous, a lot of testing is required to ensure things work reliably. Of course, you cannot ask a developer to have all sorts of screen combinations, but remember one of the strengths of FOSS: “many eyes make bugs shallow”.

openSUSE is migrating to the use of systemd for the upcoming 12.3 version, given the difficulties that emerged in trying to co-maintain two different init systems (SysV + systemd). While I am not going into the details of this choice (I leave this to more informed people), this has some consequences for software higher in the stack. As ConsoleKit is deprecated, systemd offers its own daemon to keep track of sessions and assigned seats in a system.

The KDE community has just released Beta 2 of the upcoming 4.10 release of the Development Platform, Workspaces, and Applications. Of course, distributions are providing binary packages for the adventurous… and how could the green distro be left out? In fact, it is not. Beta 2 packages were uploaded and built in the KDE:Distro:Factory repository. Updated packages have also been submitted to the development version of openSUSE (Factory) as the ultimate goal is having 4.

When I’m not on forum duty or handling openSUSE-related contributions, I try to improve my code contributions to KDE, even though I’m by no means an experienced programmer (I program all day long in Python, but I’m still a biologist after all). For the upcoming 4.10 release I’ve been polishing up Python 3 support. As you may know, Python 3 isn’t the standard in many distributions (Arch Linux excluded), but despite the slow start, it is slowly gaining steam.

Following up my [earlier post]({{ site.url }}/2012/10/whats-cooking-for-kde-in-opensuse-12-3-theming), the new openSUSE 12.3 theme has finally landed into the official openSUSE repositories  and will be part of the upcoming 12.3. A lot of work has gone into the new theme since I last posted about it, so this post will show how things look at the moment.

A few caveats:

• The theme targets the 4.10 release of the KDE Workspaces, so it may be not be perfect under 4.9;

• The default wallpaper has not been chosen yet.

Without further ado, let’s get down to seeing what’s improved.

Although the release of openSUSE 12.3 is yet to come, the people of the openSUSE community contributing to KDE are already at work to bring the best possible KDE experience for the new release.

As others, bigger members in the KDE community say, “nobody will do it for you, and therefore they will”. The patch from the title comes from such a story. Let’s give some background first: I’m really a heavy activity user, especially when working. My home PC has about five activities, my work one 3, and I managed to compartimentalize the various “topics” that each activity does pretty well. After an update a couple of weeks ago from the latest code from KDE git, I started noticing weird behavior.

Many of you know that KDE Brainstorm ideas aren’t posted straight away: they are always pre-screened to avoid repetitions, features that cannot be implemented technically, violations of the Code of Conduct, and so on. This is possible thanks to the work of the Idea Moderators, that patrol Brainstorm and evaluate the new ideas being posted. Recently, a few of them got too busy and thus we’re experiencing a backlog of ideas staying in the Vault (the staging area for evaluation) for longer times than usual.

Recently we’ve seen several blog posts on Planet KDE related to Nepomuk. Reading those I thought that I could add some (little) semantic features to [Danbooru Client]({{ site.url }}/projects/danbooru-client). Danbooru Client already makes use of Nepomuk: if enabled, tags extracted from Danbooru items are added as Nepomuk tags. But since at least some Danbooru boards are specialized in certain types of images (e.g., wallpapers only, for examples) I found it would be nice to have Nepomuk show me only the images that come from a specific Danbooru board.

Recently in the Plasma mailing list, KDE developers have discussed a new screen-locking implementation that could be added to the upcoming 4.8 release of the KDE Workspaces. The first reason to do so was to solve some security constraints of the existing implementation. As an added bonus, screen locking should be also more aestetically pleasing. There is however a trade-off: such implementation would mean that screensavers that rely on X (also called X screensavers) would not be compatible.

In one of my previous blog posts I dealt with [tagging files and resources with Nepomuk]({{ site.url }}/2010/10/pykde4-tag-and-annotate-files-using-nepomuk). But Nepomuk is not only about storing metadata, it is also about retrieving and _interrogating _data. Normally, this would mean querying the metadata database directly, using queries written in SPARQL. But this is not intuitive, can be inefficient (if you do things the wrong way) and error prone (oops, I messed up a parameter!

Recently, a question came up on the KDE Community Forums regarding the use of multiple Google Calendars with KOrganizer. The preferred access up to now has been with googledata Akonadi resource, however that doesn’t support more than one calendar, and (at least from my unscientific observation) seems to be rather unmaintained these days.

Luckily, not all’s lost. Akonadi recently gained the opportunity of accessing CalDAV resources, and Google Calendar also offers a CalDAV interface, hence this is possible.

This post will briefly describe how (thanks go to PIMster krop, which casually mentioned the possibility on IRC and prompted me to investigate).

After many years of (good) service, I’m in the process of moving from Dreamhost web hosting to a Virtual Private Server (VPS) service hosted by the folks at Linode. It’s definitely more pricey but I like the control and freedom that I have at my disposal. Thanks to a number of guides and some help, I was able to set up lighttpd and php-fpm to serve web pages, and Postfix+dovecot+amavisd-new for email.

Some of the oldest readers of this blog are well aware of [a certain hobby of mine]({{ site.url }}/category/anime). Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on. Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated?

As you may already know, recently the KDE sysadmins completely overhauled the commit hooks used with the Git infrastructure. Written in Python, they have already brought significant improvements to the current workflows. These hooks include keywords that when specified trigger particular actions: the most used are to CC specific email addresses (CCMAIL), to CC bug reports (CCBUG) or to close bug reports (BUG). With the adoption of Review Board to facilitate code reviews, there were also requests for a REVIEW keyword that could close the review requests without asking the submitters to do so manually (which is slow and not always effective).

One of the greatest strengths of KDE is undoubtedly the asynchronous and network-transparent I/O access, employed by the so-called “I/O” slaves, part of the KIO class. If you are developing an application that requires file or network access, those classes make things incredibly simple to do, and they don’t freeze your GUI when you are in the middle of a process. In this post I’ll show how to use KIO to retrieve files from network resources using PyKDE4.

Some time has passed since I last blogged… this was not only due to lack of time but also due to motivation (writing long texts can be discouraging at times). In any case, I’d like to rectify for that. In this post, I’ll talk about Nepomuk, and in particular how to use it to tag and annotate arbitrary files using its API in PyKDE4. Before starting, let me say that creating this tutorial was only possible thanks to the help of Sebastian Trueg, who helped me by pointing out some mistakes I was doing.

The rest is up to you to figure out.

With my last entry, I announced the start of the work for an OCS library for the KDE Community Forums. Today I’d like to blog again about the recent developments. First of all, now there isn’t one, but two Python modules: _ocslib, _ a pure Python module that can be used to interface with OCS-based forum systems; ocslibkde, a PyKDE4 based module that can be used to interface with OCS-based forum system in KDE applications.

For KDE developers, web-based forums are often uncommon workflows. Indeed, for communication among developers mailing lists are much better tools, especially since you can handle everything inside a client (most of the time), compared to forums where you have to use a web browser. The ways of reading, replying and interacting with posters are dramatically different. And that is why some developers find themselves uncomfortable with the KDE Community Forums.

In the past weeks and days, the KDE Community Forums staff has been working to bring new features to improve even more the user experience. A few months ago, the staff was discussing the idea of finding a way to guide users to the most appropriate forum to post their questions or discussions. Now, thanks also to the return in service of one of our admins (welcome back, sayakb!) the feature is now being implemented, as the screenshots below will show.

Those who use PyQt and PyKDE4 are certainly familiar with the syntax used to connect signals and slots: [python] from PyQt4 import QtCore from PyQt4 import QtGui from PyKDE4 import kdeui class MyGUI(QtGui.QWidget): def __init__(self, parent=None): super(MyGUI, self).__init__(parent) self.pushbutton = kdeui.KPushButton() self.pushbutton.setText("Push me!") QObject.connect(self.pushbutton, QtCore.SIGNAL("clicked()"), self.button_pushed) def button_pushed(self): print "Button clicked" [/python] The main advantage of this syntax is that it’s very close to the C++ equivalent, and so you can translate easily from C++ to Python.

Recently, I investigated how to perform some checks on web addresses using KIO for Danbooru Client. My old code was synchronous, so it blocked the application while checking, thus causing all sort of troubles (UI freezing, etc.). Therefore, making the switch to KIO was the best solution. However, I had one problem: how could I check the HTTP response? I knew already that the various ioslaves can store metadata, consisting of key-value pairs which are specific on the slave used.

With my brand-new SVN account, I just committed some code to kdeexamples, KDE’s example code module. In particular, I committed a simple example which shows how to use KConfigXT via PyKDE4, a simplified version of [what I wrote about here]({{ site.url }}/2009/10/howto-kconfigxt-with-pykde4). As most of KDE is C++, and the Python API docs are translated directly from the C++ API docs, it is essential to have good examples to help newcomers learn faster.

Sometimes answering apparently harmless questions on instant messaging can have unexpected results. In particular, I was telling about Danbooru Client to someone and a question popped up “Why don’t you support pages?”. It seemed a nice idea, so I branched off the code (yay for git!) and started working on it. Well, it took me more than a month to get this thing done… I didn’t spend every day coding, but it was a challenge.

KDE SC 4.4 Beta 1 has been released, and of course I couldn’t stay still. Thanks to the friendly openSUSE Build Service, there were packages available, so I just pointed my zypper sources to KDE:KDE4:UNSTABLE:Desktop repository, adjusted a few other things (mainly other third-party repositories) and updated.

Do you like KDE? Did you ever find yourself in a position of wanting to help, but you didn’t know what to do, or who to talk to? Do you feel you could use help to get started? Today, the KDE Community Forums would like to provide the opportunity to answer those questions by annoucing the continuation of the tutorial courses known as Klassrooms. What are Klassrooms? Klassrooms are tutorial “lessons” held in a specific area of the forum.

Well, there wasn’t a Day 1 for me (I got to the hotel too late to follow the first day of the meeting), so that is why I’m starting on day 2. To start, I need to say that I had never been to a sprint before: I am already accustomed to meeting for real someone from online, but for all the attendants, they had been just names or nicks on IRC.

A while ago I presented [“danbooru2nepomuk”]({{ site.url }}/2009/10/danbooru2nepomuk-a-nepomuk-tagger-for-danbooru-images), a small program to tag images coming from Danbooru-based image boards. Today I want to present the evolution of that program, that is a PyKDE4 client for those boards.

If you read around the KDE Techbase, or if you develop KDE applications, you may have heard about KDE’s KConfigXT. This is an extension of KDE’s KConfig, and can be used to generate nice configure dialogs with multiple pages with minimal effort, also taking care of saving and applying settings. In short, something really neat! But there are problems when using it with interpreted language bindings (such as PyKDE, which is the one I use):

• KConfigXT requires an XML file and an INI-like file to be compiled by kconfig_compiler in order to produce C++ files
• There is no such a tool (at least to my knowledge) that does the same job for bindings

So what to do? Either give up on the niceness of KConfigXT, or work around the issue. I chose the latter.

If you dabble with [anime]({{ site.url }}/category/Anime) and related things like I do, you may have heard about imageboards. A known variant, which powers sites such as moe.imouto (some links may be NSFW) or Konachan, is Danbooru, a Ruby on Rails application. One of the characteristics of this software is that images stored there can be tagged to be identified as precisely as possible: common tags are for example the magazine where the image was taken from, the characters depicted, and so on.

In line with the project’s committment to openness, the KDE developers and contributors are not a secretive bunch. In fact, the “People Behind KDE” initiative has provided the community with interviews of quite a number of the developers. And by reading those interviews, haven’t you ever felt the need of asking a specific question, outside from those prepared by the interviewer? For example, more details about what the specific developer is doing, or what his/her plans are for the next version of KDE.

While browsing around kde-look.org, I’ve stumbled upon a nice little Plasma scripted widget, and I’m publishing this to have it get more exposure. A good part of the KDE community knows at least little about Nepomuk, and its ability to attach semantic tags to your files - basically words that describe the file, be it an image, a text document, or anything you’d like. For example, you could tag all the photos from your vacation with the name of the place you’ve been.

Hello people! Yes, it’s been a while but I haven’t forgotten about it… with the Brainstorm’s new look and most technical issues resolved, I’m able to make Brainstorm Digests more often (hopefully!) Issue 3 - Special summary issue Since we have skipped a few months, what I’d like to present today (aside the usual data about the past month), is a general overview of the state of Brainstorm since the start of the initiative a while ago.

As you all know, KDE 4.3.0 has been releeased today! Now it’s the time to tell the developers “thanks” for their hard work. Join us in the KDE Community Forums and spread the word!

Up to now, the main language in which KDE applications are developed is C++. This is a perfectly valid choice: however, at least for users that don’t have a computing background (I include myself in the list: I do science) C++ can be a rather steep requirement (although Hans, fellow staff member at the KDE Community forums, is doing a nice job in explaining his learning experience). Scripted language bindings (that have a lower barrier of entry) for KDE exist: on top of my memory I can list Python, Ruby, and C# (and I’ve probably missed a few).

The KDE Brainstorm, where users can post and vote for feature requests for KDE, is the most visited area of the KDE Community Forums. In an effort to improve the experience of both users and developers, the KDE Community Forums staff is proud to present a brand new version of the KDE Brainstorm.  The new interface resembles the IdeaTorrent sites, but it is still powered by the forum software (phpBB), a clear example of the flexibility of the platform.

A few may know that I more or less maintain the Plasma FAQ page on KDE’s UserBase. Given the rapid advance of Plasma between KDE versions, each time a new version is out a new FAQ needs to be made, as the content rapidly becomes obsolete. For 4.3, unfortunately, I’m not sure I’ll be able to put a new version up in time for the 4.3 release. The reason is mostly practical: it takes a bit of work to collect and add information, and currently my free time is limited due to a rather heavy workload and some other commitments.

Today, a major upgrade of the KDE Community Forums took place. The change brings quite a number of changes to the forums themselves, and it’s a further step towards providing a better experience for KDE users (and developers too!).

At last, after months of inactivity, I pushed out a new release of [DataMatrix]({{ site.url }}/projects/datamatrix). Although the version bump is small (0.8) there are a lot of changes since last releases. The most notable include: Ability to apply functions to elements of the matrix Ability to filter rows by column contents Ability to transpose rows with columns An option to load text files produced by R (which are, by design, broken) Removed the getter for columns, using dictionary-like syntax directly A lot of bug fixes The download links on [the project page]({{ site.

Hello, and welcome to the second issue of the KDE Brainstorm Digest! This issue comes in slightly late, due to some real time commitments, but I couldn’t leave you without it, could I?

A rather big change has gone into KDE’s SVN recently: Ben Cooksley (bcooksley) and Mathias Soeken (msoeken) have committed a complete rework of System Settings.

Compared to the previous implementation, System Settings now has two operational modes, one being the current icon-based view since KDE 4 (and also seen in Kubuntu prior to KDE 4), and a second view, named “Classic”, which reimplements the old KControl look and feel. The latter change is probably very welcome to anyone who found System Settings less useful than the old KControl. The current view used can be changed in the configuration options. In addition, upon hovering an icon or module that show if there are any sub-modules associated.

Currently, the openSUSE Build Service contains Amarok 2.1 beta packages only for the KDE:KDE4:UNSTABLE repository (i.e. current trunk, soon-to-be 4.3). However, a quick search identified a repository that contains a RPM of current 2.0.90 compiled for the KDE:KDE4:Factory Desktop (which will change to 4.3 with Beta 1) andanother one for the KDE:42 repository. So you can add them using YaST or zypper and download the relevant package. I had to force a repository using zypper, otherwise zypper would complain and try to install amarok 1.

Hello, and welcome to the first “issue” of the KDE Brainstorm monthly digest. First of all, a few words of introduction. There are quite a number of ideas being posted on the KDE Brainstorm, and it would be nice to know how the initiative is faring, and important highlights, like what ideas are more popular, which are more controversial, etc. That is why the idea of a monthly digest was born (in a similar fashion as the fabolous Commit Digest).

Via Harald Hvaal’s blog I learnt that the first non-forum suggestion has been implemented! I think this shows without doubt that initiatives like the KDE Brainstorm are undoubtedly useful to the community at large, both users and developers. Keep on rocking!

In the past months I’ve always wanted to write a small Plasma applet to aid me in some boring tasks as a bioinformatician. One example (for the non-scientific crowd out there) is when I find a specific gene out of my analysis work which I want to take a look at. I am often lazy, so instead of firing up the browser to look at the online resources, I wanted to write something which could access said resources programmatically.

Now that the KDE Brainstorm has been launched, it’s time to take a look at the results so far. Currently, the forum hosts 160 threads, approximately one for each idea, and 441 posts. Not bad for the first two days of operation. At the same time, the staff has been working hard to make sure only appropriate ideas (not bug reports, not duplicates…) are on the forum. People have also begun voting, although slowly: it’s understandable, given the fact that there are so many threads in so little time.

It’s finally there: KDE Brainstorm has been launched today! Like this, it will be possible to propose features and have them voted by the community, and then submit the most voted requests to the developers. Every feature request is screened prior to posting, so duplicates, spam and flames are unlikely to occur. There is no guarantee that the voted upon features will be implemented, but as opposed to individual postings, this approach reduces the noise a lot, and allows a better communication between the “two worlds” (users and developers).

No, it’s not_ _a teen-like “I hate my life, I’m going to die tomorrow” post. I’m actually referring to the comments of a person nicknamed “I Love” that are popping up in almost all blogs that are linked to PlanetKDE which deal with Plasma or KDE4 adoption. The name “I Love” contrasts with an attitude that is unconstructive and rather trollish. This wouldn’t be such a big problem, if not for the fact that posts from said individual have had a rather negative effect: for example Aaron was forced to turn comment moderation on on his blog, Jos’ entry on the new Plasma in the upcoming KDE 4.

Mtux, of choqok fame, along with another person, has written Bilbo Blogger, a blogging utility for Blogger or any blog that supports Blogger1.0, MetaWeblog, and MovableType APIs (EDIT: also GData). It is based on the KDE4 libraries and it includes a WYSIWYG editor, an HTML editor, and a Post Preview function that can even fetch your blog’s CSS to render the entry and see how it looks. It’s not released yet, but for the daring, you can actually try and compile it.

During the course of my research work, I may obtain results that are worthy of publication in scientific journals. Since my master’s thesis I’ve been using LaTeX as my writing platform, mainly because I can concentrate on content rather than presentation (I find it useful also for writing non-scientific stuff as well). Also, I can handle bibliography (essential for a scientific publication) very well without using expensive proprietary applications (such as Endnote).

In my early days I used kLyX first, then LyX, but I found the platform to be too limited for my tastes, and also LaTeX errors were difficult to diagnose. I needed a proper editor, and that’s when I heard of kile, a KDE front-end for LaTeX. Kile is currently at version 2.0.2 and is a KDE 3 application. However, in KDE SVN work is ongoing to produce a KDE4 version (2.1) and that’s what I’ll look at in this entry.

I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

I just finished writing a new Python tutorial on KDE’s Techbase. This one deals with writing DataEngines in Python (a complement to Simon Edwards’s own Using DataEngines). Let me know what you think. As it’s a wiki, comments and suggestions are welcome.

As Simon Edwards already noted, thanks to me and him (mostly him, I have to say) starting to work on Plasma tutorials at the same time, now KDE’s Techbase has a nice set of Python Plasma tutorials. They cover creation of applets and connection to DataEngines (see the Plasma page on Techbase for more information). I plan on starting a tutorial on writing Plasma DataEngines on Thursday, if time permits.

It turned out I forgot to add the last screencast produced by the students of Kourse 2, so I’ll fix my mistake right now. Here’s Panel settings, by Kourse student TeaAge: [blip.tv ?posts_id=1653914&dest=-1]

Students from Kourse 2 fengshaun and Primoz have prepared two nice screencasts, dealing with the Zooming User Interface (ZUI) and desktop settings respectively. Without further ado, here they are: Zooming User Interface by fengshaun [blip.tv ?posts_id=1648944&dest=-1] Desktop settings by Primoz [blip.tv ?posts_id=1646835&dest=-1] As usual, both Free and non-Free versions are available. The students are also at work on subtitled versions, without the Notes plasmoid. I’ll be sure to post them once they’re done.

As some people already know,I’m mentoring a group of students on KDE Forum to create Plasma screencasts (from the upcoming KDE 4.2 version). After several adjustments back and forth, the first one (made by kourse student Primoz), showing off the various desktop settings, is complete. This version uses the Notes plasmoid to keep track of annotation, but we’re also evaluating subtitle-based versions. In the mean time, enjoy! (and spread the word).

Today I was adjusting a bit the layouts of the Activities (as defined in Plasma) to better suit my workflows. To do so I was using the brand new Activity Bar which is present in KDE 4.2. It’s very neat, but takes up space on the desktop, and while it’s not a big deal on my main PC (1280x1024 resolution), it is an issue on my recently-resuscitated EeePC (1024x600). It was then that it occured to me that such applets are, in Plasma-speak, PopupApplets, which means they adjust their behavior depending if they are in a panel or “free”.

Finally a new entry! I’ve been extremely busy with other things, that is why I did not have time to write more. One of the main reason is related to an important landmark in my professional career, but I’ll write more about it after January 1st (hint: those who follow my Twitter updates may have already understood). As a nice way to break the hiatus, I’m releasing a new version of DataMatrix, my implementation of R’s data.

Currently I have Kubuntu 8.04 (Hardy) installed on my Eee PC. Version 8.10, the Intrepid Ibex, is due on October 30th. However, I will not install it. The reason is that Kubuntu developers intentionally disabled the zoom function, and I have three activities on this machine. How come I’m supposed to use them? Also, space is pretty tight so install a build environment just to remove one patch seems overkill. So, I’m moving away from it.

Ok, ok… my definition of “tomorrow” is not like what most people use, apparently. Although I took quite a while, now [there is a static page on DataMatrix]({{ site.url }}/projects-2/datamatrix). There you will find a summary of wht I wrote in my other blog posts regarding this module. Of course, it will be kept up-to-date should I release a new version. Aside that, I put a contact form on this blog.

At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax. In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).

Today I’m in a posting spree…This clip shows how to resize and move Plasma panels around. [youtube]http://www.youtube.com/watch?v=Rmpv-S5JJI4[/youtube]

Following up on my previous post, here is another screencast showing off how to create a sidebar panel and add a few plasmoids to it. As usual, the version on Youtube has annotations. [youtube]http://www.youtube.com/watch?v=WPeFSDdt2PY[/youtube]

I’ve put together a small video that shows what you can do with zooming in and out with Plasma’s Zooming User Interface (ZUI). Enjoy. (note: the version on Youtube has also annotations that explain better what is going on) [youtube]http://www.youtube.com/watch?v=EhODrJkoidA[/youtube] If you can, please spread the link to the video. We need more correct information out there.

Those of you that follow my Linux-related posts know that I work (along with others) on a FAQ trying to explain some magic behind KDE 4.x’s Plasma. Now, especially since on the Internet, there is the need to spread correct information (most of the naysayers are not quite informed). So, if you want to help KDE, please spread the word on the Plasma FAQ! If people have questions on Plasma, just direct them to

Now even the (once respected) Steven J. Vaughan-Nichols is jumping on the bandwagon of Plasma haters. With a rather uninformed and rant-ish entry that just advocates a fork, like some other people said on the kde-devel mailinglist a week or two ago. The entry is rather dismissive of everything in KDE 4 save Plasma (and a mention on Dolphin’s single click icon), and also gets some facts and links wrong (yes, the Plasma web site is outdated, but since the developers are busy coding, someone else should step up and help).

For a long time I have tried to handle text files in Python in the same way that R’s data.frame does - that is, direct access to columns and rows of a loaded text file. As I don’t like R at all, I struggled to find a Pythonic equivalent, and since I found none, I decided to eat my own food and write an implementation, which is what you’ll find below.

After almost a month of wait (Dynamism.com doesn’t like simple order procedures), I finally got hold of an Asus Eee PC 900 (obviously - for the readers of this blog - the 20 Gb Linux version). Read more for some quick impressions and pictures.

I’ve been wondering about why FOSS is often compared to the academic world, but at least in my limited experience, I see little people that grasp its concept in the world of research. On a quick look, developing FOSS in a research environment would be very good: not only you’d get publicly available results when you publish, but at the same time you can make sure that in an extreme case your application will be carried on by someone else should you not be able to continue development.

Since my work schedule is bordering on the hectic, I was thinking on buying something to get me more organized. Rather than a PDA, I’ve been rather interested in the Asus Eee PC: small form factor, SSDs and Linux preinstalled are definitely pluses. It’s too bad that at least in Italy Asus sells only the 512M RAM version (when there are more powerful options available elsewhere). I’d like to get impressions on the Asus Eee, before considering a purchase (€ 300 are still a lot): did you try it?

To me nowadays reading KDE Dot News is a bother. Not because of the news, which are always high quality, but the comments leave a lot to be desired. Let’s take for example the recent news about Nokia buying Trolltech: 99% of the comments talk doom and gloom. This is not bad per se, but most of them bring absolutely nothing to the discussion. Truth is, it’s too early to say, so we’ll have to wait and see.

The word is official: KDE 4.0.0 has been released. Make sure to check out the Dot story, or the nicely done visual guide. And if you’re new to Plasma, have a look at the FAQ as well. Congratulations to all the KDE developers, translators, and coordinators for pushing forward our favorite desktop environment. Rock on!

Today is the tagging day for KDE 4.0.0. I think it speaks for itself. I have checked out the 4.0 branch and I’m going to use it in a full session real soon (so far I used nested X sessions with Xephyr). Aaron Seigo has a nice writeup on the release, some of the memes floating around and the future of KDE 4.

I’ve recently begun trying to create GUIs for my Python applications with PyQt, and I can say I’m absolutely loving the toolkit, relatively easy to use and featureful. As I’m trying to create a GUI for some module I wrote that deals with databases (using MySQLdb), I also learnt that Qt has a series of classes for dealing with databases, mainly QSql. My question, directed to whoever has experience with QSql and the Python DB-API, is: what are the advantages of one approach to the other?

I’ve started working on a FAQ related to Plasma, in order to ease the transition for the early adopters of Plasma when KDE 4.0 is released. That, coupled with another idea I had (offering video tutorials of operations) should make the gap smaller. Currently the FAQ is a work in progress (still a lot of TODOs, I hope to have a look after Friday as I’m really busy now) and resides in KDE’s TechBase until a more suitable solution is found.

**Notice:**Just now I realized this has been linked to to a Stack Overflow question. I recently wrote a new post that uses a different technique and a combination of R and Python. [Check it out!]({{ site.url }}/2011/05/multiscale-bootstrap-clustering-with-python-and-r)

Following up my recent post, I’ve been looking for alternatives to TMeV. So far I’ve found the R package pvclust and the Pycluster library, part of BioPython. The first one also performs bootstrapping (I’m not sure if it’s similar to what support trees do, but it’s still better than no resampling at all). I’ve found another Python project but it is still too basic to perform what I need.

As people who read my science-related posts know already, I’m not a big fan of {{post id=“software-and-biological-research” text=“software made just to support a publication”}}. Recently I’ve stumbled again into similar software. Namely, I’m talking about the TIGR Multiexperiment Viewer (TMeV), a Java-based program which is often used for microarray analysis. It’s not exactly “fit for publication”, because it has reached version 4 last year, but shows some of the problems ({{post id=“genbugg” text=“mentioned already”}}) with releasing bioinformatics software.

I use TMeV mostly because I didn’t find any other implementation of the hierarchical clustering algorithm with support trees. However, I’ve stumbled upon a very annoying bug in the most recent version. Normally I use average linkage clustering and as the distance metric I employ the Pearson’s correlation, and with gene and sample bootstrapping: with certain files this makes TMeV report errors at random during the iterations.

Yesterday I spent some of my free time to help with the KDE 4.0 Krush Day. Unfortunately, I did a lot less than what I was supposed to do, mainly because at some point the home directory ran out of space (I forgot to remove qt-copy object files), then I inadvertently removed some of the directories and I had to re-sync with SVN. Nevertheless, it was interesting and nice to be able to contribute even if you don’t speak C++.

Aseigo announced it a few days ago: on Saturday, on the Freenode IRC network, #kde4-krush channel, there will be a day-long session to triage and squash bugs in order to improve the overall quality of KDE 4.0. I will try to be there, so that I can give out my (little) contribution as non-coder. I’ll be sure to report later.

First of all let me make some disclaimers : This is **not **a Plasma bashing post (so that aseigo won’t commit suicide, should he ever read this); I’m not a KDE developer, just someone who tries out SVN and reads mailing lists; UPDATE: These statements aren’t meant to bash the collective group of the KDE developers, just to outline a bad “mood” in my opinion.

I obviously did not want to stop with a single compile of KDE4, therefore I’m updating more or less randomly my build off the SVN to check what has been changing. The first and most important change since my last post was the addition of the K-menu in the taskbar: Kickoff was moved from playground (where it resided) to kdebase. Also, kate now works perfectly, and is already usable as a full-blown text editor.

Since Beta 3 was announced a short time ago, I thought I would try testing KDE4 on my computer. Here I’m reporting on my first impressions and I’ll try to provide constructive feedback as much as possible: the developers are being already (and unjustly, in my opinion) bashed enough.

The other day I was thinking about how to make screencaps for the anime I watch. Windows users often use Media Player Classic, which can create a video contact sheet (i.e., a series of captures) out of a movie file. I had two problems with this: The biggest is that it runs on Windows, and I don’t use Windows; The frames needed to be manually cropped every time, which was slow.

After some thought, I’ve joined the fray and installed the beta version of Kubuntu 7.10 (Gutsy Gibbon) on one of my computers. It hasn’t too recent hardware (AMD Thunderbird 2100+, 512 Mb RAM and a motherboard with a Nforce 2 chipset), and it is my test system for distributions. It ran Feisty Fawn, so I tried to use the upgrader tool, which crashed when removing unsupported packages. Oh well, it was a beta, so nothing to worry about (the only worry was that it didn’t output anything at all).

At the time of writing, a lot of people (even in bioinformatics) uses Microsoft Word to write their papers. I personally think it’s not a good idea, and not just for the file formats (like Microsoft lobbying semi-legally to get OOXML approved by ISO), but because for scientific papers the WYSIWYG paradigm is not appropriate.

The title comes from some random thoughts I had while reading aseigo’s latest entry on Plasma. I was thinking about the line “who uses KDE for his/her day job, and why?”, but related perhaps to people who don’t code for a living. Here I will illustrate my point of view on why I chose KDE as my day to day desktop environment.

The reason for this post is the time I wasted this afternoon to enable DMA for a DVD burner in Windows, in order to burn a backup DVD at a decent speed. Apparently, the two optical drives are IDE while the HD is on a SATA controller. For no reason, DMA got turned off on the DVD burner (but not on the other drive). Of course I tried everything I could, of course.

Looks like my laptop doesn’t really want to keep its data in stable form. Like [I have blogged previously]({{ site.url }}/2007/05/31/borked/), the bus-reset issue apparently trashed my root partition again. I do not know the cause as it seemed a normal shutdown… but the moment I rebooted I had lost a lot of files (thankfully not on /home: I’m glad I keep data separated from the rest). Reinstalling proved less difficult, thanks to a Kubuntu DVD I burnt with my other computer.

Recently, I had to do a few scans with my old but trusty BenQ 640BU. Given that I could not use any GUI due to a long-standing Feisty bug, I tried to settle for command line scanning with the scanimage command from SANE. The main problem is that scanimage only saves images in PNM or TIFF formats. I wanted to use JPEG or PNG, but apparently that looked impossible to do.

The title will already give an idea of what happened to my laptop two days ago. Due to a bus problem and a forced reboot, my root partition got corrupted. Luckily no data was lost as I keep /usr and /home separated from the rest. However reinstalling proved to be a very difficult task. First of all, my DVD drive has some problems, and so it wouldn’t read the Kubuntu Feisty install disk I had brought from work.

Today I made a simple sed script that converts a tab-delimited text file to a format that can be pasted into a DokuWiki wiki. There is a plugin that permits to read CSV files directly, however: It doesn’t support tab-delimited text files; It’s incompatible with some plugins (one being DokuTexit, which I need). Hence the need for this script. To use it, just copy and paste the code (see below) into a new file, make it executable (chmod +x) and then invoke it with

While working through large text files for work, I found several command line tools whose existence was unknown to me before. Their usefulness is great however, expecially if you deal with comma or tab delimited files (I do, and a great deal).

On a recent dotKDE article about the weekly commit digest, someone brought up again the issue of Plasma, a component of KDE 4 whose object is to bring “revolution” to the current desktop paradigm. However, I think that many in the community had unrealistic expectations, so some people even started to think it was vaporware, like in some comments in the aforementioned article. I’ll say it again, people had unrealistic expectations.

As I’ve been working to get some results done for my Ph.D. thesis, I’ve stumbled across the problem of having different data obtained through different software. Even if it’s just a matter of text files, the fields are all different and even if dealing with the same data, trying to infer relationships is a pain.

[code lang=“bash”] lb@hardin:~$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 7.04 Release: 7.04 Codename: feisty [/code]

I just read on Slashdot that the famous RMS has now sung something against the prisoners in Guantanamo Bay (no link, I’m not giving it hits). All this while being in Cuba, for all heavens, that’s not even remotely a democracy. I don’t deny the fact that that place may have been ground for abuses, but I find it hypocritical that RMS did that in a place where people are imprisoned on a whim and human rights are not upheld constantly.

I’ve again seen how useful and powerful Python can be. The other day I had to prepare an Excel spreadsheet (sadly) which among other things needed to contain links to the GeneCards database for each gene listed. There were more than 2900 genes listed, so adding links by hand would have been suicidal. That’s when Python, through its Windows extensions, comes into play. First of all I created a module for COM objects using the makepy utility.

Recently (before my tendinitis forced me to avoid using my desktop computer) I installed the beta version of Kubuntu 7.04 (Feisty Fawn).

As I anticipated, I can finally release this small script. Its purpose is to build BED files out of tab-delimited text files. I made this because I had several files to make and moving columns left and right (not to mention writing a heading line for the Genome Browser) was becoming annoying. Its use is fairly straightforward, as the help itself says:

Today I decided to give the new Oxygen icon theme (the default icon theme for KDE 4, as Troy Unrau explains effectively on dot.kde.org) a spin. Since it’s not (obviously) available for KDE 3.x, I had to do a checkout from SVN (from trunk/KDE/kdelibs/pics, since they were recently moved there). Then it was a matter of moving the oxygen folder to /usr/share/icons and selecting the theme in kcontrol.

A recent article on dotKDE caused really a stir and a rather long (more than 430 comments!) debate. What is the reason? The decision to use the [Dolphin file manager](The Road to KDE 4: Dolphin and Konqueror) instead of Konqueror as default file manager. I found myself rather surprised at such a reaction. After all, Dolphin and Konqueror will share much of the code base (which means that they will improve both) and Konqueror won’t be removed and will be available as default file manager through configuration.

No, I’m not talking about his looks. I’m talking about him being morally disgusting. The reason? The fact that he went to Cuba and convinced them to switch to FOSS. You may want to know, why is that a bad thing? Easy answer: Cuba isn’t a democracy. Think what you want, blame the United States for the embargo how much you like, but you won’t be able to hide the fact that it is a totalitarian, oppressive regime.

Yesterday I and another person went to the server room to do the basic configuration of the Apple Xserve we have bought, along with its Xserve RAID unit. Despite the general “idea” that anything Apple does is user-friendly, our experience was plagued by problems.

In the past two days, aside studying the Python basics, I’ve been looking to find a decent GUI toolset to develop user interfaces in Python.

Reading Wesley J. Chun’s excellent Core Python Programming I realized I could definitely improve [my wallpaper checker]({{ site.url }}/2006/12/23/wallpaper-size-checker/), at least internally. That’s what I did today, and aside that, I added an option to view a thumbnail of the images contained in the lists. Note that it is not meant to be an image viewer, just a way to show the images in the list (and I suggest you filter it first if it’s long).

I’ve decided to update the wp_filter.py script. I fixed a good deal of bugs and at the same time I added a simple text-driven menu in order to simplify the program use, and I also added a readme file that describes operation and other requirements. You can download the program in [tar.gz format]({{ site.url }}/files/wp_filter.tar.gz) or in [zip format]({{ site.url }}/files/wp_filter.zip). For basic requirements, refer to my [previous blog post]({{ site.

UPDATE: Some stupid bugs had crept in the code, so I updated the archives. Sorry for the inconvenience.

I’ve writtern a small Python script to find wallpapers with right size or aspect ratio I needed, and now I’m releasing it to the public. It may come in handy especially when you download lots of desktop wallpapers (archives, torrents) and you don’t know which ones are suited for your monitor.

Two days ago I decided to install Linux on the new computer I had obtained, so I just got a Kubuntu 6.10 alternate CD and went through the steps. THe network card was not detected, but by reading around I found it was just a matter of the r1000 module not being present in the installation kernel. The problems arose when GRUB was installed. Actually, that part of the installation went fine, but once rebooted I got “error 21”, which meant “disk not found”.

I’m really saddened by the fanatic tone that a part of FOSS community is using to criticize the Novell-Microsoft deal. It should be noted that personally I don’t like the deal at all, since Microsoft has a good history of stomping on its partners when they’re no loner needed. But still, the reactions from the community are too strong, sometimes leading to (involuntary) disinformation.

In the past two days I’ve written a simple annotator program, that given an input list of RefSeq genes, automatically determines the relevant Entrez Gene IDs and annotates them using the flat files provided by the NCBI. A direct conversion was not possible due to limitations in Biopython’s parsers, but I managed to use the GenBank parser to identify and extract the references to the Gene IDs (and putting them in a list).

Finally I cleaned up my code enough to post it here. It’s probably still ugly, but not as ugly as when I wrote it down the first time. It’s all about manipulating text files, to be precise tab-delimited files. All the snippets are published under the GNU GPL v2 (not that I think that anyone would use them, but just in case…).

I’ve upgraded both leon (one of my computers at home) and quant (my work machine) to Kubuntu Edgy Eft (now in Release Candidate status, screenshots here). Leon’s upgrade went perfectly, while quant gave me some headaches. First of all there was a conflict between packages, then the nvidia module for legacy hardware wouldn’t load: $ modprobe nvidia_legacy FATAL: Module nv not found. In the end I manually compiled the nvidia module, and had to insert it via insmod or it would give out a cryptic error message (“error running install for module nvidia”).

Although I’m still studying the language, finally I managed to create a program that actually does something I need. The need arose from a gene list I was given, made up by Entrez Gene IDs. I need to annotate it, but in a form that wasn’t able to be produced by the usual functional annotation tools I have. Actually it could have been done, but what I needed was to make something that I could automate.

WARNING: This entry is somewhat political in nature.

Given the recent controversies about the GPL v3 draft, I thought I’d give my insight on the Free Software Foundation and especially its founder, Richard M. Stallman, better known as RMS. I won’t cover the GPL v3 debate as I haven’t read the license draft, though I think that the kernel developers’ standing must be at least given attention.

Jucato has some screenshots of the recently released Kubuntu Edgy Eft Knot 3. I like very much the new artwork, but it doesn’t seem that there’ll be Oxygen icons, at least from what I can gather. In any case I will try to play with it as soon as it hits a beta stage. On unrelated news, I still have got some RSI issues, so I’ll have to slow down posting.

Recently I decided to update the fglrx driver (ATI’s proprietary driver for Linux) to the latest version. I wanted to do that because the old version made switching between virtual consoles and X impossible (X would lose the correct timing of the screen, distorting it and forcing a kill to reset the settings). Also I was hoping on finally solving the hibernate issue that has been plaguing the driver for months.

A lot of my bioinformatics work involves performing functional annotation on genes. This means that given lits of genes I need to resolve their known function, or if they’re part or some metabolic pathways and so on. Even with the current trend in our laboratory, that is investigating DNA copy number changes using SNP microarrays (it’s a rather new form of analysis, but some relevant papers are out already), in the end we have to go back to the genes affected by such changes (in order to find interesting/marker genes - we study solid tumors).

I learnt recently that the Kile LaTeX environment had a new release (1.9.2) on 26th August. It is mainly a bugfix release. However no packages for Ubuntu and Kubuntu exist yet, so I decided to fill the gap by building one, as I also use Kile for S.T.E.A.L.. It is based on the packages made by Harald Sitter and Marcus Czeslinski, whom should take most of the credit, as I merely recompiled the already debianized source with the new version.

[code]lb@hardin:~$ uname -a Linux hardin 2.6.17-emission7 [/code] (the rest of the output was truncated) Thanks to some folks over at the Ubuntu Web Forums I’ve been working into rolling in my own kernel trying to solve the fact that when I’m shutting down I always get drives in an unclean state (actually only the root partition), giving rise to several errors. I wasn’t content with a vanilla kernel so I decided to use the emission patchset.

Yesterday I was trying to adjust some files in order to make a program use Affymetrix SNP arrays data (instead of arrayCGH data like the program was designed for). I had a big (116,000 rows) tab-delimited text file and I needed to use only part of the columns there.

I’ve already explained in a previous entry that I like to tweak images, extract them from backgrounds and so on. However I didn’t like that I needed Windows to perform my actions, as I want to use that operating system as less as possible. I tried then to use FOSS (Free and Open Source Software) tools available on Linux to see if I could do the same job.

305 Yesterday when I went at work I found an envelope coming from Canonical. Inside, there were the five Kubuntu 6.06 “Dapper Drake” LTS CDs I ordered from Shipit. Those are Live CDs that will run Kubuntu without any needs for installing (though I’d have preferred real install CDs). 307 I will probably try to hand out a few of those: there are already a few people using Linux where I work.

I got upgrade hardin (my laptop)’s memory at least, bringing it to 1Gb, at last. However I had two 256 Mb modules installed, that means I had to buy two 512 Mb ones. Oh well, I’ll just try to sell those ones. Everything seems snappier now, and even Firefox seems not to clog the CPU when loading pages (I need to experiment more, since I have no clue why that should have changed).

Today I’ve been trying to set up suspend to RAM and suspend to disk (also known as hibernate) on my laptop using Kubuntu 6.06 LTS. Both tries failed miserably, sadly. The machine would suspend and also wake up, but I’d get only a garbled screen. This means that the video driver failed to wake up properly: this is the well known fglrx driver, the binary only driver that ATI made for Linux.

Finally, the new version of Kubuntu 6.06 LTS (Long Term Support) is out! Not that I noticed many differences since I kept it constantly dist-upgraded since I put the beta on the desktop and the RC on the laptop. I really like it so far (save minor nags with 3D acceleration that I solved by issuing a couple of shell commands). Also, KDE 3.5.3 packages are already available from 3rd-party repositories. I will be upgrading them soon.

Yesterday I updated my laptop to Kubuntu Dapper RC. Overall the (long) process was quite smooth save a couple of problems (the use of NetworkManager for exaple, that caused me headaches to make wireless work) including the fact that the ATI drivers were looking in the wrong location (/usr/X11/lib/modules/dri instead of /usr/lib/dri) so 3D acceleration wasn’t working. It seems smooth so far, though I think the idea of NetworkManager needs polishing, as some services that are started before it connects will fail (such as autofs).

Today I found out that a computer running Windows had been “self-writing” words when an Internet Explorer window was open. This obviously led to the conclusion that there was some kind of malware running. I immediately unplugged the network cable but the typing continued - this is a good sign meaning that it was just some random program doing it. It only affected IE, no other programs. I wonder how it got there, I can only suspect the current user, as I never do any network-based activity there, only analysis (and I run a much safer Linux box - no Windows for me).

I’ve been playing a bit with Ubuntu on two computers. On the laptop, I have managed to make the email led blink when I get new mail (thanks to a tip I found online involving the use of the acerhk driver). I still need to find a way to turn it off (actually I can turn it off, just not automatically after I finish reading my mails).

Today was much more tiring than yesterday. It was a full day with courses, and especially the ones in the afternoon were rather heavy on the subjects. First of all there were some talks on networks and promoter site prediction (I liked a lot the second one) , followed by some talks on microarray data analysis (I knew a bit already of this stuff). The afternoon talks featured more statistics for bioinformatics (ugghhhh) followed by a nearly non-understandable talk that lasted for almost two hours and really drained the life out of me.

I haven’t blogged in a while, mostly because I’m either doing something else, or when I want to, I find out I’m really tired (this and the past week have been very tiring for me). In any case, I’ll make a big, random entry. I’ll start saying that I’m amazed at how badly software can be written. In the life sciences field you see very clear examples. Horrible UIs and poor documentation mostly (while the algorithms and methods implemented are usually very solid).

I’ve been migrating settings and files from the old router to the new one (check my brother’s blog to understand better what I’m talking about). I noticed the free space already dropped significantly, as you can see from this: [code] lb@hari:~$ df -h Filesystem Size Used Avail Use% Mounted on /dev/hda1 9,2G 859M 7,9G 10% / tmpfs 43M 0 43M 0% /dev/shm tmpfs 43M 13M 30M 30% /lib/modules/2.6.12-10-386/volatile /dev/hda6 83G 8,5G 70G 11% /home

As today was almost completely uneventful (and kept on raining), I’m putting together an all-in-one entry. First of all I played more with the webcam on Linux. The exposure setting and some other gamma corrections can’t be really set in real-time yet, so it tends to get a little dark. Nevertheless I can get some decent results, here’s an example picture of my desk: general/desktop.jpg I also tried to update my old Mandriva 2006.

I’ve just upgraded my blog to WP 2.0.1. Aside a little problem with the gallery images (easily fixed) everything seems to run smooth for now. If you notice any glitches please post a comment and I’ll get it fixed.

Yesterday I tried to run an electronic Italian-English dictionary I own. As I write my novel using LaTeX and I have an environment on Linux, I thought it would good to use WINE to read it. I was wrong. Wine has progressed immensely and the commercial offerings (for example CodeWeavers) are even capable of running Office in its latest incarnation: however they are totally useless in front of the extremely bad quality of those dictionaries (from a programming point of view).

I’ve just wasted an expensive DVD+R dual layer thanks to some bugs in the burning program. My laptop could handle the burning fine (hopefully) but I couldn’t read the source DVD because of the crappy quality of the DVD reader inside (I had the same exact problem with my old laptop), and on my desktop (MDV 2006.0) k3b refuses to burn, and growisofs borks mid-way with a generic error, in any case the DVD is wasted, bah.

The two items in the title aren’t really related but they sum up today’s entry. My cat had to be visited by the vet, that diagnoesed renal insufficiency and strong dehydration. Something to be worry about, but it will be at lest kept under control soon. The second part of the entry deals with the fact that I’m trying to find a decent finance program that works under Linux (no thanks to any program on Windows, sorry): I tried KMyMoney but aside the fact that it doesn’t have any Italian template, it’s a little confusing.

Recently my hosting service has been boasting service upgrades. However I didn’t see any changes in my control panel. So, I emailed them, and their reply was that it was valid only for customers signing up from November 9th (because they had set up new servers). However, I find it quite unfair, since I pay the same price as the people who will sign up, and get less. Looks like I’ll have to change hosting again in the future…

As many readers of this blog are aware, openSUSE has been offering packages of git snapshots from KDE since quite a while. They are quite useful for those wiling to test, report bugs, and / or hack on the code, but also for those who want to see what’s brewing in KDE land (without touching their existing systems). However, a major drawback for non English speakers was the lack of translations.

In the past months I’ve set up LDAP at home, to avoid having different user accounts for the services that I run on my home hardware. Rather than the venerable OpenLDAP I settled for 389 Directory Server, commercially known as Red Hat Directory Server, mainly because I was more familiar with it. Rather than describing how to set that up (Red Hat’s own documentation is excellent on that regard), this post will focus on the steps required to enable encryption using Let’s Encrypt certificates.

One thing I always wanted to do when going on holiday is to track where I go, the places I’ve been, and see how much I’ve travelled around. This is true in particular when going to places where I walk around a lot (Japan stays at the top of the list, also for other reasons that are not related to this post). Something like viewing a map showing where you were, and where did you go, with optional export to KML or GPX to import into other programs like Marble.

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others) As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in.

If I look back at the last post I made on ths blog… let’s say quite a lot of time has passed. The reason? Well, first of all, one would call it a lack of motivation1, and afterwards, the emergence of a small yet quite annoying pathogen which caused a bit of a stir worldwide. But today I’m not going to talk about viruses: perhaps some other time when you can avoid hear about it for breakfast, lunch, and dinner.

Part of this post is about openQA, openSUSE’s automated tool which tests a number of different scenarios, from installation to the behavior of the different desktop environments, plus testing the freshest code from KDE git. Recently, thanks to KDE team member Fabian Vogt, there has been important progress when testing KDE software. Testing the Dolphin file manager Those who use KDE software, either in Plasma or in other desktop environments have at least heard of Dolphin, the powerful file manager part of KDE Applications (by the way, have you checked out the recent beta yet?

As you may already know (if you don’t, please check these older posts) openQA, the automated testing system used by openSUSE runs daily tests on the latest KDE software from git. It works well and uncovered a number of bugs. However, it only tested X11. With Wayland starting to become usable, and some developers even switching to Wayland full time, it was a notable shortcoming. Until now. Why would openQA not run on Wayland?

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highlights of the new version Unbreak konachan.com support (change in URL format) Coming up next HTTPS support!

In the past three weeks, the openSUSE community KDE team has been pretty busy to package the latest release of Applications from KDE, 16.12. It was a pretty large task, due to the number of programs involved, and the fact that several monolithic projects were split (in particular KDE PIM). This post goes through what we did, and how we improved our packaging workflow. Some prerequisites In openSUSE speak, packages are developed in “projects”, which are separate repositories maintained on the OBS.

Admit it: how many times you have seen “software from this branch is completely untested, use it at your own risk” when you checked the latest code from any FOSS project? I bet you have, many times. For any reasonably modern project, this is not entirely true: Continuous Integration and automated testing are a huge help in ensuring that the code builds and at least does what it is supposed to do.

You may be aware that openSUSE Leap 42.2 is now in the release candidate stage, and there’s a lot of activity aimed at squashing those pesky bugs before they hit the final release. One particular bug proved to be quite tough to fix, and it was only solved thanks to the “heroes” mentioned in the title. This is the history of the bug. The report October 6th, 2016 - A bug iss reported against Plasma reporting a hard freeze of Plasma when using the Noveau driver, but not with the closed NVIDIA blob.

As you may know (unless you’ve been living in Alpha Centauri for the past century) the openSUSE community KDE team publishes LiveCD images for those willing to test the latest state of KDE software from the git master branches without having to break machines, causing a zombie apocalypse and so on. This post highlights the most recent developments in the area. Up to now, we had 3 different media, depending on the base distribution (stable Leap, ever-rolling Tumbleweed) and whether you wanted to go with the safe road (X11 session) or the dangerous path (Wayland):

Every day, a sizable number of people posts problems on the KDE Community Forums and the ever-helpful staff does their best to solve whatever issues they’re facing. But what exactly does one do when this happens? This post provides more insights on the process. NOTE: The following applies to my workflow for the Kontact & PIM subforum. Step 1: Someone posts a problem The questions posted are various, and range from simple tasks (“how I do XXX”) to very specific workflows.

A new version of Danbooru Client is now available! What is Danbooru Client? Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re). Highglights of the new version Support for width / height based filtering: now you can exclude posts that are below a specific width or height (or both) New dependency: KTextWidgets Coming up next Sooner or later I’ll get to finish the multiple API support, but given that there’s close to no interest for these programs (people are happy to use a browser) and that I work on this very irregularly (every 6-7 months at best), there’s no ETA at all.

Ever since the launch of Argon and Krypton, the openSUSE community KDE team didn’t really stand still: a number of changes (and potentially nice additions) have been brewing this week. This post recapitulates the most important one. I’d like the most recent Qt, please As pre-announced by a G+ post, the openSUSE repositories bringing KDE software directly from KDE git (KDE:Unstable:Frameworks and KDE:Unstable:Applications) have switched their Qt libraries from Qt 5.

As KDE software (be it the Frameworks libraries, the Plasma 5 workspace, or the Applications) develops during a normal release cycle, a lot of things happen. New and exciting features emerge, bugs get fixed, and the software becomes better and more useful than it was before. Thanks to code review and continuous integration, the code quality of KDE software has also tremendously improved. Given how things are improving, it is tempting to follow development as it happens.

Recently I’ve been setting up LDAP authentication on CentOS servers to give a shared authentication method to all the compute nodes I use for my day job. I use 389-DS as it’s in my opinion much better to administer and configure than openLDAP (plus, it has very good documentation). As I have a self built NAS at home (with openSUSE Tumbleweed), I thought it’d be nice to use LDAP for all the web applications I run there.

KDE has recently released the newest Release Candidate of the Applications 15.08 release. Among the new features and changes of this release, there is a technology preview of the new KF5-based KDE PIM suite (including reworked, faster Akonadi internals), new applications ported to KF5 (the most notable ones being Dolphin and Ark). After some consideration and thinking on how to allow users to test this release without affecting their setups too much, the openSUSE community KDE team is happy to bring this latest RC to openSUSE Tumbleweed and openSUSE 13.

Since [26th December 2005]({{ site.url }}/2005/12/up-and-running/), I’ve been runnning this blog with Wordpress. At the time there were little alternatives and finally I had got hold of a host (Dreamhost, at the time) that supported PHP and MySQL without being overly restrictive. 10 years later, things have somehow changed. The issue The main reason lies in how Wordpress has evolved over time: no, I’m not speaking about the subjective “bloat”, but the fact that it’s been moving towards a full-blown CMS, which is not what I have in mind to run my blog.

A lot has been happening on the KDE side of openSUSE… this post summarizes what’s been going on so far. Live media for Plasma 5 One of the most-often requested ways to test Plasma 5, given it can’t be coinstalled with the 4.x Workspace, is the availability of live images to test either in VM or bare metal without touching existing systems. Given that other distributions started doing so since a while, naturally openSUSE couldn’t stay still.

The ever-amazing Plasma team from KDEjust put out a new release of Plasma. I won’t spend much describing how big of an improvement it is - the release announcement at KDE has all the details needed to whet your appetite. And of course, now it’s the turn of distributions to get out packages for the users at large. This is also the case for openSUSE. The KDE:Frameworks5 repository hosts the new 5.

Following up onKDE’s announcement of the latest stable release, we have now packages available for 12.3 and 13.1 (a 13.2 repository will be made available after it is out). You will find them in the KDE:Current repository. Current users of this repository will get the new release automatically once they update. Why you should upgrade? You can take a look at the list of changes to get an idea. These fixes touch many important KDE applications, including KMail, Okular and Dolphin.

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too. I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

Since a couple of weeks the packages offered by openSUSE in the KDE:Unstable:Frameworks repository have undergone a series of changes. In particular, the packages now install to /usr. For the libraries (KDE Frameworks 5) this will mean a transparent change for the userbase as they are expected to be co-installable, but the workspace components (Plasma 5) will confict with the existing Plasma 4.11.x installation. What does this mean in practice? If you want to use Plasma 5 you will not be able to use a 4.

Requests to unlock KWallet automatically on login (assuming the wallet password and user password are the same), like gnome-keyring can do, have been going on for years: in fact, bug reports requesting this feature are quite old. Recently, thanks to the efforts of Alex Fiestas, a PAM module, which interfaces KWallet to the system authentication methods, has been developed. In parallel, the necessary glue code has been also added to the various parts of the KDE workspace so that it could make use of it.

This is a guest post by Raymond “tittiatcoke” Wooninck, with contributions from myself and Hrvoje “shumski” Senjan In the next hours the [KDE:Current]({{ site.url }}/2014/03/being-current/) repository will publish the latest release from KDE (4.13). As that this release comes with a big change (the new semantic search), we would like some simple steps in order to perform the right upgrade. Before the upgrade In order to migrate data automatically from the Nepomuk store to the new format, you will need Nepomuk up and running, and just for the time needed for the migration.

It is not news that openSUSE, through to the effort of the openSUSE community KDE team, offers several third-party repositories for those who want the latest software from KDE. Since a while, stable releases were offered in the KDE:Release:4x repositories, created with every major release of KDE software. These were meant to offer the latest and greatest to the users without having them to track KDE:Distro:Factory, which is instead used to track packaging for the next openSUSE release and is more in a state of flux.

Yesterday KDE released their first beta of the upcoming 4.13 version of Workspaces, Applications and Development platform. As usual with the major releases from KDE, it’s packed with a lot of “good stuff”. Giving a list of all the improvements is daunting, however there are some key points that stand out: Searching: KDE’s next generation semantic search is a prominent feature of this release. It’s several orders of magnitude faster, much leaner on memory and generally is a great improvement from the previous situation (this writer has been testing it for the past months and he’s absolutely delighted about it).

And so, finally openSUSE 13.1 is out of the door (I couldn’t celebrate like I wanted, as I’ve been very busy). This release has lots of improvements, and of course, the latest stable software from KDE. It is time (perhaps?) to look back and see what the team has done during this development cycle. With regards to the KDE software packaging, the past 8 months have seen quite an increase in the involvement of poeple from the community.

As you may know, there is an ongoing effort to rearrange and adjust the openSUSE KDE repositories. In line with the previously announced deletions, and more recent adjustments, a number of changes went into the organization and layout of the KDE repositories: KDE:Distro:Factory and KDE:Release:4xy will now hold the “core” KDE packages: this means the base Development Platform, Workspaces and Applications, and additional applications for a basic desktop experience.

Summer is ending soon (at least for those living in the northern hemisphere) and while usually cleaning is done during spring, the KDE team decided to do what I’d call… autumn cleaning of repositories. You may know that the KDE presence in openSUSE, aside being the default desktop, is quite a long one. In the past years different repositories were created by the members of the openSUSE KDE team (at the time mostly made up by KDE people hired by Novell) in order to review and test packages, like newer Qt versions, KDE software, and so on.

In the past few days, the openSUSE KDE team has been working hard, following the footsteps of the nice work done by the Kubuntu and Arch Linux communities, to provide Qt5 packages for the distribution. In fact, work was already done in the past, but the packages were not coinstallable with the existing Qt4 installation. Thanks to a renewed effort, the OBS holds now Qt5 packages that won’t overwrite the existing Qt4 install: they currently live in the KDE:Qt51 repository (Factory and openSUSE 12.

The latest release of the KDE Platform, Workspaces, and Applications (4.11) is around the corner: in fact, the last RC was recently made available. We’re almost there, but it doesn’t mean that testing and reporting should stop: on the contrary, it is needed even more to ensure that no bad bugs crawl up in the final release. As part of this effort, openSUSE packages for RC2 have been released through the OBS, and are available in the KDE:Distro:Factory repository.

The latest release from KDE moved from beta to RC stage, thus finding and reporting bugs is more important that ever. At the same time, the distribution packaging teams are also working in polishing their packages. As far as openSUSE is concerned (not dissing other distros, just mentioning the one I’m involved in ;), you can kill two birds with one stone by installing the packages provided in the KDE:Distro:Factory repository.

KDE released the second beta of the KDE Platform, Workspaces and Applications 4.11, and after the necessary time for the OBS to build packages from the released tarballs, packages are available for openSUSE 12.3 and openSUSE Factory. Like the previous beta, they are available through the KDE:Distro:Factory repository. 4.11.x is is targeted for inclusion in the upcoming openSUSE 13.1. So far 4.11 has been pretty stable for me, but you should never forget these packages are for testing and bug reporting purposes: don’t use them on production systems.

As a consequence of [the recent changes in the repositories]({{ site.url }}/2013/06/upcoming-changes-to-opensuse-kde-repositories), the openSUSE KDE team is happy to announce the availability of packages containing the first beta of the KDE Platform, Workspaces and Applications 4.11. Packages are available in the KDE:Distro:Factory repository. As it is beta software, it may have not-yet-discovered bugs, and its use is recommended only if you are willing to test packaging (reporting bugs to Novell’s bugzilla) or the software (reporting bugs directly to KDE).

Since KDE has released the first beta of Platform, Workspaces, and Applications 4.11, there will be some changes in the packages offered in the openSUSE repositories. In short: KDE:Distro:Factory will now start tracking 4.11 betas and RCs: packages are being worked on. Use this version to test packages and to report bugs upstream. KDE:Release:410 has been decoupled from KDE:Distro:Factory. If you were using 4.10 packages from KDF, you’re highly encouraged to move to this repository.

These posts kind of sound like a broken record, right? ;) Anyway, since KDE has released new versions of Platform, Workspaces and Applications as part of the stable release cycle, thanks to the OBS we have packages available for openSUSE 12.2 and 12.3. The 4.10.4 update will also be released as an official update for 12.3 in due time. Where you can get the packages? Two places, as usual: KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release; KDE:Release:410 (openSUSE 12.

KDE released 4.10.3 versions of the Platform, Workspaces and Applications yesterday, with more than 70 bugs being fixed. Notably: Several fixes in handling encrypted mails in KMail Fixes for KDEPIM syncing and ownCloud A number of improvements in Dolphin, including crash fixes Optimizations in the Plasma Workspaces [The full list](https://bugs.kde.org/buglist.cgi?query_format=advanced&bug_status=RESOLVED&bug_status=VERIFIED&bug_status=CLOSED&bugidtype=include&chfieldfrom=2013-01-01&chfieldto=Now&chfield=cf_versionfixedin&chfieldvalue=4.10.3&order=Bug Number&list_id=638034) has other important changes. As usual, there are two different repositories from which you can get them:

KDE has released its monthly update for the 4.10 release, and after a brief wait while the Open Build Service worked over the released tarballs, the openSUSE KDE team is pleased to announce the availability of the 4.10.2 release packages for openSUSE 12.2 and 12.3. []({{ site.url }}/images/2013/04/757111961.png) Despite being a minor release, more than 100 bugs were fixed, in particular there were many KDEPIM fixes touching both the low level stack and KMail/KAddressbook/Kontact.

Hot on the heels of the announcement from KDE, the openSUSE KDE team is happy to announce the availability of packages for the latest stable release of the KDE Platform, Workspaces, and Applications. Packages are available in the KDE:Distro:Factory repository (which is where the packages to land in 12.3 are tested) for openSUSE Factory (soon to be 12.3) and openSUSE 12.2 and soon (when the Open Build Systen finishes rebuilding a number of packages) in the KDE:Release:410  repository for openSUSE 12.

During the discussions for the release of openSUSE 12.3, the topic of update notifications and applets was brought up again. Originally openSUSE shipped with a custom update applet, but since it was basically unmaintained, the decision was made to switch to Apper for openSUSE 12.2 The original Apper used in that version had a number of issues, which the upstream developer (Daniel Nicoletti) fixed in a newer version, which also had a lot of other improvments.

Following up on the announcement from KDE, the openSUSE KDE team is happy to announce the availability of 4.10 RC3 packages. Remember that they are packages meant for testing and reporting bugs, so that the next release will be as polished as possible. You will find the packages in the KDE:Distro:Factory repository. An updated live media based on the upcoming openSUSE 12.3 ([see previous post]({{ site.url }}/2013/01/test-the-upcoming-opensuse-12-3-and-kde-workspace-applications-and-platform-4-10-rc2)) is also available (files named KDE4-4.

Following up on my previous post, a different type of image has been made by the openSUSE KDE community members. In particular, alin has created images sporting the same software from KDE (4.10 RC2) but using the upcoming openSUSE 12.3 as base. Download links: 32 bit version 64 bit version Release directory (in case the above links go 404; the files are named KDE4-.4.10.RC2-Live) These images are provided not only to test 4.

The 4.10 release for the KDE Development Platform, Workspaces and Applications is drawing nigh… as you may have read, there is now an additional release candidate in order to test some last-minute changes. Of course, the KDE developers can only do so much: it’s impossible to test all possible combinations. That is, unless the community at large helps by finding and reporting issues the developers can fix. But doing so requires a 4.

Yesterday Alex Fiestas showed on his blog a video of a recent development version of the KScreen library, created to handle easily multiple monitor setups in KDE, almost in an “automagic” way. As this is a project where configurations and setups are highly heterogeneous, a lot of testing is required to ensure things work reliably. Of course, you cannot ask a developer to have all sorts of screen combinations, but remember one of the strengths of FOSS: “many eyes make bugs shallow”.

openSUSE is migrating to the use of systemd for the upcoming 12.3 version, given the difficulties that emerged in trying to co-maintain two different init systems (SysV + systemd). While I am not going into the details of this choice (I leave this to more informed people), this has some consequences for software higher in the stack. As ConsoleKit is deprecated, systemd offers its own daemon to keep track of sessions and assigned seats in a system.

The KDE community has just released Beta 2 of the upcoming 4.10 release of the Development Platform, Workspaces, and Applications. Of course, distributions are providing binary packages for the adventurous… and how could the green distro be left out? In fact, it is not. Beta 2 packages were uploaded and built in the KDE:Distro:Factory repository. Updated packages have also been submitted to the development version of openSUSE (Factory) as the ultimate goal is having 4.

Following up my [earlier post]({{ site.url }}/2012/10/whats-cooking-for-kde-in-opensuse-12-3-theming), the new openSUSE 12.3 theme has finally landed into the official openSUSE repositories  and will be part of the upcoming 12.3. A lot of work has gone into the new theme since I last posted about it, so this post will show how things look at the moment.

A few caveats:

• The theme targets the 4.10 release of the KDE Workspaces, so it may be not be perfect under 4.9;

• The default wallpaper has not been chosen yet.

Without further ado, let’s get down to seeing what’s improved.

Like everything, openSUSE is not perfect. Bugs crop here and there, or there is missing / quirky functionality that users may run into. Being a distribution of heterogeneous software, this means that bugs fall into these categories: Upstream bugs in the software shipped by openSUSE Bugs in the packaging Bugs in distribution-specific setups or that derive from interactions with these setups (e.g. kernel, low level software stack, etc.

Although the release of openSUSE 12.3 is yet to come, the people of the openSUSE community contributing to KDE are already at work to bring the best possible KDE experience for the new release.

Recently Fedora’s Lukas Tinkl pushed to kdelibs (for the 4.10 release) a patch that enabled Solid to talk to udisks2, which is a replacement for udisks. Fedora already moved to udisks2 (and killed HAL) and future GNOME releases will only use udisks2, so the need for a working backend was a necessity, and at the same time they acted like good open source citizens, and pushed the code both to 4.

Because changes occur when one least expects them. This post is about one such change.

While reading the statistics for my blog, I noticed that a number of searches looked for hierarchical clustering with Python, which [I covered quite a while ago]({{ site.url }}/2007/11/data-clustering-with-python). Today I’d like to present an updated version which uses more robust techniques.

 My Akademy talk proposal was not accepted, but the organizers were kind enough to offer me the chance to hold a BoF on the same subject. Now I bet you wonder on what I’m going to discuss, and I think the title already gives you an idea: KDE and bioinformatics: the missing link Although in the KDE community we have our fair share of scientists (hey there, Stuart!

At last, after months of inactivity, I pushed out a new release of [DataMatrix]({{ site.url }}/projects/datamatrix). Although the version bump is small (0.8) there are a lot of changes since last releases. The most notable include: Ability to apply functions to elements of the matrix Ability to filter rows by column contents Ability to transpose rows with columns An option to load text files produced by R (which are, by design, broken) Removed the getter for columns, using dictionary-like syntax directly A lot of bug fixes The download links on [the project page]({{ site.

In the past months I’ve always wanted to write a small Plasma applet to aid me in some boring tasks as a bioinformatician. One example (for the non-scientific crowd out there) is when I find a specific gene out of my analysis work which I want to take a look at. I am often lazy, so instead of firing up the browser to look at the online resources, I wanted to write something which could access said resources programmatically.

Some say that all good things must come to an end. I’m not entirely sure that this is a universal truth, but I can say that at some point in life there are decisions that need to be taken. In this case I made my own: today was the last day inDr.Cristina Battaglia’s laboratory, a place where I spent my three-year Ph.D. course and one year as a post-doc research fellow.

During the course of my research work, I may obtain results that are worthy of publication in scientific journals. Since my master’s thesis I’ve been using LaTeX as my writing platform, mainly because I can concentrate on content rather than presentation (I find it useful also for writing non-scientific stuff as well). Also, I can handle bibliography (essential for a scientific publication) very well without using expensive proprietary applications (such as Endnote).

In my early days I used kLyX first, then LyX, but I found the platform to be too limited for my tastes, and also LaTeX errors were difficult to diagnose. I needed a proper editor, and that’s when I heard of kile, a KDE front-end for LaTeX. Kile is currently at version 2.0.2 and is a KDE 3 application. However, in KDE SVN work is ongoing to produce a KDE4 version (2.1) and that’s what I’ll look at in this entry.

I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

Finally I can lift the curtain of silence and tell the reason why I’ve been very busy before Christmas: it all lies in the publication of a paper, “Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments”, which is finally out on this week’s issue of PLoS ONE. It’s different from [the previous paper I mentioned]({{ site.url }}/2008/01/phd) (which was not my first publication, either), for two main reasons:

Finally a new entry! I’ve been extremely busy with other things, that is why I did not have time to write more. One of the main reason is related to an important landmark in my professional career, but I’ll write more about it after January 1st (hint: those who follow my Twitter updates may have already understood). As a nice way to break the hiatus, I’m releasing a new version of DataMatrix, my implementation of R’s data.

Recently I had to annotate a large (10,000+) number of genes identified by Entrez Gene IDs. My goal was to avoid “annotation files” (basically CSV files) that a part of wet lab group likes, because I wanted to stay up-to-date without having to remember to update them. So the obvious solution was to use a service available on the web, and in an automated way. For reference, I just tried to attach gene symbol, gene name, chromosome and cytoband.

At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax. In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).

For a long time I have tried to handle text files in Python in the same way that R’s data.frame does - that is, direct access to columns and rows of a loaded text file. As I don’t like R at all, I struggled to find a Pythonic equivalent, and since I found none, I decided to eat my own food and write an implementation, which is what you’ll find below.

I wanted to write this earier, but I couldn’t: I’m now in a hotel in Maastricht, Netherlands, and waiting to get back tomorrow. I’ve been attending the 4th NuGO hands-on advanced microarray data analysis course and I even wanted to blog about it… but the hotel’s connection did not resolve any non-European web page until late today.

I’ve been wondering about why FOSS is often compared to the academic world, but at least in my limited experience, I see little people that grasp its concept in the world of research. On a quick look, developing FOSS in a research environment would be very good: not only you’d get publicly available results when you publish, but at the same time you can make sure that in an extreme case your application will be carried on by someone else should you not be able to continue development.

I’m often wondering why people only resort to R when working with microarrays. I can understand that Bioconductor offers a plethora of different packages and that R’s statistical functions come in handy for many applications, but still, I think people underestimate the impact of performance. R is not a performing language at all, it doesn’t parallelize well when using HPC (at least from the talks I’ve had with people studying the matter), and in general is a memory and resource hog.

Fourteen days since my last post. Quite a while, indeed. Mostly I’ve been stumbled with work and some health related issues. Anyway, I thought I’d follow up on the meta analysis matter I discussed in my last post. It turns out that it’s a fault of both limma and the data sets, because apparently the raw data found in the Stanford Microarray Database have different length, gene-wise (a result of not all spots on the array being good?

Again in the past days I’ve been banging my head thanks to the fact that doing meta-analysis with microarray data is more difficult than what it seems. The problem sometimes lies in the data, sometimes lies in the analysis software and sometimes in a combination of factors. When doing work on a public data set (Zhao et al., 2005), I had to start analysis from raw data. Now, I tried using both the limma and marray Bioconductor packages, but both of them bail out with cryptic error messages.

The title says it all. After all these years, I was finally able to get my Ph.D. in Molecular Medicine this morning, with my thesis “Identification of disregulated metabolic pathways by transcriptomic analysis in renal carcinoma samples” (yes, that’s a long title). The defense was a success and I admit I was surprised when the commitee actually expressed a significant interest in my work. In any case, I’m happy that it’s over, as the past period has been rather hectic.

There is always a lot of talk about “brain drain” (fuga di cervelli in Italian) from my country. I keep on reading disgruntled comments of low pays and poor research, and that going abroad is the only solution for an Italian scientist to be successful.

While I believe that research done outside of my country can be handled better (but it’s impossible to know for sure: never tar everyone with the same brush), I think that, also thanks to the way the media and the scientists themselves handle it, in everyone’s view it has almost become like the El Dorado. And that, in my opinion, is incorrect.

While working today on an annotation class in Python I stumbled on a problem. Normally I work with lists of genes that are consistent, i.e. all Entrez Gene IDs (or RefSeq IDs, or Genome Browser IDs…), but today I had a list of mixed identifiers. The subsequent idea was “let’s implement auto-detection of common identifiers in the class”. The problem is… is there any actual documentation on how identifiers are made?

**Notice:**Just now I realized this has been linked to to a Stack Overflow question. I recently wrote a new post that uses a different technique and a combination of R and Python. [Check it out!]({{ site.url }}/2011/05/multiscale-bootstrap-clustering-with-python-and-r)

Following up my recent post, I’ve been looking for alternatives to TMeV. So far I’ve found the R package pvclust and the Pycluster library, part of BioPython. The first one also performs bootstrapping (I’m not sure if it’s similar to what support trees do, but it’s still better than no resampling at all). I’ve found another Python project but it is still too basic to perform what I need.

As people who read my science-related posts know already, I’m not a big fan of {{post id=“software-and-biological-research” text=“software made just to support a publication”}}. Recently I’ve stumbled again into similar software. Namely, I’m talking about the TIGR Multiexperiment Viewer (TMeV), a Java-based program which is often used for microarray analysis. It’s not exactly “fit for publication”, because it has reached version 4 last year, but shows some of the problems ({{post id=“genbugg” text=“mentioned already”}}) with releasing bioinformatics software.

I use TMeV mostly because I didn’t find any other implementation of the hierarchical clustering algorithm with support trees. However, I’ve stumbled upon a very annoying bug in the most recent version. Normally I use average linkage clustering and as the distance metric I employ the Pearson’s correlation, and with gene and sample bootstrapping: with certain files this makes TMeV report errors at random during the iterations.

My supervisor has given me an OK for my thesis (save for a couple of cosmetic changes), therefore now I have just to wait for the verdict of the Ph.D. council then fill in some paperwork: the next step is the defense, sometime in January. After that I’ll probably put my thesis online and post a few articles on the concept of group testing for microarray data.

Today I started working on a data set published on GEO. As the sample data were somehow inconsistent (they mentioned 23 controls when I found 28), I decided to parse the SOFT file from GEO in order to get the exact sample information. I did a grave mistake. First of all, Biopython’s SOFT parser is horribly broken (doesn’t work at all) and quite undocumented: I could work around the lack of documentation (API docs) but not with the fact that it wouldn’t work.

Today I was looking for an easy way to do some calculations of raw expression data on Affymetrix arrays, but I didn’t want to use R: I have already mentioned how I don’t like its design and implementation. While looking for some documentation, I stumbled upon this nifty little program called RMAExpress.

The title of this post tries to give some insight on a problem that I’ve stumbled upon a lot of problems when doing microarray data analysis: the plethora of different file formats. In “conventional” (as I call it) bioinformatics this is less problematic, as FASTA or PDB are quite standardized by now.

After little more than a year, I’ve been moved to a new office, because new people needed to be put in the room I was in. The new place is slightly bigger (four desks instead of six) and for now quieter. I spent most of the morning fixing things and setting up network connections. This is how it looks now: []({{ site.url }}/images/2007/09/016.JPG) [![A closer look]({{ site.

At the time of writing, a lot of people (even in bioinformatics) uses Microsoft Word to write their papers. I personally think it’s not a good idea, and not just for the file formats (like Microsoft lobbying semi-legally to get OOXML approved by ISO), but because for scientific papers the WYSIWYG paradigm is not appropriate.

After giving in the summary of my thesis today, I also started writing the actual thing. Of course this is not something I will finish in a few days. It’s a long journey that will go on until I deliver it. Aside that, I’ve been having some problems with R, a language which I really don’t like and I hope to use as less as possible. I was obtaining a list of differentially expressed genes (DEGs) out of some data files with SAM, and of course I had to supply a matrix with expression values for every gene.

The idea to blog about this common phenomenon came after I read a post over at Bioinformatics Zen on the matter of open science. There, Mike describes the situation quite clearly: mostly, you need a middle ground between complete secrecy and absolute openness. That said, I still think science should be more open, at least in the field of life sciences. Publication should be a way to let others know, benefit and also build upon your work, not just a way to obtain funding or improve one’s career.

As the people who read my science related posts already know,[ I’m in the middle of doing meta-analysis]({{ site.url }}/2007/05/28/more-meta-analysis-difficulty/). That brought up a problem, so to speak, and it’s related to annotations.

UPDATE: Today I found out that J Brooks (the corresponding author of Zhao’s paper) has agreed to send the data I needed. Thanks a lot! When you do bioinformatics, you often test your own procedures not only on your data, but also on datasets provided by other people and publicly available. [As I stated previously]({{ site.url }}/2006/11/10/the-joy-of-meta-analysis/), that’s what meta-analysis is. I’m doing a bit of that for my thesis and recently I noticed that some datasets, while being public, are far from complete.

I’ve been able to complete most of the analysis for my Ph.D. thesis work, at last. I need a few runs more but I am arranging to work at a location of one of our research partners, as I don’t have a powerful enough computer to handle the calculations (apparently, 1Gb of RAM isn’t enough). At least the results I have look promising. Now all it’s left (and that’s not an easy task, heh).

As I’ve been working to get some results done for my Ph.D. thesis, I’ve stumbled across the problem of having different data obtained through different software. Even if it’s just a matter of text files, the fields are all different and even if dealing with the same data, trying to infer relationships is a pain.

I’ve again seen how useful and powerful Python can be. The other day I had to prepare an Excel spreadsheet (sadly) which among other things needed to contain links to the GeneCards database for each gene listed. There were more than 2900 genes listed, so adding links by hand would have been suicidal. That’s when Python, through its Windows extensions, comes into play. First of all I created a module for COM objects using the makepy utility.

This post sums up my frustration in trying to use Python for my daily work. Like Perl and Ruby, it has its own Bio version to deal with biological data. However, the current implementation leaves a lot to be desired. A lot of stuff that doesn’t deal with sequence analysis, even for simple tasks such as fetching annotations from Entrez Gene, is missing (but present in Bioperl, for example). Also, documentation for some modules is lacking or non-existant (why keeping a parser for Affymetrix CEL files when there are no information on how to use it, let alone know which formats does it support?

This entry already shows what I think of a popular open source pathway analysis and visualization program, GenMAPP. It’s quite used to map gene expression data coming from microarrays to metabolic pathways, and in addition to that you can also evaluate enrichment for both pathways and Gene Ontology terms. Last but not least you can create and contribute new metabolic maps. So why the title of the post? Because, despite being actively developed and with conscious developers that don’t want to break the software with new features, it’s extremely buggy.

As I anticipated, I can finally release this small script. Its purpose is to build BED files out of tab-delimited text files. I made this because I had several files to make and moving columns left and right (not to mention writing a heading line for the Genome Browser) was becoming annoying. Its use is fairly straightforward, as the help itself says:

Today I went over my old Python code, back when I first started programming. I’d say that I found what I had written to be largely amusing to say the least. Loads of ugly hacks all over the place, duplicated functions, etc… in short, a real mess. I’m quite happy of the results I achieved in the past month, since I finally learnt how to code properly and started making my own classes (this book was immensely helpful).

I just learnt today that the paper I’m writing with my colleague has to be in an acceptable state (almost submission ready) by the 20th. Considering I’m still behind with the analysis, it will be certainly challenging to complete the task, considering I also have other duties to attend to. In primis I need to study more and more papers (I add more and more to my TODO list). Also, probably next week the new infrastructure for authentication (which includes a Primary Domain Controller for Windows clients) will be put in place and I’ll have to make sure that the data handling for our group will be without problems.

Work is getting hectic as we’re finally gathering a lot of data for a new publication. This means reading a lot of literature, choosing the figures and planning results and discussion properly. On top of that, I’m starting to study pathway analysis for my thesis, and of course, seeing how I can use that to study our own data. I also have some other non research duties to attend to, such as being the person repsonsible for data handling of our group in relation to the [server that we bought recently]({{ site.

I’ve just came back from a two days’ trip in Firenze. On the first day we had a long (4.30 hours) meeting on some interesting research topics, such as cellular aging and about oxidative damage in yeast. On the second day I attended part of a workshop on pathway analysis and related topics. Many speakers were from the NuGO project funded by the European Community, but the talks were still quite general.

Yesterday I and another person went to the server room to do the basic configuration of the Apple Xserve we have bought, along with its Xserve RAID unit. Despite the general “idea” that anything Apple does is user-friendly, our experience was plagued by problems.

In the past two days I’ve been tackling an annotation problem. I’m trying to provide annotations for genes found in regions that are significantly altered, DNA copy-number wise (thanks to the STAC method). The idea would be to annotate those regions (that span one megabase) using UCSC Table Browser. However, the task was impractical, so I decided to automate it a bit. I converted the data into ranges and then used the KnownGene annotation file (downloaded from UCSC) to obtain which genes were in which reagion.

A post I wrote ended up on the front page of nodalpoint.org. I liked that, even though it may not seem a lot to many: at least it shows that some of my concerns are shared with other people in the scientific community. Also after viewing some presentations about Web 2.0 at the EMBL, I decided to make a del.icio.us account. I find it quite handy so far to organize bookmarks and such.

In the past two days I’ve written a simple annotator program, that given an input list of RefSeq genes, automatically determines the relevant Entrez Gene IDs and annotates them using the flat files provided by the NCBI. A direct conversion was not possible due to limitations in Biopython’s parsers, but I managed to use the GenBank parser to identify and extract the references to the Gene IDs (and putting them in a list).

Since recently (thanks to my brother) I got a new cellular phone with better capabilities, photo-wise, I decided to take a few photos of my workplace. I changed office a while ago, now I’m located on the first floor of the building, sharing the office with 5 other people: Raoul, Michele, Giorgio, Roberta and Alessandro. This photo shows my current computer setup: 429 Quant was running a screensaver when I took this photo: the mouse pad and that other black thing next to the keyboard are gel pads to help me with my tendinitis.

EURASIP Journal on Bioinformatics and Systems Biology is having a special issue on text mining for biology. My boss wants to publish something there, and asked if I and a colleague could work on that. I’ll probably focus on evaluation methods, since I’m not an expert in text mining or language processing. And that’s where the problem comes in: I know almost nothing on text mining. Which means this will add up to the ever growing pile of papers and books I have to study, including but not limited to Python programming, microarray analysis and XML…

Recently, I’ve been in need to retrieve some records regarding renal cell carcinoma referenced in papers by Zhao et al. and Higgins et al. The records of the former were hosted on NCBI’s Gene Expression Omnibus, while the latter records were uploaded to EBI’s ArrayExpress database. Getting data from others and using it for your own analysis is called meta-analysis, and it’s often used to validate methods and algorithms with different data sets.

After discussing my second PhD year today, and after noticing that not even a single professor from the commitee was there (save my boss and a person that joined later on), I realized that the situation for students like me isn’t really the best. A PhD program is supposed (at least here) to be a cross between a research job and a student’s position, since you should study but at the same time conduct research and (if you’re lucky) also get paid for it.

I’ve noticed that the journal Science code for Biology and Medicine has finally launched. While some said that would be a journal if someone is desperate for a publication, I think it fills in a gap that’s very felt in bioinformatics: the availability of source code.

Finally I cleaned up my code enough to post it here. It’s probably still ugly, but not as ugly as when I wrote it down the first time. It’s all about manipulating text files, to be precise tab-delimited files. All the snippets are published under the GNU GPL v2 (not that I think that anyone would use them, but just in case…).

Although I’m still studying the language, finally I managed to create a program that actually does something I need. The need arose from a gene list I was given, made up by Entrez Gene IDs. I need to annotate it, but in a form that wasn’t able to be produced by the usual functional annotation tools I have. Actually it could have been done, but what I needed was to make something that I could automate.

A lot of my bioinformatics work involves performing functional annotation on genes. This means that given lits of genes I need to resolve their known function, or if they’re part or some metabolic pathways and so on. Even with the current trend in our laboratory, that is investigating DNA copy number changes using SNP microarrays (it’s a rather new form of analysis, but some relevant papers are out already), in the end we have to go back to the genes affected by such changes (in order to find interesting/marker genes - we study solid tumors).

I’m finally back from holidays and since there’s almost no one in the office here I thought I’d write a little mixed entry, while quant is busy compiling a patched 2.6.17 kernel (but quant as an odd overheating problem that I will describe in another entry, so I have to compile it by steps). Work is somewhat slow, as the people I need to contact are still on holiday. In the mean time, I’m reading an interesting paper on some GPLed software for Single Nucleotide Polymorphism analysis, written in Perl and R.

In the past few months I’ve been wondering about the state of bioinformatics and computational biology in general. When I attended the school in Bertinoro (as [I wrote about previously]({{ site.url }}/2006/03/19/bertinoro-arrival-day-1/)). The development in this field can be regarded as quite astounding, just a look at journals like BMC Bioinformatics, Bioinformatics or others can give an insight of that. However, and talks at Bertinoro seemed to confirm this impression, it looks like that many in the computational field forget that we’re talking about biology.

Our paper’s completion has probably been delayed till September or so pending some (in my opinion puzzling) organizational issues within a group that works with us. My research work is also pending due to the fact that I’m waiting for someone to prepare a “data matrix” for me, and the person doesn’t seem to know that leaving other people hanging is somewhat impolite. So, I decided that as a person that works in bioinformatics I could learn something new.

Yesterday I was trying to adjust some files in order to make a program use Affymetrix SNP arrays data (instead of arrayCGH data like the program was designed for). I had a big (116,000 rows) tab-delimited text file and I needed to use only part of the columns there.

I got upgrade hardin (my laptop)’s memory at least, bringing it to 1Gb, at last. However I had two 256 Mb modules installed, that means I had to buy two 512 Mb ones. Oh well, I’ll just try to sell those ones. Everything seems snappier now, and even Firefox seems not to clog the CPU when loading pages (I need to experiment more, since I have no clue why that should have changed).

I haven’t been writing a lot here mostly because of the rather hectic work schedule I’m having. We’re nearing the completion phase of a paper that includes quite a bit of my work (and also a lot of other people’s contributions), and I’m also swamped with PhD classes (two weeks to go). Also, one of my bosses has assigned me another project which I’ve yet to tackle, and I got to help my colleague with a poster as well.

This week has been absolutely exhausting. I’ve been having PhD classes (statistics, effective writing, and more statistics) almost every day (save tomorrow) and also heaps of work piled up. I’ve got new data to work on, and also I’ve been assigned to do something else along with my current bioinformatics work. I also need to get in touch with the Partek software representative to let him know what I think of their genomics software.

Today I obtained a trial license of a data analysis program. I plan on using it for the next two weeks to see if it could improve the analysis workflow in our laboratory. I noticed this software uses the Tk widget set to achieve cross-platform capability (in fact, it can run on Linux, which is a big plus for me). However, in my opinion, Tk widgets look rather ugly. I wonder why the company didn’t consider using Trolltech’s Qt widgets.

This has been a rather stressful period work-wise. Things are looking extremely confusing on the (upcoming) paper we need to write and even a small doubt can cause huge time losses (I spent the whole morning checking to see if my analysis was correct or not while in fact it was correct in the first place). I’ve been shown a new software for microarray analysis, well, at least some brochures. I’m going to inquire about pricing (the most important part) and platform availability (I’d love if it could run on Linux).

Today I found out that a computer running Windows had been “self-writing” words when an Internet Explorer window was open. This obviously led to the conclusion that there was some kind of malware running. I immediately unplugged the network cable but the typing continued - this is a good sign meaning that it was just some random program doing it. It only affected IE, no other programs. I wonder how it got there, I can only suspect the current user, as I never do any network-based activity there, only analysis (and I run a much safer Linux box - no Windows for me).

This week has been quite busy at work. As I finally got the two lists of differentially expressed genes that I needed, I started my analysis work. Perhaps analysis is not quite appropriate, as what I to is mostly to annotate the genes (i.e. I try to find out everything about them, or certain features I need) and to see if the lists are “enriched” by a particular feature. From this I try to see if what I see has a biological relevance, or not.

Today one of our desktops won’t turn on at all. I didn’t even see the POST lights turning on (this is a Dell computer), so I assume that the PSU is dead. I’d have already called for support but since the box has been bought in the USA (part of a bundle of our GeneChip systems) I had to request a warranty transfer (notice that I don’t even know if there’s still a warranty!

Finally, we have windows in the office. Before that it was just a room with walls, and it looked a little claustrophobic. It took a good deal of time (4 months) to get these works done, but I think the result is worth it. At least the whole room looks a little more human, now. I will be spending tomorrow’s work day analyzing data with an extremely bad piece of software, at least design-wise (the algorithm used inside it’s very solid, instead).

I haven’t been writing on this blog as much as I wanted, partly because of tiredness, partly because of my always-present tiredness. Today I delivered the receipts from the Bertinoro school and also from Trieste: I hope I get a refund fairly quickly (although usually “fairly quickly” means around 3-4 months if I’m lucky). Also, these days I’m working on the DNAcopy package from Bioconductor (a series of add-on packages for R) to see if I can use the data from Affymetrix’s Chromosome Copy Number Analysis Tool to get a genome-wide view on copy number aberrations (CNAT only permits you to see one chromosome at a time).

Talks, talks, talks. That’s all about this day. Some were also extremely difficult to understand, and I’m not sure I took good notes. Talks went on from 8.30 to 18.00 (excluding lunch break) and then a workshop until 19.30. I’m really beat. I retired to my room while the others wanted to play karaoke, but I was too tired. Tomorrow is the last day, thank goodness! I’m tired of waking up at 6.

I just came home and I’m terribly tired, so I’ll be rather brief. This morning we had four lectures, including two interesting ones on protein structure prediction, though one speaker was too fast and I almost couldn’t take notes. Then we went in the afternoon to Ravenna. I took some pictures during the sightseeing and I’ll post them when I get home. We visited the “Mausoleo of Teodorico”, the “Basilica di S.

Finally I got hold of a stable Internet connection so I can post about my experience in Bertinoro di Romagna so far.

I haven’t blogged in a while, mostly because I’m either doing something else, or when I want to, I find out I’m really tired (this and the past week have been very tiring for me). In any case, I’ll make a big, random entry. I’ll start saying that I’m amazed at how badly software can be written. In the life sciences field you see very clear examples. Horrible UIs and poor documentation mostly (while the algorithms and methods implemented are usually very solid).

Finally I have some time to give an insight of what happened Tuesday and Friday, when I left for Trento to attend to the ITC-irst’s meeting called “Biobanks for functional genomics”. The trip was mostly uneventful, though we had to wait a lot once we arrived at the ITC-irst because we were way earlier than expected. I spent time talking to some people there, they work in an interesting field: applying computational methods to microarray expression data.

After sorting out the bureaucracy, finally I was able to enroll for the 6th Course in Bioinformatics for Molecular Biologists that will take place in Bertinoro di Romagna in three weeks. I’m glad I was able to, the course program looks really interesting and perhaps I’ll be finally able to learn bioinformatics in the right way, since so far I’m entirely self-taught, and sadly, it shows. On another topic, the ceiling is going to be fixed by tomorrow, I hope, so I’ll be able to get back to my old office at last.

Not everything can be fun in the life of a scientist. For example, my work in the bioinformatics field of our laboratory makes me see a lot of annoying problems related to files, to be precise file formats. A lot of sofware in the biological sciences uses plain text files to export data to other programs (sometimes binary data, but that’s another matter). The problem comes when you have to use the output into another program.

First of all, the strangest oddity ever. On Friday once at the laboratory I was contacted by an Affymetrix representative regarding [this entry ]({{ site.url }}/2006/01/26/badly-written-software-or-policy/). She wanted to know why I wrote it and that it seemed that I “didn’t contact Affymetrix to see if the problem could be solved”. She wasn’t offended or anything (she will even get me in touch with someone from the software department), but nevertheless this is my blog and I’m entitled to my personal opinions.

That was the only noteworthy event of today’s work. I arrived late (took 1 hour and 30 just to get there) and then during lunch break we moved again to the LITA to celebrate. We got a sort of necklace for her which she liked quite a lot, and we got time to have a toast and eat some cake. It took way more than I expected - I was back at the CISI at around 15.

Today while working I got stuck in what probably is an intentional flaw of the software we’re using. When we scan Affymetrix’s GeneChips there are a number of files produced by the GeneChip Operating Software (GCOS in short) including raw acquisition images and various analyses. Now, a certain number of people need to use those data to work (including myself), but I don’t want people to fiddle on the scanner workstation unless they know what they’re doing.

Now that the office is more or less in working order (if we exclude the lack of chairs) I thought I’d post something about it. I finally finished setting everything up (including the 250 Gb network drive) today, so I can finally resume my real work next week (that is, bioinformatic analysis). I plan on buying a cheap chair this weekend so I can get at least a place to sit: there are two chairs only for 6 stations.

Finally today there was the (largely) anticipated move from the LITA to the CISI. I actually showed up at the CISI first, to do some research work, then after the lunch break I and a colleague went to the LITA to pack things up. We almost looked like robbers (and for sure got some funny looks from people as we moved to put things in the car): we had four computers, four monitors and keyboards, lots of cables, my notebooks, and more.

I haven’t been able to write because I always end up extremely tired from work. Since I’m moving to the CISI next week, it looks like everyone needs me. I managed to study a bit, then I had to help a couple people with a protocol, then work on the firewall/router migration (we’re restructuring our Intranet once I move a few computers there) then help with a software, etc. And tomorrow looks the same.

Today I thought I was going to move from my current location (LITA building, University of Milano ) to the new one, the CISI. However I didn’t think up that some stuff (including the arrival of 3 new people at our laboratory, Sarah, Guya and Alessandra) would have held me back. I won’t relocate till next Monday. In the mean time I spent the day testing out some procedures and creating a draft proposal for the new laboratory’s network structure, and getting the equipment to put that in place.