Initial import of new posts

_posts/1999-12-31-temporary-post-used-for-style-detection-title-1133825971.markdown

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+---
+author: einar
+comments: true
+date: 1999-12-31 23:00:00+00:00
+layout: post
+slug: temporary-post-used-for-style-detection-title-1133825971
+title: Temporary-Post-Used-For-Style-Detection-Title-1133825971
+wordpress_id: 722
+categories:
+- General
+---
+
+Temporary-Post-Used-For-Style-Detection-Content-1133825971

_posts/2005-12-26-up-and-running.markdown

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+---
+author: einar
+comments: true
+date: 2005-12-26 19:23:14+00:00
+layout: post
+slug: up-and-running
+title: Up and running
+wordpress_id: 2
+categories:
+- General
+---
+
+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.

_posts/2005-12-31-new-books.markdown

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+---
+author: einar
+comments: true
+date: 2005-12-31 15:26:37+00:00
+layout: post
+slug: new-books
+title: New books
+wordpress_id: 8
+categories:
+- Anime
+---
+
+I recently got myself a couple of new books, thanks to the folks at [Archonia](http://www.archonia.com):
+  
+
+[![Sakura Taisen V Original & Format Collection](http://www.dennogumi.org/wp-content/gallery/_stvbook.jpeg)](http://www.dennogumi.org/wp-content/gallery/stvbook.jpeg) 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. It's nice to have such an addition in my collection, considering that books in Italy are impossible to find.
+  
+
+[![T2 Works - Sora no iro, Mizu no iro](http://www.dennogumi.org/wp-content/gallery/_t2.jpg)](http://www.dennogumi.org/wp-content/gallery/t2.jpg) T2 is a well known artist so I got it... too bad I didn't know it was full of H content, even though I have it filtered when browsing Archonia. I'll send them a mail about it. Nice art, but mostly unviewable (almost vomit-inducing in my case). 

_posts/2006-01-01-new-year.markdown

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+---
+author: einar
+comments: true
+date: 2006-01-01 13:11:24+00:00
+layout: post
+slug: new-year
+title: New Year
+wordpress_id: 9
+categories:
+- General
+---
+
+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. Well, mostly because I've seen some people even struggle to **show** that they would be celebrating. 
+
+But enough with the angry stuff. I wish a Happy New Year to whoever is reading this.

_posts/2006-01-02-roc-star-yet-again.markdown

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+---
+author: einar
+comments: true
+date: 2006-01-02 15:58:18+00:00
+layout: post
+slug: roc-star-yet-again
+title: Roc Star... yet again
+wordpress_id: 14
+categories:
+- Final Fantasy XI
+---
+
+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.
+Next window will open tomorrow: not sure I will be there, though.

_posts/2006-01-03-unfair-treatment.markdown

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+---
+author: einar
+comments: true
+date: 2006-01-03 10:14:51+00:00
+layout: post
+slug: unfair-treatment
+title: Unfair treatment?
+wordpress_id: 15
+categories:
+- Linux
+---
+
+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...
+
+

_posts/2006-01-04-cats-and-finances.markdown

@@ -0,0 +1,15 @@
+---
+author: einar
+comments: true
+date: 2006-01-04 14:52:12+00:00
+layout: post
+slug: cats-and-finances
+title: Cats and finances
+wordpress_id: 16
+categories:
+- General
+- Linux
+---
+
+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](http://kmymoney2.sourceforge.net/index-home.html) but aside the fact that it doesn't have any Italian template, it's a little confusing. I'll keep on looking for something similar that works under KDE.

_posts/2006-01-05-drawing-commissions.markdown

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+---
+author: einar
+comments: true
+date: 2006-01-05 19:15:32+00:00
+layout: post
+slug: drawing-commissions
+title: Drawing commissions
+wordpress_id: 18
+categories:
+- Anime
+- S.T.E.A.L.
+---
+
+The few people who know me may have heard of one of my pet projects, [S.T.E.A.L.](http://www.dennogumi.org/interests/), whose draft PDF is available [here](http://www.dennogumi.org/steal/steal.pdf). I've been trying for ages to get an illustrator to do some b/w art for it (a la [Slayers](http://www.tokyopop.com/dbpage.php?propertycode=SLY&categorycode=BNV)), 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...

_posts/2006-01-05-dvd-burning.markdown

@@ -0,0 +1,14 @@
+---
+author: einar
+comments: true
+date: 2006-01-05 19:05:33+00:00
+layout: post
+slug: dvd-burning
+title: DVD burning
+wordpress_id: 17
+categories:
+- Linux
+---
+
+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. 
+Next time I'll just move the ISO over to my laptop....

_posts/2006-01-07-money-oddities.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-01-07 14:55:57+00:00
+layout: post
+slug: money-oddities
+title: Money oddities
+wordpress_id: 19
+categories:
+- General
+- S.T.E.A.L.
+---
+
+Some things strike me as being really odd. Regarding the [commission post](http://www.dennogumi.org/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? I'm not sure. Perhaps people were too busy? A simple "no" would have been better. 
+But I think it all boils down to the bad habits of people on the Internet. And having read around about Mark Shuttleworth (of [Ubuntu](http://www.ubuntulinux.org) fame) offering money to help the [GIMP](http://www.gimp.org) project and then being forced to withdraw it, perhaps I shouldn't be so surprised.
+Nevertheless, I'll keep on trying.

_posts/2006-01-08-programming-quality.markdown

@@ -0,0 +1,14 @@
+---
+author: einar
+comments: true
+date: 2006-01-08 14:32:03+00:00
+layout: post
+slug: programming-quality
+title: Programming quality
+wordpress_id: 20
+categories:
+- Linux
+---
+
+Yesterday I tried to run an electronic Italian-English dictionary I own. As I write my novel using [LaTeX](http://www.latex-project.org) and I have an environment on Linux, I thought it would good to use [WINE](http://www.winehq.com) 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). They only work in Windows because the underlying (crappy) environment can compensate for an equally crappy program.
+For now I'll use an online dictionary I found. At least that only requires a browser.

_posts/2006-01-09-moving-not-yet.markdown

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+---
+author: einar
+comments: true
+date: 2006-01-09 20:16:07+00:00
+layout: post
+slug: moving-not-yet
+title: Moving? Not yet
+wordpress_id: 21
+categories:
+- S.T.E.A.L.
+- Science
+---
+
+Today I thought I was going to move from my current location (LITA building, [University of Milano](http://www.unimi.it) ) 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.
+I've had an overload of information and I'm really tired, for having just done my first day of work after the holidays. And it looks like I'll be wanted by many people this week...
+
+On another note, I sent some more mails for the commission work. I hope to get some replies.

_posts/2006-01-11-always-needed.markdown

@@ -0,0 +1,15 @@
+---
+author: einar
+comments: true
+date: 2006-01-11 20:44:17+00:00
+layout: post
+slug: always-needed
+title: Always needed
+wordpress_id: 22
+categories:
+- General
+- Science
+---
+
+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. Guess I'll have to bear with it.

_posts/2006-01-14-new-steal-snapshot.markdown

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+---
+author: einar
+comments: true
+date: 2006-01-14 15:52:06+00:00
+layout: post
+slug: new-steal-snapshot
+title: New S.T.E.A.L. snapshot
+wordpress_id: 23
+categories:
+- S.T.E.A.L.
+---
+
+After about six months of inactivity, I finally got myself to write more (thanks also for WINE so I can use a dictionary on Linux), and this takes form of a new snapshot of the novel. Changes are mostly in the last part, and include some paragraphs adjusted and rewritten from scratch (I didn't like them at all). Plans are to complete the next part of the chapter soon (more action packed). Completion level is 50%. 
+You can find a link to the current snapshot in the sidebar.

_posts/2006-01-16-fatestay-night.markdown

@@ -0,0 +1,17 @@
+---
+author: einar
+comments: true
+date: 2006-01-16 21:25:30+00:00
+layout: post
+slug: fatestay-night
+title: Fate/stay night
+wordpress_id: 25
+categories:
+- Anime
+---
+
+[![Saber from the opening animation](http://www.dennogumi.org/wp-content/gallery/_saber.png)](http://www.dennogumi.org/wp-content/gallery/saber.png)
+
+
+I just got around to see the first two episodes of this anime, which is an animated version of [TYPE-MOON](http://www.typemoon.com)'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.
+Also, the opening theme (disillusion by Number 201) is quite catchy, and I'll be looking forward to the single's release (22th Jan).

_posts/2006-01-16-moved.markdown

@@ -0,0 +1,14 @@
+---
+author: einar
+comments: true
+date: 2006-01-16 21:15:18+00:00
+layout: post
+slug: moved
+title: Moved
+wordpress_id: 24
+categories:
+- General
+- Science
+---
+
+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. It took an hour to pack things, and another 30 minutes to unpack them at the new location. That is, they're in place but they're not actually _working_ - I'll have to do that tomorrow (and I hope everything works). 

_posts/2006-01-20-office-take-2.markdown

@@ -0,0 +1,37 @@
+---
+author: einar
+comments: true
+date: 2006-01-20 22:01:36+00:00
+layout: post
+slug: office-take-2
+title: Office, take 2
+wordpress_id: 27
+categories:
+- General
+- Science
+---
+
+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.
+
+Last but not least, there are some pictures (taken with my cell phone, so the quality is low):
+
+general/0118_124128.jpg An overview of the office.
+
+
+general/0118_124105.jpgThe (still offline) AFFY2 workstation and my own computer, Quant.
+
+
+
+
+
+
+
+general/0912_154843.jpgThe heart of the acquisition system, [Affymetrix's](http://www.affymetrix.com) GeneChip Scanner (the box next to the computer) and the ATG-1 Dual Xeon acquisition station.
+
+
+
+
+I will post more later.
+
+
+

_posts/2006-01-22-wild-arms-4.markdown

@@ -0,0 +1,18 @@
+---
+author: einar
+comments: true
+date: 2006-01-22 10:37:37+00:00
+layout: post
+slug: wild-arms-4
+title: Wild ARMs 4
+wordpress_id: 28
+categories:
+- Anime
+- General
+---
+
+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. I'm not too impressed with the story, though. The characters are really 2D personality-wise - they don't really have any depth and the plot seems hole-ridden so far.
+
+More on this when I finish it.

_posts/2006-01-25-of-life-and-pets.markdown

@@ -0,0 +1,20 @@
+---
+author: einar
+comments: true
+date: 2006-01-25 18:19:20+00:00
+layout: post
+slug: of-life-and-pets
+title: Of life and pets
+wordpress_id: 30
+categories:
+- General
+---
+
+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 guess I grew attached to it, even if it was "just" a pet. Friday is going to be tough somehow on this aspect, everyone in the family is feeling sad to some extent. I hope I won't see it in its last moments.
+
+**Update**: At 1.00 GMT+1, it passed away because of a respiratory crisis, even before the vet (called urgently on the phone) could come. I'll just add its photo here... taken years ago before this mess even started.
+
+
+general/pucci 028.jpg

_posts/2006-01-25-the-end-of-wild-arms-4.markdown

@@ -0,0 +1,15 @@
+---
+author: einar
+comments: true
+date: 2006-01-25 18:12:23+00:00
+layout: post
+slug: the-end-of-wild-arms-4
+title: The end of Wild ARMs 4
+wordpress_id: 29
+categories:
+- General
+---
+
+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. Oh well, let's see what will happen with Wild ARMs - The Vth Vanguard...

_posts/2006-01-26-badly-written-software-or-policy.markdown

@@ -0,0 +1,18 @@
+---
+author: einar
+comments: true
+date: 2006-01-26 20:40:09+00:00
+layout: post
+slug: badly-written-software-or-policy
+title: Badly written software, or policy?
+wordpress_id: 31
+categories:
+- General
+- Science
+---
+
+Today while working I got stuck in what probably is an intentional flaw of the software we're using. When we scan [Affymetrix](http://www.affymetrix.com)'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. So I bought a network hard drive a week ago and I decided to sync the data from the workstation to the network drive. Affymetrix has a proprietary solution to access data in a centralized fashion, but it costs € 65,000, plus the MS SQL2000 Enterprise Edition license and not including the actual server machine! They also have a stand alone tool (Data Transfer Tool) but it doesn't support unattended operations (obviously). I thought by copying over files and using one mode of operation of this software to transfer data to the other machines (some data are stored in a database, that's why you can't just copy the flles over).
+
+I was wrong because the software "detected" the type of files and refused to proceed further. I really wanted to put an unattended sync from the scanner to the network drive, but it's impossible now. I need to manually make special archive files and then copy them over.
+
+Poor programming practice, or vested interests in selling the server class product?

_posts/2006-01-29-more-about-steal.markdown

@@ -0,0 +1,15 @@
+---
+author: einar
+comments: true
+date: 2006-01-29 15:22:46+00:00
+layout: post
+slug: more-about-steal
+title: More about S.T.E.A.L.
+wordpress_id: 32
+categories:
+- General
+---
+
+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.
+
+I admit I'm a little anxious to see something, the various failures in the past with finding someone to do the art that I will set my mind at rest only when I see something done.

_posts/2006-01-30-clarissas-birthday.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-01-30 22:33:48+00:00
+layout: post
+slug: clarissas-birthday
+title: Clarissa's birthday
+wordpress_id: 33
+categories:
+- General
+- Science
+---
+
+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. I managed to get more stuff done, and so I'm more or less on time with my work schedule.
+
+No pictures of the event, no one took any.

_posts/2006-02-01-knightly-earring.markdown

@@ -0,0 +1,45 @@
+---
+author: einar
+comments: true
+date: 2006-02-01 22:27:30+00:00
+layout: post
+slug: knightly-earring
+title: 'Knightly Earring '
+wordpress_id: 34
+categories:
+- Final Fantasy XI
+---
+
+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. Vigieous, our thief, delivered the finishing blow: not sure if it's myth or not, but I admit we were extremely lucky. [Knightly Earring](http://ffxi.allakhazam.com/db/item.html?fitem=8213) (my target) dropped, and also the [Heavy Lance](http://ffxi.allakhazam.com/db/item.html?fitem=5580). Heavy Lance will go to one of our dragoons, I'll inform the linkshell's council soon.
+
+In any case, finally I got one of MY _endgame_ items. The rest are the Valor relic armor and/or the AF+1, much harder to get...
+
+Here's a picture of my group after the fight:
+
+
+ffxi/img_0042.png
+
+
+
+
+
+
+
+And here's the earring in all its glory:
+
+
+
+
+
+
+
+
+
+
+ffxi/knightly.png
+
+
+
+
+
+

_posts/2006-02-05-all-in-one-entry.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-02-05 17:47:05+00:00
+layout: post
+slug: all-in-one-entry
+title: All-in-one entry
+wordpress_id: 35
+categories:
+- Anime
+- General
+- Science
+---
+
+First of all, the strangest oddity ever. On Friday once at the laboratory I was contacted by an Affymetrix representative regarding [this entry ](http://www.dennogumi.org/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. Hence, any IP from affymetrix com (and its European branch affymetrix.co.uk) is now banned from accessing this page.
+
+On unrelated topics, my brother finished assembling his mini-ITX router/server today. No OS installed yet, but I found a nice Ubuntu Linux installation image to be run from an USB stick. I backed up things from the current server/router and once we have time we'll try installing Ubuntu again.
+
+Tonight online I have a Gration run with Heaven's Inferno. That giant is really tough and I predict multiple deaths (just as we wiped embarassingly against Seiryu yesterday). I hope to finish before going to bed, so I can watch the latest episode of Fate/stay night (really nice series so far!).

_posts/2006-02-06-woes-of-a-scientist.markdown

@@ -0,0 +1,21 @@
+---
+author: einar
+comments: true
+date: 2006-02-06 22:55:18+00:00
+layout: post
+slug: woes-of-a-scientist
+title: Woes of a scientist
+wordpress_id: 36
+categories:
+- Science
+---
+
+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. As a matter of fact, all kinds of programs use differently formatted text files, making a conversion or integration a pain. That is, unless you use some shell scripting (on Linux, obviously) to handle them. Today my editing window looked like this:
+
+
+general/file-making.png
+
+
+Where I was fixing by hand some text files. I should have used GNU sed and join earlier, as it would have saved loads of time, bah. With the changes (thanks, Raoul) the files made are almost perfect (one more tab than necessary but I'll fix it tomorrow).
+
+Also, I have to complete a couple of things for the paper we're submitting, should be done tomorrow I hope.

_posts/2006-02-08-it-lives.markdown

@@ -0,0 +1,21 @@
+---
+author: einar
+comments: true
+date: 2006-02-08 17:09:45+00:00
+layout: post
+slug: it-lives
+title: It lives!
+wordpress_id: 37
+categories:
+- S.T.E.A.L.
+---
+
+Finally some news in the S.T.E.A.L. front! First of all one of the artists I asked confirmed his commitment (he's first busy with higher-priority company commissions), and a second one just gave me a preliminary sketch here:
+
+
+steal/yumiko.jpg
+
+
+
+
+I'm way happy to see that finally the characters are taking life from words to drawings!

_posts/2006-02-11-new-steal-snapshot-2.markdown

@@ -0,0 +1,22 @@
+---
+author: einar
+comments: true
+date: 2006-02-11 11:52:33+00:00
+layout: post
+slug: new-steal-snapshot-2
+title: New S.T.E.A.L. snapshot
+wordpress_id: 38
+categories:
+- S.T.E.A.L.
+---
+
+As the post says, I've uploaded a new snapshot of S.T.E.A.L., finally closing a part that had been open since last summer, and hopefully paving the way for the big things to come for the rest of chapter 4.
+
+
+
+
+As usual, the most current version can be downloaded from the links on the sidebar.
+
+
+
+

_posts/2006-02-12-webcam-on-linux.markdown

@@ -0,0 +1,23 @@
+---
+author: einar
+comments: true
+date: 2006-02-12 14:10:20+00:00
+layout: post
+slug: webcam-on-linux
+title: Webcam on Linux, success!
+wordpress_id: 39
+categories:
+- General
+---
+
+
+
+
+
+general/webcam_work.jpg
+
+
+I have this [Trust Mini-Webcam WB-1200p](http://www.trust.com/products/product.aspx?artnr=13405) 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). Most of the few drivers around had little or no documentation, were binary-only, or looked completely unmantained. Then I took a look at [spca5xx](http://mxhaard.free.fr/spca5xx.html) again. This driver was born to support the SPCA webcam chipsets (like Creative's PC-CAM 600) but over the time it grew bigger and now supports a whole load of different cameras.
+
+Ubuntu has an outdated version that doesn't recognize my camera. I tried first downloading the most recent snapshot from the site, but it threw a bunch of errors after compiling (i.e. it wouldn't run) I then decided to get the most recent Debian package and install it with module-assistant. And it **worked**! Finally I can use my webcam on Linux and avoid using Windows even more.
+

_posts/2006-02-13-wordpress-201.markdown

@@ -0,0 +1,14 @@
+---
+author: einar
+comments: true
+date: 2006-02-13 22:05:40+00:00
+layout: post
+slug: wordpress-201
+title: Wordpress 2.0.1
+wordpress_id: 40
+categories:
+- General
+- Linux
+---
+
+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.

_posts/2006-02-15-fatestay-night-06.markdown

@@ -0,0 +1,27 @@
+---
+author: einar
+comments: true
+date: 2006-02-15 18:30:36+00:00
+layout: post
+slug: fatestay-night-06
+title: 'Fate/stay night #06'
+wordpress_id: 41
+categories:
+- Anime
+---
+
+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.<!-- more -->But let's look in detail of what happens in this episode.
+
+
+anime/fate06_1.pnganime/fate06_2png.png
+
+
+First we see Shiro in trouble (though the small comical elements from the past episode are luckily gone) and then when he intentionally puts himself into trouble by trying to look for the person who tried to kill Rin (and hit his arm instead).
+
+
+anime/fate06_3.pnganime/fate06_4.png
+
+
+_Of course_ the troublemaker is a Servant (Rider to be precise) and of course she tries to kill the incredibly stupid main character. He manages to survive somehow and gets home safely thanks to the help of Rin. The episode closes with a confrontation (a verbal one) between him and Archer.
+
+Overall, I liked the episode. I hope I can see more soon.

_posts/2006-02-17-opo-opos-and-hyppogriphs.markdown

@@ -0,0 +1,31 @@
+---
+author: einar
+comments: true
+date: 2006-02-17 23:06:24+00:00
+layout: post
+slug: opo-opos-and-hyppogriphs
+title: Opo-opos and Hyppogriphs
+wordpress_id: 42
+categories:
+- Final Fantasy XI
+---
+
+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.<!-- more -->After a while the bard disconnected and didn't get back, so we just warped away. Later in the day, a few people were trying to get hyppogriph tailfeathers for PM4-2. They had no tank, so I took the place of my brother and joined them. These images show both events.
+
+
+
+
+
+
+ffxi/img_0045.png
+
+
+ffxi/img_0047.png
+
+
+
+
+
+
+
+In the  end we got 24 tailfeathers, enough to grant us 12 mistmelts for the upcoming battle. A group is doing it now as I type, the rest will do it Sunday. I hope everything goes smoothly and we get more people further ahead in the Chains of Promathia missions.

_posts/2006-02-19-rain.markdown

@@ -0,0 +1,23 @@
+---
+author: einar
+comments: true
+date: 2006-02-19 19:19:10+00:00
+layout: post
+slug: rain
+title: Rain
+wordpress_id: 43
+categories:
+- Final Fantasy XI
+- General
+- Linux
+---
+
+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](http://www.mandriva.com) 2006.0 installation on the desktop (shown in the image) but I couldn't get urpmi to update the unofficial KDE repository. Sadly I think those packages are too broken for my tastes, I should have used direct backports from the development version. I guess I'll reinstall the new version over the old one as soon as I get the chance.
+As the sidebar shows, I got Grandia III a few days ago. I'm playing it and I like it so far, I just hope it isn't too short (Wild ARMs 4 was a real disappointment in that sense) and that the story doesn't suck. I'm putting Magna Carta on hold because the plot (and the game system) is terribly slow.
+Later today I have a KS30 run in FFXI, hoping to get some good items. I also have to watch Fate/stay night #7, I'll do that tomorrow night.

_posts/2006-02-21-ceiling.markdown

@@ -0,0 +1,13 @@
+---
+author: einar
+comments: true
+date: 2006-02-21 23:45:07+00:00
+layout: post
+slug: ceiling
+title: Ceiling
+wordpress_id: 45
+categories:
+- General
+---
+
+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). Well, the CISI is supposed to be brand new, but then such things happen... I guess as usual in the public sector, something didn't go as planned...

_posts/2006-02-21-valor-coronet-relic-armor-15.markdown

@@ -0,0 +1,31 @@
+---
+author: einar
+comments: true
+date: 2006-02-21 23:30:58+00:00
+layout: post
+slug: valor-coronet-relic-armor-15
+title: Valor Coronet! Relic armor 1/5
+wordpress_id: 44
+categories:
+- Final Fantasy XI
+---
+
+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.<!-- more -->The run started at 19.45, when people started to gather in Bastok Mines. I don't know how much later we started but it wasn't that much with regards to the specified time. Things went smoothly immediately, as we started taking down Effigies and Vanguards without problems, and with very little deaths.
+
+
+[![img_0048](http://www.dennogumi.org/d/85-2/img_0048.png?g2_GALLERYSID=ee72fa4dabbf45f3a187a40b0709e06b)](http://www.dennogumi.org/v/ffxi/img_0048.png.html)[![A pause after a battle](http://www.dennogumi.org/d/88-2/img_0049.png?g2_GALLERYSID=ee72fa4dabbf45f3a187a40b0709e06b)](http://www.dennogumi.org/v/ffxi/img_0049.png.html)
+
+
+
+
+At first nothing dropped but currency (which only goes to the sponsors). Then some relic armor started to drop: some for Monks, Summoners, Dark Knights. Then a single valor coronet (Paladin relic armor, for the head) dropped. There were two Paladins there (me included) so we just cast lots. I won the lot by just 30 (189 vs 219) and finally I got one of my "endgame" items! Now I need four more pieces to make it complete.
+
+
+
+
+Of course Dynamis didn't stop with that item. We went further and we even managed to get to the so called "Mega Boss" and defeat it. Not bad, considering that we were just 25 people (considered sub-optimal for Dynamis). I didn't die a single time, which is good considering the loss in experience points (since I usually don't do parties to get them back).
+
+
+
+
+[![After interloping](http://www.dennogumi.org/d/91-2/img_0050.png?g2_GALLERYSID=ee72fa4dabbf45f3a187a40b0709e06b)](http://www.dennogumi.org/v/ffxi/img_0050.png.html)[![Valor coronet](http://www.dennogumi.org/d/94-2/img_0051.png?g2_GALLERYSID=ee72fa4dabbf45f3a187a40b0709e06b)](http://www.dennogumi.org/v/ffxi/img_0051.png.html)

_posts/2006-02-28-bertinoro-di-romagna.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-02-28 22:24:05+00:00
+layout: post
+slug: bertinoro-di-romagna
+title: Bertinoro di Romagna
+wordpress_id: 46
+categories:
+- General
+- Science
+---
+
+After sorting out the bureaucracy, finally I was able to enroll for the [6th Course in Bioinformatics for Molecular Biologists](http://www.eurogene.org/body.php?t=1&l=l&p=pages/train/courses/crsprogr.php&r=72) 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.

_posts/2006-03-02-it-lives-part-2.markdown

@@ -0,0 +1,18 @@
+---
+author: einar
+comments: true
+date: 2006-03-02 23:17:38+00:00
+layout: post
+slug: it-lives-part-2
+title: It lives! (part 2)
+wordpress_id: 47
+categories:
+- S.T.E.A.L.
+---
+
+I'm very happy to write that I got a second drawing from [firekitty](http://firekitty.deviantart.com)! I liked the first one but I like the second one better. Now I'm just waiting for [too](http://toounit.deviantart.com) to show me the character designs he has made... I hope he manages to scan them quickly as I'm rather anxious to see them...
+
+For now, enjoy the new unfinished sketch. I'll probably try to write more of the novel this weekend.
+
+
+steal/yumiko-2.jpg

_posts/2006-03-05-migrating.markdown

@@ -0,0 +1,34 @@
+---
+author: einar
+comments: true
+date: 2006-03-05 17:44:51+00:00
+layout: post
+slug: migrating
+title: Migrating
+wordpress_id: 48
+categories:
+- General
+- Linux
+---
+
+I've been migrating settings and files from the old router to the new one (check [my brother's blog](http://www.jumpjoe.com/?p=131) 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
+
+[/code]
+
+Already 30 Gb gone... I wonder how much will be remaining after I move all the data.
+
+I also managed to update the LDAP database with the old values and update authentication accordingly. In principle everything **should** work out of the box, but somehow I'm being skeptical... (and code tags aren't shown properly in the blog, I wonder why)

_posts/2006-03-11-trento-march-7th-8th.markdown

@@ -0,0 +1,21 @@
+---
+author: einar
+comments: true
+date: 2006-03-11 11:40:02+00:00
+layout: post
+slug: trento-march-7th-8th
+title: Trento, March 7th-8th
+wordpress_id: 49
+categories:
+- Science
+---
+
+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. I was the only one with a biological background there, the rest had degrees in mathemathics or physics.
+
+The conference started with a very interesting talk by Chris Stoeckert from the University of Pennsylvania, a member of the [MGED](http://www.mged.org) society.  He is a funny and extremely smart person and I even managed to exchange opinions with him.
+
+After the talks we headed out to the hotel [Villa Madruzzo ](http://www.villamadruzzo.it)where we had a very pleasant dinner (not to mention it was free!). We finished around midnight, I went to sleep but at 2 in the morning the fire alarm sounded. There was no fire, just the alarm, for some odd reason. The same happened at 7.
+
+After a nice breakfast, the 8-hour-long talk session started. Some were really too difficult for me, others were easier but overall it was an interesting session. Once we were done, someone brought us to the station, and then I got my train home.
+
+Tiring experience, but definitely interesting.

_posts/2006-03-16-random-entry.markdown

@@ -0,0 +1,23 @@
+---
+author: einar
+comments: true
+date: 2006-03-16 18:17:25+00:00
+layout: post
+slug: random-entry
+title: Random entry
+wordpress_id: 50
+categories:
+- General
+- Linux
+- Science
+---
+
+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). Our friends at Affymetrix have shown me again something like that. I was trying to combine the data from two different [SNP](http://en.wikipedia.org/wiki/Single_nucleotide_polymorphism) arrays (since they complement each other) and the documentation was pointing in the exactly opposite direction of what I needed to do. Shame, that costed me an hour of tries.
+
+I'll be departing for Bertinoro this Saturday, but I'll be probably able to post things here, since I'll have a wireless connection.
+
+On the Final Fantasy XI front, I managed to coordinate 18  people and we took Bahamut down. Now all that's left is the final mission, "The Last Verse", then I can wait for Treasures of Aht Urghan to come out.
+
+On a finishing note, I finished Grandia III a while ago. Good game system, but the difficulty is extremely unbalanced, and the story is down right **awful**.

_posts/2006-03-19-bertinoro-arrival-day-1.markdown

@@ -0,0 +1,26 @@
+---
+author: einar
+comments: true
+date: 2006-03-19 17:57:54+00:00
+layout: post
+slug: bertinoro-arrival-day-1
+title: Bertinoro - Arrival & Day 1
+wordpress_id: 51
+categories:
+- General
+- Science
+---
+
+Finally I got hold of a stable Internet connection so I can post about my experience in Bertinoro di Romagna so far.<!-- more -->
+
+I took the train yesterday at 17.00 and I arrived in Bologna at 18.42, on time (that is rare for Trenitalia). There I found the [EGF](http://www.eurogene.org) people and some of the course members, and we took a small van to Bertinoro. It's far from Bologna, much more than I imagined: the whole trip took about one hour. Then we got assigned to our rooms, and given a keycard. This opens all doors of the university center (save the main door for me, and I don't know why) and my own room. I'm sharing it with a nice guy from Cameroon that's studying in the Netherlands.
+
+Dinner was a buffet of cold stuff (I just got some fruid and a piece of cake) and I talked a bit with also two other Italian girls (one is studying in my same PhD program). I was terribly tired, so then I just went to my room (but I spent a while trying to make the wireless connection work).
+
+I woke up at 6.30 - ick - and had breakfast around 7.30 in the dining hall of the Center. Then, I moved towards the Rook where the courses would have taken place. There were immediately some difficulties with a projector, so the starting lecture was delayed by 30 minutes (and we had it in the computer room). We had overall five talks today the first were a general introduction followed by a still general talk on the applications and uses of sequence analysis, and a  **very** hard to follow talk on gene prediction.
+
+We then had lunch break in the Center's main canteen (quite nice) then thirty minutes off before the next round of talks. I took the time to get a network cable here so I could use my laptop (that's where I'm writing from now).
+
+The afternoon talks were about protein-protein interaction, and a devastatingly long dissertation on statistical methods for bioinformatics. I came back an hour ago and I'm very tired. I have plans to go with the Italian people, my roommate and two of his colleagues somewhere to eat, I have a € 15 coupon to use for food in local restaurants.
+
+I took some photos, but they'll have to wait until I come back. Overall, this looks interesting. I wonder how the next days willl be...

_posts/2006-03-20-bertinoro-day-2.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-03-20 20:33:34+00:00
+layout: post
+slug: bertinoro-day-2
+title: Bertinoro - Day 2
+wordpress_id: 52
+categories:
+- General
+- Linux
+---
+
+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.
+
+The day ended with a tutorial on R. Nice language, I'll experiment more once I'm at home.  I had dinner, but I'm too tired to do something now, I'll go to bed soon and have a read.

_posts/2006-03-21-bertinoro-day-3.markdown

@@ -0,0 +1,18 @@
+---
+author: einar
+comments: true
+date: 2006-03-21 22:06:22+00:00
+layout: post
+slug: bertinoro-day-3
+title: Bertinoro - Day 3
+wordpress_id: 53
+categories:
+- General
+- Science
+---
+
+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.Apollinare in Classe" and the Arian Baptistery. Then we had an hour of free roaming (couldn't see much) and then came back to our bus. Getting back to the rooms was a pain, thanks to an extremely steep slope. I was dead tired, and so were the others, but we managed to go to a nice pizzeria near our place. Extremely nice food, and I didn't get to pay anything. It was also a great fun.
+
+Now I'm going to hit the bed, as tomorrow there's another wake-up call at 6.45...

_posts/2006-03-22-bertinoro-day-4.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-03-22 21:03:57+00:00
+layout: post
+slug: bertinoro-day-4
+title: Bertinoro - Day 4
+wordpress_id: 54
+categories:
+- General
+- Science
+---
+
+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 6.45.

_posts/2006-03-30-mixed-entry-yet-again.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-03-30 21:56:31+00:00
+layout: post
+slug: mixed-entry-yet-again
+title: Mixed entry (yet again)
+wordpress_id: 55
+categories:
+- Final Fantasy XI
+- General
+- Science
+---
+
+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](http://www.bioconductor.org) (a series of add-on packages for [R](http://www.r-project.org)) 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). It's quite heavy on computational resources, and for no reason quant (my work machine) reboots after a while, so I had to run it on another computer.
+
+On the Final Fantasy Front, I'm preparing to help my friend Sechs to do the Zilart Missions 14 and 16. This will finally enable me to get my group and complete the Chain of Promathia Mission 8-5, the last one (at last!).

_posts/2006-04-01-upgrades.markdown

@@ -0,0 +1,13 @@
+---
+author: einar
+comments: true
+date: 2006-04-01 12:35:12+00:00
+layout: post
+slug: upgrades
+title: Upgrades
+wordpress_id: 56
+categories:
+- General
+---
+
+I've upgraded the theme (now it uses a non-hacked version of Regulus), the image gallery with the new [Gallery](http://gallery.menalto.com) v2.1, and also the new[ WPG](http://www.dennogumi.org/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.

_posts/2006-04-06-windows-and-missions.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-04-06 22:13:28+00:00
+layout: post
+slug: windows-and-missions
+title: Windows and Missions
+wordpress_id: 57
+categories:
+- Final Fantasy XI
+- General
+- Science
+---
+
+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). It means that I'll have to move around tons and tons of text files, take images and then compile spreadsheets (I wonder **why** all the reports in our laboratory are Excel-based... I'd much prefer tab delimited formats).
+
+On the Final Fantasy XI front, finally I managed to get Sechs past ZM16. This means we can start the quests that will lead us to the final (for now) battle in the Empyreal Paradox. Finally, it's the time!

_posts/2006-04-10-orz.markdown

@@ -0,0 +1,17 @@
+---
+author: einar
+comments: true
+date: 2006-04-10 21:28:07+00:00
+layout: post
+slug: orz
+title: Orz!
+wordpress_id: 59
+categories:
+- Final Fantasy XI
+---
+
+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. Getting the first one (the magic user) down is not too hard, although if his magic is not stunned the damage is pretty high. However, every time we managed to defeat this, people started dying very fast with the other. Some moves can actually one-shot people (me included).
+
+We're retrying this Wednesday, and this time I'll be doing it with my original group (one of us wasn't there thanks to a power outage). I really want some revenge!

_posts/2006-04-10-outage.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-04-10 21:32:32+00:00
+layout: post
+slug: outage
+title: Outage
+wordpress_id: 60
+categories:
+- General
+- Science
+---
+
+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!). I'll probably call support tomorrow.
+
+This has the unwanted side effect of slowing down my analysis work, since the workstation that "died" was used by a person who now is using my analysis station (which is not my work computer, by the way).

_posts/2006-04-22-sickness.markdown

@@ -0,0 +1,13 @@
+---
+author: einar
+comments: true
+date: 2006-04-22 07:16:10+00:00
+layout: post
+slug: sickness
+title: Sickness
+wordpress_id: 61
+categories:
+- General
+---
+
+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.

_posts/2006-04-24-cursing.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-04-24 11:52:49+00:00
+layout: post
+slug: cursing
+title: Cursing
+wordpress_id: 62
+categories:
+- Final Fantasy XI
+---
+
+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).
+
+The issue was brought up again at a sackholder's meeting yesterday (the person was missing) but no one raised particular concerns in being a little respectful when we were around regarding those things (note: anyone could have said anything when people not offended by this hadn't been around). Then, on the forum discussing the meeting minutes this person raises hell, claiming censorship.
+
+I'm not very fond of a certain North American way of thinking and this person represents it very well: prideful and self-righteous. In any case, there were other and more urgent matters to discuss of rather than bitching (excuse the term) for something that would require 0.01 seconds of thinking. I'm really amazed that a person could get so upset when asked for a little more respect towards the others. Certain Americans should learn they aren't the only beings on this planet.

_posts/2006-04-30-treasures-of-aht-urghan.markdown

@@ -0,0 +1,34 @@
+---
+author: einar
+comments: true
+date: 2006-04-30 13:30:50+00:00
+layout: post
+slug: treasures-of-aht-urghan
+title: Treasures of Aht Urghan
+wordpress_id: 63
+categories:
+- Final Fantasy XI
+- General
+---
+
+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);
+
+	
+  * There are new jobs (Corsair and Puppetmaster). Aside everyone taking them now, I'm not interested in either;
+
+	
+  * Assault missions can be fun, but require you to get to the _staging points_ around, and that is the longest part (some aren't really easy to reach);
+
+	
+  * Besieged (namely beastmen attacking the town) is fun, but the novelty effect actually impairs it. I mean, last time there were about 400 people while the beastmen horde was around 30. It was so lagged that people didn't see the monsters, nor they saw them die.
+
+
+Overall, it's fun, but not as challenging as Chains of Promathia, so far. I'll have to see as I continue my exploration.

_posts/2006-05-01-ubuntu-games.markdown

@@ -0,0 +1,29 @@
+---
+author: einar
+comments: true
+date: 2006-05-01 13:42:52+00:00
+layout: post
+slug: ubuntu-games
+title: Ubuntu games
+wordpress_id: 64
+categories:
+- Linux
+---
+
+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).<!-- more -->
+
+On the desktop i installed the beta of [Kubuntu](http://kubuntu.org/announcements/dapper-beta.php) and I've been using it for a while. It's quite stable, despite the occasional breakage here and there, though the real testing will be when I'll install it on the laptop (but I'm waiting on the official stable release for that). A lot of hype is being put on Ubiquity, the new installer from liveCD. However I'd have preferred more work also on the install CD, since I prefer always to install from scratch (and to keep /home on a separate partition, this is something that in my opinon should be asked by default).
+
+Here is a snapshot of my current desktop there:
+
+
+
+
+
+
+
+
+257
+
+
+

_posts/2006-05-05-continuous-analysis.markdown

@@ -0,0 +1,22 @@
+---
+author: einar
+comments: true
+date: 2006-05-05 19:33:24+00:00
+layout: post
+slug: continuous-analysis
+title: Continuous analysis
+wordpress_id: 65
+categories:
+- Science
+---
+
+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. In practical terms this means I use a lot of web-based tools and some basic statstics to evaluate my work. A typical session on my computer is shown by this image.
+
+
+263
+
+
+
+
+
+I've been doing a lot of this, and also graphing my results (not without some difficulties, as Excel sucks and R is not really suited to do what I need to do - anyone knows of a good Linux-based program for histograms and other plots?). More to come next week, where things will probably get more hectic as we're aiming to have a publication ready for submission by the end of June.

_posts/2006-05-08-security-breach.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: false
+date: 2006-05-08 20:17:29+00:00
+layout: post
+slug: security-breach
+title: Security breach
+wordpress_id: 66
+categories:
+- General
+- Linux
+- Science
+---
+
+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).
+
+Tomorrow I'll have to clean it, as the antivirus obviously ignores it. Luckily I got some of the excellent tools provided from [Mark Russinovich's site](http://www.sysinternals.com) so I already killed the suspected processes (a remote control application and what seems to be a worm).
+
+On other news, the brightness on this monitor was really getting to me, but even when set at minimum it was still too high. Luckily NVIDIA provides an utility called nvidia-settings to handle color regulation and such. I compiled it from source (because the one bundled in Dapper wanted to uninstall nvidia-glx for some odd reason) and now I just put a small bash script running it in ~./kde/Autostart. I also need to put some more eye candy on the desktop but that will come later.

_posts/2006-05-17-stress.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-05-17 17:54:11+00:00
+layout: post
+slug: stress
+title: Stress
+wordpress_id: 67
+categories:
+- General
+- Science
+---
+
+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). I'll also ask for a demonstration if possible.
+
+On unrelated and useless news, I renewed my driving license. € 75 was surely a steep price... thank goodness I need to do this only once every 10 years.

_posts/2006-05-20-antispam-or-inconvenience.markdown

@@ -0,0 +1,15 @@
+---
+author: einar
+comments: true
+date: 2006-05-20 10:32:36+00:00
+layout: post
+slug: antispam-or-inconvenience
+title: Antispam, or inconvenience?
+wordpress_id: 68
+categories:
+- General
+---
+
+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. And now you have to pay also to remove yourself? Bah.
+
+What's worse is that my own ISP doesn't care a lot about such issues.  But that's another matter entirely.

_posts/2006-05-20-xolotl-xtrapolator.markdown

@@ -0,0 +1,33 @@
+---
+author: einar
+comments: true
+date: 2006-05-20 11:00:35+00:00
+layout: post
+slug: xolotl-xtrapolator
+title: Xolotl Xtrapolator
+wordpress_id: 69
+categories:
+- Final Fantasy XI
+---
+
+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:<!-- more -->
+
+
+
+
+
+[![Kokba Hostel](http://www.dennogumi.org/gallery2/d/268-2/img_0059.png?g2_GALLERYSID=1ea7bd99ed35fedfaf1f25884a29d823)](http://www.dennogumi.org/v/ffxi/img_0059.png.html)[ ![Rice cakes](http://www.dennogumi.org/gallery2/d/271-2/img_0060.png?g2_GALLERYSID=1ea7bd99ed35fedfaf1f25884a29d823)
+](http://www.dennogumi.org/v/ffxi/img_0060.png.html)
+
+
+272
+
+
+
+
+Two days ago I got to fight Xololtl, a corse undead notorious monster that walks around Attohwa Chasm at night. Despite a terrible start (one of the white mages there got attacked before we were ready and we wiped big time), and some rather _unconventional _way of fighting (Xolotl summons two undead minions that weren't dealt with properly) we managed to kill it (and I found out I can handle it well, despite all the Paladin-bashing talks that are so common recently). The Bandomusha Kote dropped, also: (image taken from Allakhazam but mirrored here - I don't steal bandwidth)
+
+
+
+
+![Bandomusha Kote](http://www.dennogumi.org/Bandomusha-Kote.jpg)

_posts/2006-05-25-biological-software-and-hig.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-05-25 15:37:18+00:00
+layout: post
+slug: biological-software-and-hig
+title: Biological software and HIG
+wordpress_id: 70
+categories:
+- General
+- Science
+---
+
+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](http://www.trolltech.com/products/qt) widgets. Mind, I don't have any ties with TT but I appreciate their toolkit (licensed either under the GNU GPL or a commercial license) in the [KDE](http://www.kde.org) desktop environment.
+
+But let's get to the point of this entry. This software, but not  only this one, has a rather unintuitive user interface (though not as bad as other products I've seen in my career). I see that a lot of software in the life sciences has rather poor  UI design, up to being almost completely unusable. There is a lot of non commercial software released just for obtaining a publication, then completely unmantained. I wonder if the authors of such software want really to help the scientific community by releasing their work or they do so just to obtain one more paper in their curriculum vitae. Commercial software isn't any better either. I'd expect at least commercial companies to follow _HIG_ (Human Interface Guidelines) to produce usable UIs. Usabilty is kept in high regard in free and open source software. Why can't companies listen? They surely have more resources. This is even more important considering that not all biologists are computer-savy, and can't waste their time fighting with poor user interfaces.

_posts/2006-05-28-dist-upgrade-fun-dns-drama.markdown

@@ -0,0 +1,21 @@
+---
+author: einar
+comments: true
+date: 2006-05-28 10:37:09+00:00
+layout: post
+slug: dist-upgrade-fun-dns-drama
+title: dist-upgrade fun, DNS, drama
+wordpress_id: 71
+categories:
+- Final Fantasy XI
+- General
+- Linux
+---
+
+Yesterday I updated my laptop to [Kubuntu](http://www.kubuntu.org) 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 also moved my blog to a new hosting yesterday (I didn't like the old one's Terms of Service). However my ISP is terribly slow in updating the DNS records: actually the secondary server obtained the update, but not the primary... since the installation was broken after the move to this server, I had to fumble around so I could fix it. I really like the new hosting so far, I'm also liking the fact that I can log in via SSH and use a shell - it simplifies a lot of maintenance operations.
+
+To end this entry, in Heaven's Inferno there is a huge debate over the readmission of a player. This person was rather rude, often played drunk and said bad thing to others because of that, and  in general caused a lot of unnecessary grief. The readmission wasn't publicly discussed so basically the linkshell is torn in two. So far most of the council wants to kick him out. His supporters are threatening to leave, but well, I do not care. I risk losing loyal members because of this person. I wouldn't care even if 75% of the linkshell broke up... I did already my fair share of fixing.

_posts/2006-06-02-kubuntu-606-lts-dynamis-xarcabard.markdown

@@ -0,0 +1,23 @@
+---
+author: einar
+comments: true
+date: 2006-06-02 08:52:51+00:00
+layout: post
+slug: kubuntu-606-lts-dynamis-xarcabard
+title: Kubuntu 6.06 LTS / Dynamis-Xarcabard
+wordpress_id: 72
+categories:
+- General
+- Linux
+---
+
+Finally, the new version of [Kubuntu 6.06 LTS](http://kubuntu.org/announcements/6.06-lts-release.php) (**L**ong **T**erm **S**upport) 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](http://kubuntu.org/announcements/kde-353.php) packages are already available from 3rd-party repositories. I will be upgrading them soon.<!-- more -->
+
+I didn't use the new live CD installer but from the screenshots it looks quite good. I'll probably test it soon enough, since I ordered (for free) 5 Kubuntu CDs from [Shipit](htp://shipit.kubuntu.org), the free CD delivery services from Canonical.
+
+On the FFXI related news, I did Dyamis-Xarcabard for the first time last Tuesday. The music is nice and a welcome change from the monotonous tone of the other areas. Unluckily no Paladin relic dropped (yet again.... I hate when it's so rare), and I ended up dying about five times because of the massive links that some pullls generated. Next Tuesday is Dynamis-San d'Oria, perhaps I can hope for the relic hands to drop...
+
+Some screenshots:
+
+
+275278

_posts/2006-06-03-the-problem-with-binary-only-drivers.markdown

@@ -0,0 +1,18 @@
+---
+author: einar
+comments: true
+date: 2006-06-03 20:04:38+00:00
+layout: post
+slug: the-problem-with-binary-only-drivers
+title: The problem with binary only drivers
+wordpress_id: 73
+categories:
+- General
+- Linux
+---
+
+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.
+
+Even without mentioning the extremely sloppy quality of ATI's drivers in general (both Windows and Linux), this shows a fundamental problem with binary drivers, as many have said. Without the source, I can't fix/ask for help. I need to rely on the vendor input, which is quite scarce in this case. And if they decide to drop support, I'll be screwed.
+
+I'm not thinking that everything should be open source, but having a parallel, open implementation of video drivers with **clear**, documented specs would be extremely helpful... not to mention that competition would also help.

_posts/2006-06-08-classes-and-meetings.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-06-08 17:02:33+00:00
+layout: post
+slug: classes-and-meetings
+title: Classes and meetings
+wordpress_id: 74
+categories:
+- General
+- Science
+---
+
+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. In all honesty it's quite nice, however it lacks the ability of apply Significance Analysis of Microarrays ([SAM](http://www-stat.stanford.edu/~tibs/SAM/))  which is essential for our work. It's a shame, because both the gene expression module (very fast Robust Multichip Analysis - RMA - implementation) and the copy number variation module are good, but alone they won't justify the price.

_posts/2006-06-08-the-gods-themselves.markdown

@@ -0,0 +1,17 @@
+---
+author: einar
+comments: true
+date: 2006-06-08 17:21:25+00:00
+layout: post
+slug: the-gods-themselves
+title: The gods themselves
+wordpress_id: 75
+categories:
+- Final Fantasy XI
+---
+
+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. All I can say is to quote Asimov:
+
+_Against stupidity, the gods themselves contend in vain?_

_posts/2006-06-16-books.markdown

@@ -0,0 +1,32 @@
+---
+author: einar
+comments: true
+date: 2006-06-16 16:47:53+00:00
+layout: post
+slug: books
+title: Books
+wordpress_id: 76
+categories:
+- Anime
+- General
+---
+
+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.<!-- more -->
+
+First of all there is Aoi Nanase's "The Seven Colors of the Wind":
+
+
+281
+
+
+It is a great illustration book from this artist, mostly featuring illustrations related to novels where she does drawings for. Aoi Nanase is a great artist and this book really gives her some justice, since all the ilustrations are beautiful and in color. Definitely worth the wait (I ordered it in February and it arrived just now).
+
+Then, there is Kanan's Galaxy Angel Beta manga:
+
+
+284
+
+
+Nice drawings, but not too good story, which is mostly a filler.
+
+P.s.: I wrote this entry a week ago but I forgot to publish them when my notebook's battery run out. Oops!

_posts/2006-06-17-busy-busy-busy.markdown

@@ -0,0 +1,17 @@
+---
+author: einar
+comments: true
+date: 2006-06-17 14:52:49+00:00
+layout: post
+slug: busy-busy-busy
+title: Busy busy busy!
+wordpress_id: 77
+categories:
+- General
+- S.T.E.A.L.
+- Science
+---
+
+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.
+
+In short, I've been extremely busy and with little will to stay at the computer and write.  However yesterday when I was going back home I got an interesting idea for S.T.E.A.L. to replace the latest junction (which I'm not very satisfied with). I hope to get some will to work on it soon.

_posts/2006-06-20-upgrade.markdown

@@ -0,0 +1,20 @@
+---
+author: einar
+comments: true
+date: 2006-06-20 17:51:34+00:00
+layout: post
+slug: upgrade
+title: Upgrade
+wordpress_id: 78
+categories:
+- Anime
+- General
+- Linux
+- Science
+---
+
+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).
+
+On other things, I'm still very busy. The PhD  classes aren't over yet (one more week) and I need to do more work on the paper still, only halfway done (plus the revision, which will take a long time). I also need to read a lot of papers and work on other projects, I'm not sure when I'll manage fo finish...
+
+On an ending note, i finished watching Fate/stay night. Such a good series, such an awful ending, which is also sad. I wish the anime would have drifted from that, but I guess it had to be like that, bah.

_posts/2006-06-25-implosion.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-06-25 11:25:53+00:00
+layout: post
+slug: implosion
+title: Implosion
+wordpress_id: 79
+categories:
+- Final Fantasy XI
+---
+
+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. When one of the leaders acts like leaving, most of the members move like sheep. Flames also erupted in the forums. There was still a certain number of people inside, however one of the former sack holders went in and started mass kicking them out - probably to have them leave regardless if they wanted it or not.
+
+As it stands now, there are just 3 people or less in Heaven's Inferno. All of this was caused by the so called _endgame_ that made people behave quite bad, a combination of arrogance, greed, childishness and plain old stupidity. I'll be shutting down the site next week: funny how people said that I wasn't doing anything while I paid the bills and spent the time to make it running...
+
+In the end I care little. I saved this linkshell from breaking three times since Inferno, there won't be a fourth. I have another pearl for a social linkshell, where hopefully this stupid issues will arise less, if they ever will.

_posts/2006-06-25-poyoyon-rock-magical-canan.markdown

@@ -0,0 +1,34 @@
+---
+author: einar
+comments: true
+date: 2006-06-25 16:44:46+00:00
+layout: post
+slug: poyoyon-rock-magical-canan
+title: Image editing
+wordpress_id: 80
+categories:
+- Anime
+- General
+---
+
+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.<!-- more -->
+
+And now I present the latest adjustment I made, extracting one of the characters of _[Magical Canan](http://www.animenfo.com/animetitle,1642,vccuqa,magical_canan.html)_ (character designer Poyoyon Rock; the series sucks, but the art doesn't):
+
+
+299
+
+
+The original image had another girl and the annoying cute sidekick over the girl's right leg. You can use this image in any way you want, and if you request it in comment I can give you the full resolution PNG (around 6Mb) or the PSD file (30 Mb).
+
+I know there may be a lot of problems with my work, since I'm self taught and I don't practice this often (it's time consuming). However, this is not Minitokyo, where people are flamed if they don't post grade A pictures: it's merely my own page. As such, please bear with the (many) errors.
+
+Also, I've found another edit I did back in the days and I uploaded it too, this time it's Luna from [_Chojuushin Gravion_](http://www.animenfo.com/animetitle,1088,sbcixy,gravion.html):
+
+
+302
+
+
+It's a transparent PNG, so it doesn't display properly in Internet Explorer: though luck folks, go to Microsoft and complain about releasing a standards-compliant browser.
+
+I'll be probably posting more images in the near future.

_posts/2006-07-01-kubuntu-dapper-arrived.markdown

@@ -0,0 +1,22 @@
+---
+author: einar
+comments: true
+date: 2006-07-01 10:17:33+00:00
+layout: post
+slug: kubuntu-dapper-arrived
+title: Kubuntu Dapper arrived
+wordpress_id: 83
+categories:
+- Linux
+---
+
+305
+
+
+Yesterday when I went at work I found an envelope coming from [Canonical](http://www.canonical.com). Inside, there were the five [Kubuntu](http://www.kubuntu.org) 6.06 "Dapper Drake" LTS CDs I ordered from [Shipit](http://shipit.kubuntu.org). 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. Also, one or two will be useful to keep as install discs and to perform maintenance (though systems such as [Knoppix](http://www.knoppix.net) are perhaps better suited for this). I plan on testing one of these today or tomorrow, to see how they perform on certain hardware.

_posts/2006-07-01-widget-fun.markdown

@@ -0,0 +1,13 @@
+---
+author: einar
+comments: true
+date: 2006-07-01 21:11:35+00:00
+layout: post
+slug: widget-fun
+title: Widget fun
+wordpress_id: 84
+categories:
+- General
+---
+
+As you may have noticed the theme and the layout changed slightly. I updated the [Regulus](http://www.dennogumi.org/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](http://automattic.com/code/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.

_posts/2006-07-02-image-editing-using-foss-tools.markdown

@@ -0,0 +1,53 @@
+---
+author: einar
+comments: true
+date: 2006-07-02 17:07:52+00:00
+layout: post
+slug: image-editing-using-foss-tools
+title: Image editing using FOSS tools
+wordpress_id: 85
+categories:
+- Anime
+- General
+- Linux
+---
+
+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.
+
+<!-- more -->
+
+Notice that this is not meant to be a tutorial, just a description of what I did: I'm a beginner myself, though I can answer questions if anyone (if any) posts them here. Don't bring comparisons with Photoshop, either. It doesn't run on Linux natively.
+
+The two most famous image manipulation programs I know in Linux are the [GIMP](http://www.gimp.org), GTK+ based, and [Krita](http://www.koffice.org/krita/), which integrates into the KDE environment. I like Krita a lot more than GIMP, because it has a much saner user interface, however it's still under heavy development and some features are not yet present (but it's evolving at a very high pace, the developers are doing a fantastic job). Therefore, I had to stick with the GIMP.
+
+For the job I picked up an image from _[My-HIME](http://www.animenfo.com/animetitle,1493,hafpby,mai_hime.html)_. Very nice art, but again a disappointing series. Here's how it looked at the start.
+
+
+
+
+
+310
+
+
+
+
+
+I found this image somewhere on the net. It's quite big, so it was perfect for my needs. In GIMP, I created an additional layer so I could avoid ruining the image. Then I selected a blue color and started painting around the contour of the figure of Mai, like this:
+
+
+314
+
+
+I know there are probably better ways to do it, I'm doing what I'm used to, that luckily is Photoshop-agnostic. Once I finished the contours, I merged down the layers and selected the blue area with the magic wand. The tool tends to keep a smaller contour than expected, so I grew the selection by three pixels using the Grow command. After this I inverted the selection, cut the figure out of the background and pasted it into a new image. The contour had been damaged, so I used the [Layer Effects](http://users.telenet.be/ev1/gimp/gimplayereffects_en.html) script to add an outer glow with a small blur:
+
+
+320
+
+
+All I needed to do then was to resize the image, cut out the white background and save it as a PNG image. Here is the finished result:
+
+
+317
+
+
+I have the original XCF (GIMP's layered file), if anyone wants it.

_posts/2006-07-08-the-power-of-the-shell.markdown

@@ -0,0 +1,28 @@
+---
+author: einar
+comments: true
+date: 2006-07-08 08:16:30+00:00
+layout: post
+slug: the-power-of-the-shell
+title: The power of the shell
+wordpress_id: 86
+categories:
+- General
+- Linux
+- Science
+---
+
+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.
+
+<!-- more -->
+
+Most people would just try to use Excel (ugh) but since it has way too many limitations, it is unstable, and runs on Windows, I had to use other ways. The _awk_ command is what I needed, given the fact that my input was a text file:
+[code]awk ' { print $1"\t"$7 } ' CAKI1_CNAT.txt  > CAKI-1.txt
+awk ' { print $1"\tchr"$2"\t"$3"\t"$3 } ' CAKI1_CNAT.txt  > CAKI-1.ann [/code]
+
+With two commands I created the two files I needed for the obscure software I was testing and without a single headache. The first one created a file with only columns 1 and 7, while the second only with the first three columns, adding "chr" to the text in the second column.
+
+A simpler and more elegant solution would have probably been using _cut_ for the first file:
+[code]cut -f1,7 CAKI1_CNAT.txt > CAKI-1.txt[/code]
+
+Either way, these are things that make my job easier. Try doing that with cmd.exe.

_posts/2006-07-10-new-happenings-on-asura.markdown

@@ -0,0 +1,23 @@
+---
+author: einar
+comments: true
+date: 2006-07-10 19:29:04+00:00
+layout: post
+slug: new-happenings-on-asura
+title: New happenings on Asura
+wordpress_id: 87
+categories:
+- Final Fantasy XI
+---
+
+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.
+
+<!-- more -->
+
+Still, I managed to do a few things these weeks. I completed a couple of Assaults, mostly to get points and get items I could sell to raise my in game balance. Also, last week the Astral Candescence was lost for the first time on Asura. Since the server is quite lazy, I tried to recover it with a pick up group I got on the way. We managed to get up to the three Mamool Ja generals:
+
+
+335
+
+
+The fight is _hard_. The enemy I targeted, a black mage, spams level IV magic, ancient magic and tier III -ga magic. The others can't be slept reliably, and they hit hard. In other words, we got defeated pretty easily. Still, it was fun.

_posts/2006-07-14-finally.markdown

@@ -0,0 +1,38 @@
+---
+author: einar
+comments: true
+date: 2006-07-14 22:50:47+00:00
+layout: post
+slug: finally
+title: Finally!
+wordpress_id: 88
+categories:
+- S.T.E.A.L.
+---
+
+Finally I get to blog about S.T.E.A.L. after so many months! That's because finally _I have illustrations for the novel after all these years!_ As I said on my [previous post on the matter](http://www.dennogumi.org/2006/02/08/it-lives/), I had been in talks with two artists at the time. One simply disappeared after a while (and then I read on her deviantart page that drawing is not a priority... it would have been nicer if she had told me at least), while the other took a good deal of time (around seven months). But now, thanks to the incredible drawing skill of [Too](http://toounit.deviantart.com), I have the first set of seven pictures I commissioned (out of nine)!
+
+<!-- more --> Actually, I had some drafts since a few months, but considering that I've been extremely unlucky with art commissions in the past four years, I've kept quiet until I had at least some definitive art. Here are some samples:
+
+
+338
+
+
+The picture above is from one of the first scenes in the novel (want to know more? [Go and take a look!](http://www.dennogumi.org/steal/steal.pdf)) depicting Yumiko (center), Saiyuki (left) and Michiru (right).
+Too has changed a bit how Yumiko looks with respect to the original description, but both me and Marco are OK with it, so I'll update the description accordingly.
+
+
+341
+
+
+This drawing shows the other female main character of the story, Satsuki Ford. Too used as reference an old drawing someone made for me, but made the character a little sexier.
+
+
+344
+
+
+More Yumiko here, slightly risque. This comes from approximately one third into the novel and in this case it is a faithful representation of the description.
+
+I love Too's style and art, it's really perfect for the novel. The remaining images, watermarked to avoid "theft", are available in the gallery (see the tab on the top of the page). The complete images will be available in the next build of the PDF, which I'll make once I get the remaining two pictures.
+
+Now, it's time to finish this novel... it's been almost 10 years (I started in 1997).

_posts/2006-07-17-additions-and-changes.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-07-17 17:52:35+00:00
+layout: post
+slug: additions-and-changes
+title: Additions and changes
+wordpress_id: 89
+categories:
+- S.T.E.A.L.
+---
+
+I've been writing a lot in the past weekend. The fact that I have some definitive art gave me the impulse after many months of inactivity. Being totally dissatisfied with the state of chapter 4 (the latest I'm writing), I completely reorganized it, moving one section to the top and rearranging the behavior of some characters (like Satsuki, who was a little too hysterical) and cut off part of a flashback. And finally I'm getting to one of the most action-packed parts of the novel.
+The snapshot on the links page is terribly outdated, I'm afraid. I'm waiting for the rest of the art from Too to put it up, but if I don't get any by next week I'll put it up anyway, so that the (few) people that read this page will be able to appreciate the changes.
+
+I've been thinking of making a web page about S.T.E.A.L. to promote the project better. The downside is that I can't put images of the characters or the like around, because of course they exist only through Too's art and my description. If anyone comes up with a good design suggesions, please say it in a comment.

_posts/2006-07-17-under-observation.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-07-17 21:42:12+00:00
+layout: post
+slug: under-observation
+title: Under Observation
+wordpress_id: 90
+categories:
+- Final Fantasy XI
+---
+
+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. The smaller ones use single target fire magic (Fire II) while the big one uses both single target and area of effect (AOE) fire magic (Firaga). All three spam a very annoying move, Hex Eye, that paralyzes everyone that is facing directly towards them.
+
+Mercredi employed a different strategy than usual: him and Rezo came as blue mages, while my brother was a ninja. BLU (short hand for Blue Mage) is  really suited for this battlefield. The trick was to have my brother and Rezo hold the two small gazers without facing them, while Mercredi kited the big one and succesfully bound it with Pinecone Bomb.
+
+Rezo and my brother used either blue magic or ninjutsu to kill the small ones, and then all three focused on the remaining gazers. Head Butt was used to stun it before it could cast Firaga. The strategy failed on the first run, but was succesful in other three. The Peacock Charm didn't drop, but they got Utsusemi: Ni and Erase, which sold and gave a respectable amount of 500,000 gil to each one.

_posts/2006-07-21-rsi.markdown

@@ -0,0 +1,13 @@
+---
+author: einar
+comments: true
+date: 2006-07-21 21:36:08+00:00
+layout: post
+slug: rsi
+title: RSI
+wordpress_id: 91
+categories:
+- General
+---
+
+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.

_posts/2006-07-24-clarification.markdown

@@ -0,0 +1,15 @@
+---
+author: einar
+comments: true
+date: 2006-07-24 12:37:35+00:00
+layout: post
+slug: clarification
+title: Clarification
+wordpress_id: 93
+categories:
+- General
+---
+
+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).

_posts/2006-07-27-im-still-alive.markdown

@@ -0,0 +1,13 @@
+---
+author: einar
+comments: true
+date: 2006-07-27 21:15:45+00:00
+layout: post
+slug: im-still-alive
+title: I'm still alive
+wordpress_id: 94
+categories:
+- General
+---
+
+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.

_posts/2006-07-28-perspectives.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-07-28 17:44:40+00:00
+layout: post
+slug: perspectives
+title: Perspectives
+wordpress_id: 95
+categories:
+- Science
+---
+
+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. That is why I've decided to learn [Python](http://www.python.org). The fact that it forces you to use proper indentation and its syntax seems ideal for me, who has little programming experience save bash shell scripting and a few PHP (terrible). I've found a nice [tutorial](http://honors.montana.edu/~jjc/easytut/easytut/) for it and so far it's going OK.
+
+I've taken a look at the [Biopython](http://biopython.org) project as a reference for future work, but it mostly deals with sequence analysis, which is not my field. I wonder if there are Python tools for microarray data analysis, because I really don't like R (it's slow and it's more of an environment than a programming language) and the only ones I know are from the [Bioconductor](http://www.bioconductor.org) project, in R, as I wrote. Not only that, but I work on proprietary high density oligonucleotide arrays, not the most common two-color (Cy3 + Cy5) variants.
+
+If that's not the case, I could look into annotation, probably, which is something I do extensively to filter out biologically non relevant data (always a problem when you deal with complex algorithms).  Still, there's more time before I get to doing something relevant to my work, so the chances are that I'll find something by then.

_posts/2006-07-29-computational-biology-wheres-the-biology.markdown

@@ -0,0 +1,21 @@
+---
+author: einar
+comments: true
+date: 2006-07-29 08:29:08+00:00
+layout: post
+slug: computational-biology-wheres-the-biology
+title: Computational Biology...  biology?
+wordpress_id: 96
+categories:
+- Science
+---
+
+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](http://www.dennogumi.org/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,](http://www.biomedcentral.com/bmcbioinformatics/) [Bioinformatics](http://bioinformatics.oxfordjournals.org) 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_. Aside people that apply data analysis tecniques to different subjects (not only biology), that can be excused if they don't know much about biological meaning, I think that a lot of people working in bioinformatics deal with biological data without knowing that it means.
+
+In my opinion, this is a mistake that should be corrected. I understand that, for example, a computational biologist that works on algorithms to find transcription factor binding sites isn't required to know the chemistry of the interaction between transcription factors and the DNA: however he/she should have a _good_ knowledge of what ehnancers and silencers are, and at least an idea on how the transcription mechanism works.
+
+It really puzzled me when a while ago there was someone talking about algorithms to find regions of aneuploidy (DNA copy number change) who talked about "disomy" and "trisomy" _without actually knowing their meaning_. Same for people that study docking and protein-protein interaction that know almost nothing about  their targets.
+
+Biologists in this field are making an effort to understand IT (I do my best to help my colleagues, for example), it would be nice if the computational field would do a similar effort.

_posts/2006-08-02-departure.markdown

@@ -0,0 +1,15 @@
+---
+author: einar
+comments: true
+date: 2006-08-02 17:54:25+00:00
+layout: post
+slug: departure
+title: Departure
+wordpress_id: 97
+categories:
+- General
+---
+
+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.

_posts/2006-08-04-holidays.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-08-04 09:43:56+00:00
+layout: post
+slug: holidays
+title: Holidays
+wordpress_id: 98
+categories:
+- General
+- S.T.E.A.L.
+---
+
+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](http://www.loano.net), in Liguria, for about 17 days, and I'll spend the rest traveling around central Italy (Arezzo, Perugia, Assisi, Todi, Gubbio, Siena).
+
+As "parting gift" I uploaded [a new snapshot of S.T.E.A.L.](http://www.dennogumi.org/steal/steal.pdf), which includes Too's fantastic art. Take a look, I hope you appreciate it. As usual, comments are welcome!

_posts/2006-08-29-im-back.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-08-29 08:52:45+00:00
+layout: post
+slug: im-back
+title: I'm back
+wordpress_id: 99
+categories:
+- General
+- S.T.E.A.L.
+- Science
+---
+
+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. I have some test data so I'll soon give it a try (after reading the paper, [published in BMC Bioinformatics](http://www.biomedcentral.com/content/pdf/1471-2105-7-25.pdf) earlier this year). It may be what I need to perform some comparison analysis between different kinds of tumor samples.
+
+On a different matter, the summer has been quite productive for S.T.E.A.L., as I've been writing quite a lot, and I set an internal deadline for completion (31st October), while text revision will take me more time before putting up the finished work. I'll be uploading a new snapshot soon.
+I also have some photos from my week-long cultural trip in Toscana and Umbria, I'll put them online as soon as I scan them (I had to use a single-use camera).

_posts/2006-08-30-new-steal-snapshot-released.markdown

@@ -0,0 +1,42 @@
+---
+author: einar
+comments: true
+date: 2006-08-30 21:11:56+00:00
+layout: post
+slug: new-steal-snapshot-released
+title: S.T.E.A.L. snapshot released
+wordpress_id: 100
+categories:
+- S.T.E.A.L.
+---
+
+As promised, I put up a new snapshot of S.T.E.A.L. (available [here](http://www.dennogumi.org/steal/steal.pdf)) Highlights include:
+
+
+
+	
+  * Interpolated drawings. This should reduce the pixelation effect, but it will make them more blurry. I can't fix this until Too sends me the actual art;
+
+	
+  * Revisions throughout the text, to remove some parts where Yumiko acted out of character;
+
+	
+  * A new part in New York, preparing the background for the more action-oriented parts that will follow;
+
+
+Still TODO:
+
+	
+  * Add more dialogue between Satsuki and Jim Clark, as the latter is an important character and now it looks underdeveloped;
+
+	
+  * Revise some older parts that I haven't looked at since they were written;
+
+	
+  * Fix the question marks. This is actually a Kile bug with quotations;
+
+	
+  * Of course, go on with the story!
+
+
+I'm also trying to make a S.T.E.A.L. page, but I need to think about a design that's not graphic-intensive. Suggestions are appreciated.

_posts/2006-09-03-new-kernel.markdown

@@ -0,0 +1,21 @@
+---
+author: einar
+comments: true
+date: 2006-09-03 15:57:07+00:00
+layout: post
+slug: new-kernel
+title: New kernel
+wordpress_id: 101
+categories:
+- Linux
+---
+
+[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](http://www.ubuntuforums.org) 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](http://www.evolution-mission.org). This enables extra functions like a framebuffer splash (pity about vesafb-tng not working on my video card), suspend2 (an enhanced suspend-to-disk functionality), low latency patches and so on.
+
+I have to say that Debian's kernel-package is wonderful, in the sense that it automates kernel packaging up to the point of being brain dead almost, and it also automatically compiles out-of-tree modules that have been installed using the *-kernel-source packages. In any case, I'm very happy of the result so far, with the only problem being the inability of setting 16:10 resolutions on the framebuffer. If anyone knows how, please leave a comment.
+
+All is well, however the drives **still** aren't unmounted cleanly. Is there a way you can remount a partition read-only just the moment before shutting down?

_posts/2006-09-04-the-black-coffin-and-a-static-merit-party.markdown

@@ -0,0 +1,21 @@
+---
+author: einar
+comments: true
+date: 2006-09-04 20:22:47+00:00
+layout: post
+slug: the-black-coffin-and-a-static-merit-party
+title: The Black Coffin and merits
+wordpress_id: 102
+categories:
+- Final Fantasy XI
+---
+
+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. I was the first to go down, followed by our ranger. Then we took a while to find the correct entrance to the Arrapago Reef. In the end, I had to leave out one person because there wasn't enough time available to do a run twice (we were in 7).
+
+The fight itself proved to be pretty fun. We had to fight five Fomors, then followed by another wave of Fomors. No one of us was in real danger save Mercredi, who got hit by Vorpal Blade with Counterstance on (but a quick Cure V saved him). The cutscenes after the fight were pretty interesting, but it's a shame that we won't see more story until October at least.
+
+My brother made a movie out of the fight (around 15 minutes long, 90 Mb), it's available on [Google Video](http://video.google.it/videoplay?docid=966962734279622489).
+
+On a related topic, I'm trying to assemble a static party (me, Eithin, Mercredi, Rezo, Sechs and Billyism) to gain some merit points. Our first run should be on Friday, I'll be sure to report about it.

_posts/2006-09-07-dynamis-buburimu.markdown

@@ -0,0 +1,37 @@
+---
+author: einar
+comments: true
+date: 2006-09-07 22:05:19+00:00
+layout: post
+slug: dynamis-buburimu
+title: Dynamis-Buburimu
+wordpress_id: 104
+categories:
+- Final Fantasy XI
+---
+
+UPDATED: Now a movie showing the run is hosted at [Google Video](http://video.google.it/videoplay?docid=6873951092724468622).
+
+On Tuesday there was my second attempt at doing Dynamis-Buburimu with [United Dynamis.](http://www.illuminaire-asura.com/forum) 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.<!-- more -->
+
+
+387
+
+
+At first only three members entered, to locate the ??? spot that would re-enable support jobs (disabled when you enter one of these areas). It was found relatively quickly. Then there was the matter of the dragons. Seven dragons roam the area, plus one which is the so-called mega boss. Killing the dragons deprives the mega boss of certain special abilities. We killed four of them, we couldn't do more because of the time limit (you have one hour as soon as you enter, with no extensions until you kill the boss). After that, we took on the Apocalyptic Beast.
+
+It was a hard fight, with numerous deaths (mine included) but we eventually won. Therefore I cleared the area, but it wasn't over yet. It was time to kill some regular enemies in order to obtain some good items. We started fighting "Nightmare Ravens". They aren't hard by themselves, but groups can be problematic. Our puller, Confuse, did a good job, but even him couldn't fight against bad luck. One of the pulls was so unlucky that it brought around 50 of these monsters. The image below outlines the (obvious) result (thanks to Sephris for letting me use this one):
+
+
+384
+
+
+As you can see, it wasn't a good result. Nevertheless, the whole run was successful, with 4 pieces of tattered relic armor, one warrior waist piece and one samurai relic piece among the drops (not counting around 50 pieces of Dynamis currency). As my luck always runs out, there weren't any paladin pieces. Dynamis-Xarcabard is scheduled for next week, and that also is the day where I will fully regain my lotting rights within United. I'm hoping for a Valor Surcoat drop...
+
+Closing this post, here's a group shot of some United members after the victory:
+
+
+390
+
+
+My brother should work on a movie of the run soon.

_posts/2006-09-10-kile-192-for-kubuntu-dapper.markdown

@@ -0,0 +1,70 @@
+---
+author: einar
+comments: true
+date: 2006-09-10 09:09:29+00:00
+layout: post
+slug: kile-192-for-kubuntu-dapper
+title: Kile 1.9.2 for Dapper
+wordpress_id: 105
+categories:
+- Linux
+---
+
+I learnt recently that the [Kile LaTeX environment](http://kile.sourceforge.net) 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. <!-- more -->
+The package is available on [here](http://www.dennogumi.org/deb/kile_1.9.2-0kubuntu1_i386.deb) (if the link is no longer working, leave a comment and I'll host it elsewhere), along with the [languages package](http://www.dennogumi.org/deb/kile-i18n_1.9.2-0kubuntu1_all.deb:). It has been signed with [my own GPG key](http://www.dennogumi.org/lb.key), which is also available on the wwwkeys.pgp.net keyserver (key ID   EC445369).
+
+I built the package for myself. It should also work for you, but I am not to be held responsible if it causes some breakage. Use it at your own risk.
+
+**UPDATE**: If you have trouble installing those packages, make sure you have the latest version of KDE as installed from [kubuntu.org](http://kubuntu.org/announcements/kde-354.php)'s repositories.
+
+A list of changes, taken from the original version announcement on Kile's web page, is available below:
+
+version 1.9.1 -> 1.9.2
+**Fixes:**
+
+
+
+	
+  * Add autoref command to standard reference commands (#130037)
+
+	
+  * Remember the setting of MakeIndexOptions checkbox in the project settings
+dialog. (debian #337550)
+
+	
+  * Added utf-8 and other encodings to the quickdocument dialog. (#131402)
+
+	
+  * Make the "New Tool" dialog box big enough. (#132425)
+
+	
+  * Check if masterdocs in kilepr files exist, should fix some problems with upgrades from kile 1.8.
+
+	
+  * Searching for environments in Edit functions improved.
+
+	
+  * Take array as math environment instead of tabular in Configure->Latex Environments.
+
+	
+  * Don't crash if a user changes the icon of a toolbar item. (debian #382317)
+
+	
+  * Allow a few more punctuation in codecompletion of citation keys. (#130148)
+
+	
+  * Remember last working directory in 'find in files' dialog. (debian #359932)
+
+	
+  * Tabular wizard should insert all entered elements. (#132736)
+
+	
+  * Only autosave files which have been modified.
+
+	
+  * Delete comma of last bibtex entry if Bibliographie->Clean is called. (#129499)
+
+	
+  * Quick Preview fails if graphics are included in selection (#126019)
+
+

_posts/2006-09-13-annotations-and-linux.markdown

@@ -0,0 +1,32 @@
+---
+author: einar
+comments: true
+date: 2006-09-13 17:27:58+00:00
+layout: post
+slug: annotations-and-linux
+title: Annotations and Linux
+wordpress_id: 106
+categories:
+- Linux
+- Science
+---
+
+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](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16897747&query_hl=3&itool=pubmed_docsum) 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).<!-- more -->
+
+For part of my work I use the excellent [DAVID 2006](http://niaid.abcc.ncifcrf.gov/) software by the NIAID, which can perform a lot of analyses including functional annotation, clustering, and more. Its output is usually a tab-delimited text file with the fields of interest. But that's just part of the work I need to do, as I usually have to filter and analyze the lists using different critera (depending on the analyses I do). And that's when Linux helps me a lot in doing this job.
+
+For example, today I had a lists of annotated genes, around 300, and I wanted to filter the list so that only the ones including the [Entrez Gene](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) description. I know that DAVID had the sixth column as the description identifier. So all I had to do was:
+
+[code] awk ' BEGIN { FS="\t"} { if ( $6 !="") { print }} '  infile > outfile [/code]
+
+$6 is the 6th field, which corresponds to the Entrez Gene description in the text file I obtained from DAVID. This line of code will print all the lines where $6 is not empty.  Once I did that, I obtained all the genes where the description was available. However, there were still fields I wouldn't need:
+
+[code]  awk ' BEGIN { FS="\t"}{ print $1"\t"$2"\t"$4"\t"$6 } ' infile > outfile [/code]
+
+That stripped two fields that weren't useful for me. I could have probably merged this on the other one. Even with this done, the file was hardly readable, both using less or oocalc to display it better. I needed to convert it to an HTML table! But how to do it? After a quick googling, I found the answer in the form of [t2t](http://www.scholnick.net/t2t/), a Perl script that converts text files to HTML tables. After installing it, I invoked it with:
+
+[code] t2t --header file_to_be_converted [/code]
+
+and I had immediately an usable HTML file.
+
+I'm pretty sure there are more tricks I could learn to improve my work.

_posts/2006-09-16-ati-drivers-and-linux.markdown

@@ -0,0 +1,17 @@
+---
+author: einar
+comments: true
+date: 2006-09-16 07:58:45+00:00
+layout: post
+slug: ati-drivers-and-linux
+title: ATI drivers and Linux
+wordpress_id: 107
+categories:
+- Linux
+---
+
+Recently I decided to update the fglrx driver ([ATI](http://www.ati.com)'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](https://support.ati.com/ics/support/KBAnswer.asp?questionID=22059) that has been plaguing the driver for months.
+
+Alas, nothing of the sort was observed in the latest version. It surely added a bunch of new features, but some irritating bugs are still not fixed (and still no AIGLX support). I have to say this is a common behavior regarding ATI products, even on Windows: the hardware is usually top-notch but the software components are insanely buggy. And they (like NVIDIA) won't publish open specifications in fear of having them exposed to competition... too bad that their competition has been always using reverse engineering methods to obtain information, so I don't think it would change anything.
+
+This, [as I blogged about previously](http://www.dennogumi.org/2006/06/03/the-problem-with-binary-only-drivers/), is a sore problem of binary-only drivers, with even important bugs staying present until the vendor decides to fix them. With AMD buying ATI I think that the situation will only become worse, reducing even the little competition there is in this essentially duopolistic market.

_posts/2006-09-16-steal-related-news.markdown

@@ -0,0 +1,21 @@
+---
+author: einar
+comments: true
+date: 2006-09-16 16:53:11+00:00
+layout: post
+slug: steal-related-news
+title: S.T.E.A.L. related news
+wordpress_id: 108
+categories:
+- S.T.E.A.L.
+---
+
+As I checked my messages on deviantart this morning, I got some news from Too. Aside some delay in obtaining the actual artwork he did (not his fault, probably some quirk of the postal system) he provided me with a tentative sketch of the cover. It impressed me a great deal, so I already gave out the "green light" for coloring it. Here is the sketch (watermarked, as usual):
+
+
+393
+
+
+Too's skill is evident.
+
+Work continues on the text, and if I can I will try to publish a new snapshot by tomorrow, or next week. I'm finally getting to the parts I want to write, btu I found that connecting those to the flow of narration requires more work than I thought. Also, I've registered the domain stealsaga.net in order to give a proper place to the novel. I'm still unsure how to design and implement it, though.

_posts/2006-09-17-another-steal-snapshot.markdown

@@ -0,0 +1,29 @@
+---
+author: einar
+comments: true
+date: 2006-09-17 16:49:22+00:00
+layout: post
+slug: another-steal-snapshot
+title: Another S.T.E.A.L. snapshot
+wordpress_id: 109
+categories:
+- S.T.E.A.L.
+---
+
+As promised, I got around to write for a while during this weekend and here is the result, a new S.T.E.A.L. snapshot ready for [download](http://www.dennogumi.org/steal/steal.pdf).
+
+Notable changes include:
+
+
+
+	
+  * New dialogue between Jim and Satsuki at the start of chapter 4. This should show better that Jim is and will be an important character during the story development;
+
+	
+  * Text revisions throughout chapter 4;
+
+	
+  * A whole new part of the chatper 4 story, that can be considered now roughly halfway.
+
+
+On a related topic, I'm still working on the stealsaga domain, and I think it should be ready at least in alpha form in a week or two.

_posts/2006-09-21-kubuntu-edgy-knot-3-artwork.markdown

@@ -0,0 +1,16 @@
+---
+author: einar
+comments: true
+date: 2006-09-21 19:03:50+00:00
+layout: post
+slug: kubuntu-edgy-knot-3-artwork
+title: Kubuntu Edgy Knot 3 artwork
+wordpress_id: 110
+categories:
+- General
+- Linux
+---
+
+[Jucato](http://jucato.multiply.com/blog) has [some screenshots](http://jucato.multiply.com/photos/album/24) 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](http://oxygen-icons.org) 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. Bah.

_posts/2006-09-24-cooperation-and-stupidity.markdown

@@ -0,0 +1,17 @@
+---
+author: einar
+comments: true
+date: 2006-09-24 08:36:25+00:00
+layout: post
+slug: cooperation-and-stupidity
+title: Cooperation and stupidity
+wordpress_id: 111
+categories:
+- Anime
+---
+
+While I was viewing [Yamato Video](http://www.dennogumi.org/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](http://www.animenfo.com/animetitle,1261,pipkkd,chrno_crusade.html). As a few may know, it's written _Chrno_ and not Chrono for some obscure reason. What it matters though is that [Planet Manga](http://www.paninicomics.it/Home.jsp) already edited the relevant manga with the name Chrono Crusade (same as what AD Vision did in the United States).
+
+Of course, Yamato didn't bother changing the title to stir interest from people who already bought the manga. I can bet the adaptation will alos be different and nothing like the manga. This is not new in the Italian market, which is basically a mafia. Everyone knows each other, there are stupid, petty rivalries between the head sections of different companies which basically means that any good idea of cooperation - for mutual advantage - is scrapped  because of stupidity.
+
+Healthy competition and cooperation help. In this case there is _no_ competition, just mutual ignorance. The fact that sales' figures are kept hidden should tell something. I hope that someday a  _real_ company, whith a sensible business plan (so, nothing like [Shin Vision](http://www.shinvision.com) is doing, for example) will come and force the others to act accordingly.

_posts/2006-09-28-on-free-software-and-fsf.markdown

@@ -0,0 +1,23 @@
+---
+author: einar
+comments: true
+date: 2006-09-28 19:36:24+00:00
+layout: post
+slug: on-free-software-and-fsf
+title: On Free Software and FSF
+wordpress_id: 113
+categories:
+- General
+- Linux
+---
+
+**WARNING**: This entry is somewhat political in nature.
+
+Given the [recent controversies](http://lwn.net/Articles/200422/) about the [GPL v3 draft](http://gplv3.fsf.org/draft), I thought I'd give my insight on the [Free Software Foundation](http://www.fsf.org) 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.<!-- more -->
+
+The FSF has done a good job in creating free (as in freedom) tools from UNIX, and also for creating the GPL v2, a license that mostly reminds me of good, fruitful scientific work because it encourages sharing and improvement. I always recommend the GPL as the license of choice for academia-developed software. I like the license because it encourages competition, puts everyone on a level playing field where everyone can improve. That said, the political views of the FSF and RMS really are questionable.
+
+RMS is an idealist, but his views in my opinion clash with reality, not to mention that his "no compromise" attitude is not always the best option. I can understand his desire to have free software for everyone, but every time someone does not behave in such a way, he's extremely critic. He should understand as well that **pluralism** is actually **a good thing**. You can't force people to make free software as much as you can't force people to make proprietary software (I like the former better, but that's my idea only). Instead, he is always on a rampage to promote his ideas through activism. Sometimes it seems only he has the right view on something, which is down right irritating.
+I hate activism. When you have a democratically elected government, it's a lot less useful than it may seem. Why always bypassing the people you have elected? What's the role of the government then? And not only that, the FSF has been present at activities promoted by certain parties, notably the Green Party, because of their stance on software patents. Going with a party whose most incarnations show a total and complete ignorance of environment just because they support part of their cause is insane. Personally I am not represented by the Greens, nor I want to. The FSF should concentrate on the technical, and legal aspects of free software, and leave out the extreme left/anarchist ideals.
+
+Last but not least, what can I think when RMS himself says that he wants to[ "liberate everyone in the cyberspace"](http://www.groklaw.net/article.php?story=20060625001523547)? Has he been reading too much W.Gibson, perhaps?

_posts/2006-10-02-valor-gauntlets.markdown

@@ -0,0 +1,32 @@
+---
+author: einar
+comments: true
+date: 2006-10-02 16:18:21+00:00
+layout: post
+slug: valor-gauntlets
+title: Valor Gauntlets!
+wordpress_id: 112
+categories:
+- Final Fantasy XI
+---
+
+At least, after six long months of wait, I obtained a new piece of the Paladin relic set.<!-- more -->
+
+It all happened in United Dynamis' last San d'Oria run. Things started a little late (around thirty minutes), but everything went smoothly. After killing the last notorious monster required for spawning the so called "Mega Boss", the sponsor decided to farm more, so we moved to try a shot with the Ninja NM on the west side of the area. That's when the Valor Gauntlets dropped. I admit I got lucky, as I casted a lot of 770, while the others got only 47 and 350. And after the usual 5 minutes' wait, they went from the treasure pool into my inventory. Here they are:
+
+
+
+
+
+399
+
+
+
+
+
+Now I only need two more parts of the relic set. Next week there is Beaucedine Glacier scheduled, where the Valor Breeches drop. One can hope to be lucky...
+
+And last, here is how I look with this new addition:
+
+
+401

_posts/2006-10-04-a-disappointment-galaxy-angel-ii.markdown

@@ -0,0 +1,33 @@
+---
+author: einar
+comments: true
+date: 2006-10-04 19:23:46+00:00
+layout: post
+slug: a-disappointment-galaxy-angel-ii
+title: 'A disappointment: Galaxy Angel II'
+wordpress_id: 116
+categories:
+- Anime
+---
+
+Recently, [Galaxy Angel II](http://www.animenfo.com/animetitle,3716,hmgxur,galaxy_angel_ii.html) 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.<!-- more -->
+
+The series features a brand new cast, with only loose relationships (as far as I could tell) with the original series. The episode opens with two of the new characters, one being Millefuille Sakuraba's (one of the original GA cast) relative.
+
+
+405
+
+
+What disappointed me at first was the presence of _fan service_, that had been completely absent in the original series. I find it to be a bad point since the show had worked so well without the need of anything even remotely risque. The second important feature is that the episodes are now full-length, i.e. 23 minutes, instead of half-length. This has severe impact on the humor, that held for short time but that grows tiring on the long run. And as far as I could see, the humor is nowhere near the craziness of the original GA (save for the opening, perhaps).
+
+
+408
+
+
+I found the show to be rather dull and boring for the first part. I almost didn't smile while watching the various gags. BUt the worst, in my opinion, was yet to come. That is because there is actually a more serious part of the story, that shows up briefly near the end of the episode, where the new Angel Tai gets on their frames.
+
+
+411
+
+
+Despite some rather unsuccessful humor during this part, the "serious", as I can call it, part looks really out of place. It would have been better to do either totally humorous or not, as these last minutes look completely out of place. In short, I was really disappointed. BROCCOLI made a bad move this time. For sure I won't be watching more of this.

_posts/2006-10-04-dutch-weekend.markdown

@@ -0,0 +1,19 @@
+---
+author: einar
+comments: true
+date: 2006-10-04 20:03:19+00:00
+layout: post
+slug: dutch-weekend
+title: Dutch weekend
+wordpress_id: 114
+categories:
+- General
+---
+
+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've been to a museum, but I (sadly) couldn't go to the Van Gogh Museum. In the night we had a nice dinner but we were too tired to go around, so we opted to watch a film. My brother's girlfriend had a somewhat biographic one on the explorer Shackleton, made by UK's Channel 4. While I liked Kenneth Brannagh's acting, the extremely slow pace (200 minutes long) made me quit in advance and go to bed.
+
+On the following day we went to see the Space Expo, a permanent exhibition near my brother's work place at [ESTEC](http://www.esa.int/esaCP/SEMOMQ374OD_index_0.html). And in the evening we went around Leiden, which I find much more interesting than Amsterdam. I left on the following day at 4.50 in the morning.
+Overall this has been a pleasant experience, and I look forward to seeing my brother again on October 12th, when he'll get back to Italy again for a few days.
+I took some photos, but I have to wait for my brother to send them to me so I can put it online.