Posts on dennogumi.org

Out with the old, in with the new (??)

Wed, 30 Sep 2026 00:00:00 +0000

Note: this article contains anime-style AI generated illustrations. If that bothers you… feel free to stop reading (although you might miss out… or not?).

Leave of absence?
#

Soo… the last post here was approximately four (or was it five?) years ago. What the heck happened?

An art-challenged individual's perspective on AI (anime) generated art

Sun, 20 Nov 2022 22:17:41 +0100

You might have heard it in the past few months: some areas of the Internet are buzzing with discussions on “generative art”, that is, artwork generated from “AI” models that were fed with an absurdly large amount of images as training as a base. There are supporters, there are critics, and techology advances: among all this, this post offers my humble experience with computer-generated imagery.

In this post, you’ll be guided by Yumiko, Satsuki, and Maya: the first two are characters created by someone else I know (who wants to remain anonymous) which I then expanded, cooperating with their creator in a certain project from a few years ago; the latter is… well, a character with an interesting history, which will be explained later.

Translations available for KDE unstable packages

Fri, 07 Oct 2022 23:10:14 +0200

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

Setting up Let's Encrypt certificates for the 389-ds LDAP server

Fri, 22 Oct 2021 21:04:52 +0200

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

Setting up OwnTracks Recorder and OAuth2 with nginx, oauth2-proxy and podman

Sun, 01 Aug 2021 00:30:28 +0200

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

Blast from the past: 超獣機神ダンクーガ (Super Beast Machine God Dancougar)

Sun, 13 Jun 2021 00:26:43 +0100

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

Partings

Thu, 25 Feb 2021 23:19:33 +0100

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

DIY KVM over IP with pikvm

Sun, 07 Feb 2021 09:19:47 +0100

(Note: this post also appears in Planet KDE and Planet openSUSE because I thought this might be interesting to others)

As I mentioned in some other posts, I have a small “server” which I use as a NAS to provide archiving for photos and other files of interest. As it runs in a remarkably small (and quiet) enclosure, I’ve managed to put it in an incospicuous part of the room it is in. For the most part, it runs without a hitch: but in some (rare) occasions it needs to be looked at, and sometimes either logging via SSH is not possible, or it is not enough to diagnose the problem. In other words, I need to check what’s on the display. And the position it is in means that attaching a monitor and a keyboard can be inconvenient at best. In other words, I needed out-of-band management.

Quick tips: Server Name Indication for internal domains with Turris Omnia

Sat, 30 Jan 2021 01:05:17 +0100

Omnia?
#

The Turris Omnia is quite a nice (although a little pricey) OpenWRT-based router from CZ.NIC. It provides a fairly powerful CPU, relatively unconstrained eMMC space, and quite a lot of hackability (some revisions even have GPIO ports to play with). It runs a modified version of OpenWRT, named TurrisOS.

The problem
#

A few years ago, I built a custom NAS for my storage needs, using a cheap Intel SoC (J1900 chipset) and a (much pricier) mini-ITX small form factor server tower. While I want it to be primarily a NAS, I wanted to run a few services on it, for example Nextcloud or Pymedusa. Of course, in these days it’s better to use HTTPS, and the process is both cheap and fast using Let’s Encrypt. I also wanted to use SNI with multiple subdomains (files.example.com, medusa.example.com, etc.) pointing to the same internal LAN IP (because some of the software I used is much harder to set up with subpaths of a single domain).

Fixed comments

Sat, 09 Jan 2021 02:14:57 +0100

The migration happened and well… it turns out that it was not as smooth as I expected. In particular, comments weren’t working at all due to a filesystem permission on the database (which meant nothing would get written at all). That is now fixed. Sorry for the problems.

To add problems over problems, I had a hardware failure (RAID card) last June, which wrecked the root filesystem and I had to reinstall everything from scratch. When I looked back to recover the last comment backup… Well… it wasn’t being backed up. I was able to recover the ones up to 2015-2016 or so because I had still my old Disqus export laying around.

Refreshed look

Wed, 06 Jan 2021 00:30:09 +0100

You might have noticed that the blog has a markedly different look than before. It has not only changed visually, but also under the hood. This (brief) post summarizes the reasons behind the change.

Why?
#

Simply put, the previous solution was unmaintainable. “But,” you might say, “it was a static site generator! How could it become unmaintainable?”.

Providing KDE software updates from git for fun and profit in openSUSE

Tue, 05 Jan 2021 15:23:49 +0100

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

New server: away from Kolab

Fri, 07 Jun 2019 23:47:42 +0000

Yesterday I finally flipped the switch on the MX record and moved to a new server (still aptly named after another character from アキハバラ電脳組). The machine was found through Hetzner’s server auctions and has quite a good configuration for the price paid:

Intel Xeon CPU E31245 @ 3.30GHz
16G ECC RAM (ECC was the deciding factor)
LSI Hardware RAID 1 with two 3x2T disks

Now, since the old server has been chugging along since 2011, the 5 eurocent question is why did you move at all? It turns out there were a pretty good number of reasons (to me, at least).

Hack of the day: extracting comments from Nicovideo

Thu, 03 Jan 2019 23:07:42 +0000

Header image credit: 1840151sudarshan (Wikimedia Commons, CC BY-SA)

A while ago I posted a way to download 実況動画 from Nicovideo. One of my acquaintances publishes videos there, and he wanted to collect the various comments to reply in a follow up video (what the Nico users call the コメント返し). When the comments are more than just a few, it’s hard to find where they refer to without watching them on Nicovideo itself, and its UI is suboptimal. Ideally one would check comments ordered by their position in the video. There are existing programs but their user interface is utterly confusing at best. This called for something simpler, and that’s what I tried to do.

Dolphin and openQA and other assorted bits

Sat, 28 Jul 2018 23:20:48 +0000

Part of this post is about openQA, openSUSE’s automated tool which tests a number of different scenarios, from installation to the behavior of the different desktop environments, plus testing the freshest code from KDE git. Recently, thanks to KDE team member Fabian Vogt, there has been important progress when testing KDE software.

Testing the Dolphin file manager
#

Those who use KDE software, either in Plasma or in other desktop environments have at least heard of Dolphin, the powerful file manager part of KDE Applications (by the way, have you checked out the recent beta yet?). A couple of weeks ago, in the #opensuse-kde channel, Fabian mentioned the possibility of writing new openQA tests: although there are many tests already, the desktop ones are all but comprehensive given the many possible scenarios. After some discussion back and forth, the consensus was to test Dolphin as it’s a very commonly used in many everyday tasks.

Hack of the day: downloading VOICEROID実況 from Nicovideo

Tue, 23 Jan 2018 23:15:48 +0000

実況? Is it something edible?
#

In recent times, I’ve been watching a lot of VOICEROID実況 (じっきょう, jikkyou, literally “commentary”) videos from the rather famous (in Japan) video service ニコニコ動画, better known as “Nicovideo”. In this case, the commentary actually refers to games: they’re basically a Japanese version of the Let’s Play videos that are all around other places like YouTube.

There can never be enough testing

Mon, 07 Aug 2017 14:49:35 +0000

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

Why would openQA not run on Wayland? The reason lies in the video driver. openQA runs its tests in a virtual machine (KVM) which uses the “cirrus” virtual hardware for video display. This virtualized video card does not expose an interface capable of interfacing with the kernel’s Direct Rendering Manager (DRM), which is required by kwin_wayland, causing a crash. To fix it, “virtio”, which presents a way for the guest OS to properly interface with the host’s hardware, is needed. Virtio can be used to emulate many parts of the VM’s hardware, including the video card. That would mean a working DRM interface, and a working Wayland session!

Danbooru Client 0.6.1 released

Wed, 01 Mar 2017 20:43:48 +0000

A new version of Danbooru Client is now available!

What is Danbooru Client?
#

Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition).

It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re).

Announcing a new project

Sun, 15 Jan 2017 21:00:00 +0000

If you look through this blog’s archives, you may notice that although Free and Open Source Software is what I write most about, it is not the exclusive topic. I’ve written on science (my day job) as well as other interests. And today I’d like to lift the wraps on another project which I take part on, unrelated to the above.

Notice for those who read my blog coming from FOSS aggregators like Planet KDE: this is fairly different than most recent topics from me, so be warned before you continue reading.

Killing the redundancy with automation

Sun, 18 Dec 2016 11:51:57 +0000

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

Some prerequisites
#

In openSUSE speak, packages are developed in “projects”, which are separate repositories maintained on the OBS. Projects whose packages will end up in the distro, that is where they are being developed to land in the distribution, are called devel projects. The KDE team uses a number of these to package and test:

Testing the untestable

Sun, 27 Nov 2016 09:27:13 +0000

Admit it: how many times you have seen “software from this branch is completely untested, use it at your own risk” when you checked the latest code from any FOSS project? I bet you have, many times. For any reasonably modern project, this is not entirely true: Continuous Integration and automated testing are a huge help in ensuring that the code builds and at least does what it is supposed to do. KDE is no exception to this, thanks to build.kde.org and a growing number of unit tests.

The heroes we deserve

Sat, 29 Oct 2016 16:43:23 +0000

You may be aware that openSUSE Leap 42.2 is now in the release candidate stage, and there’s a lot of activity aimed at squashing those pesky bugs before they hit the final release. One particular bug proved to be quite tough to fix, and it was only solved thanks to the “heroes” mentioned in the title. This is the history of the bug.

The report
#

October 6th, 2016 - A bug iss reported against Plasma reporting a hard freeze of Plasma when using the Noveau driver, but not with the closed NVIDIA blob. Although the effect is deleterious to Plasma and not other desktop environments, there is evidence that the issue is in the driver itself, but there’s only partial indications, and no conclusive proof.

Two in one

Sat, 25 Jun 2016 14:11:01 +0000

As you may know (unless you’ve been living in Alpha Centauri for the past century) the openSUSE community KDE team publishes LiveCD images for those willing to test the latest state of KDE software from the git master branches without having to break machines, causing a zombie apocalypse and so on. This post highlights the most recent developments in the area.

Up to now, we had 3 different media, depending on the base distribution (stable Leap, ever-rolling Tumbleweed) and whether you wanted to go with the safe road (X11 session) or the dangerous path (Wayland):

I have a problem...

Sun, 29 May 2016 09:48:50 +0000

Every day, a sizable number of people posts problems on the KDE Community Forums and the ever-helpful staff does their best to solve whatever issues they’re facing. But what exactly does one do when this happens? This post provides more insights on the process.

NOTE: The following applies to my workflow for the Kontact & PIM subforum.

Step 1: Someone posts a problem
#

The questions posted are various, and range from simple tasks (“how I do XXX”) to very specific workflows. It covers a large spectrum. The first thing I do when reading a post, is to go through a “mental checklist”:

Danbooru Client 0.6.0 released

Sun, 01 May 2016 14:59:16 +0000

A new version of Danbooru Client is now available!

What is Danbooru Client?
#

Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition).

It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re).

Of gases, Qt, and Wayland

Sat, 27 Feb 2016 16:13:11 +0000

Ever since the launch of Argon and Krypton, the openSUSE community KDE team didn’t really stand still: a number of changes (and potentially nice additions) have been brewing this week. This post recapitulates the most important one.

I’d like the most recent Qt, please
#

As pre-announced by a G+ post, the openSUSE repositories bringing KDE software directly from KDE git (KDE:Unstable:Frameworks and KDE:Unstable:Applications) have switched their Qt libraries from Qt 5.5 to the recently released Qt 5.6. This move was made possible by the heroic work of Christophe “krop” Giboudeaux, who was able to beat QWebEngine into submission and make it build in the OBS.

Where are my noble gases? I need MORE noble gases!

Fri, 19 Feb 2016 21:03:25 +0000

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

HOWTO: Configure 389-ds LDAP server on openSUSE Tumbleweed

Sat, 23 Jan 2016 21:28:41 +0000

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

Danbooru Client 0.5.0 released

Tue, 08 Dec 2015 00:20:05 +0000

A new version of Danbooru Client is now available!

What is Danbooru Client?
#

Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition).

It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re).

Tip: opening and closing ports needed by a systemd service

Sun, 18 Oct 2015 16:54:25 +0000

Recently I’ve been testing out murmur, http://wiki.mumble.info/wiki/Main_Page server component, on my CentOS 7 server. Murmur requires specific ports being open to operate, and when using it I would open them manually, and close them after the session had been completed.

I found it pretty tedious: I wanted to wrap it into a single call to the service, so I could enable my user (via sudoers) to be able to start and stop the service without worrying about elevating permissions to start and stop the firewall. After reading a bit systemd’s documentation I found about ExecStartPre and ExecStopPost that would work perfectly for the job.

The Big Forum Cleaning

Sat, 26 Sep 2015 20:32:06 +0000

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

Danbooru Client 0.4.0

Wed, 12 Aug 2015 16:32:23 +0000

Taking advantage of the holidays, I’ve managed to land a number of fixes in Danbooru Client, and therefore I think it’s time for a new version, 0.4.0!

What is Danbooru Client?
#

Danbooru Client is an application to access Danbooru-based image boards (Wikipedia definition). It offers a convenient, KF5 and Qt5-based GUI coupled with a QML image view to browse, view, and download images hosted in two of the most famous Danbooru boards (konachan.com and yande.re).

KDE Applications 15.08 RC for openSUSE

Sat, 08 Aug 2015 17:57:15 +0000

KDE has recently released the newest Release Candidate of the Applications 15.08 release. Among the new features and changes of this release, there is a technology preview of the new KF5-based KDE PIM suite (including reworked, faster Akonadi internals), new applications ported to KF5 (the most notable ones being Dolphin and Ark). After some consideration and thinking on how to allow users to test this release without affecting their setups too much, the openSUSE community KDE team is happy to bring this latest RC to openSUSE Tumbleweed and openSUSE 13.2¹.

GPG transition statement

Sun, 07 Jun 2015 14:39:58 +0000

(Inspired by http://viccuad.me/blog/GPG-transition-statement/)

This exact same text can be found at this location.

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Sun Jun  7 14:12:39 CEST 2015

For a number of reasons, i've recently set up a new OpenPGP key, and
will be transitioning away from my old one.

The old key will continue to be valid for some time, but i prefer all
future correspondence to come to the new one.  I would also like this
new key to be re-integrated into the web of trust.  This message is
signed by both keys to certify the transition.

the old key was:

pub   rsa4096/6E1A4E79 2009-05-11
      Key fingerprint = CBD6 EEE3 7132 027A A237  9659 013F A50B 6E1A 4E79

And the new key is:

pub   rsa4096/A29D259B 2015-06-05 [expires: 2016-06-04]
      Key fingerprint = DBC1 07DC 8601 B275 835F  9178 FBE5 5AED A29D 259B

To fetch the full key (including a photo uid, which is commonly
stripped by public keyservers), you can get it with:

  wget -q -O- https://www.dennogumi.org/A29D259B.txt | gpg --import -

Or, to fetch my new key from a public key server, you can simply do:

  gpg --keyserver pgp.mit.edu --recv-key A29D259B

If you already know my old key, you can now verify that the new key is
signed by the old one:

  gpg --check-sigs A29D259B

If you don't already know my old key, or you just want to be double
extra paranoid, you can check the fingerprint against the one above:

  gpg --fingerprint A29D259B

If you are satisfied that you've got the right key, and the UIDs match
what you expect, I'd appreciate it if you would sign my key:

  gpg --sign-key A29D259B

Lastly, if you could upload these signatures, i would appreciate it.
You can either send me an e-mail with the new signatures (if you have
a functional MTA on your system):

  gpg --armor --export A29D259B | mail -s 'OpenPGP Signatures' lbeltrame at kde.org

Or you can just upload the signatures to a public keyserver directly:

  gpg --keyserver pgp.mit.edu --send-key A29D259B

Please let me know if there is any trouble, and sorry for the
inconvenience.

Regards,
        Luca Beltrame
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2

iQIcBAEBCgAGBQJVdDmaAAoJEAE/pQtuGk55uKoP/1orTlEgSNC7HCIJECkkBxqR
F64VMegugEFIe2nUyTf13wjtMDXluCy6hpY7+3iaOAHfMFBCOlPe0INrUTiuqwir
GnP/PQyzXU41yDqd7ytvNKqV8UkkW6NBcL7vCx810zSbnxpSV5L1N8dDy3GG5ZkE
iUm5AH+JJHzZGA7Cn90aA5VcemGCTu5buoJTu2rWWU4ahm3WMHnpuUsYP2mCNnU3
EOc94jlayqiLUTsnjTbpiPbJ7mcxBoufhjg1RHI5uK9BU5db8aUI619nGlTdvHHE
pZ4rXYWJqAhjeuDPmAk8poIeITi8qdiY5W5UibajhV2OchAuyOBGYv/Cddx36Xnk
rUyxlupZsWXriqo79+DgXsVjTgzBjCpkz+QVnBlq3rboXpgpCh6mZWoECGPBj8dN
E0uqsO5CmDxwYv1Yv3EpTvn2rf00pKEAUTq6cfEZAZ7ZhZih7XQdB4qlve4GD8M0
42wQUpFiyRiV0WrXEjN/EyrI0CiY9Rt/wNj+JLKC7NhELyC0q4oRzjvYCJdZHMhH
ydM8YiyWVOLUX5b3Y5xqlmRwPQydmjrGv2NAI7y4z0k1yc9pn/K4m5z2sxTunmQk
jaYxQ5DkQMpoSxaIYxmAYC5vjAa7U5nlg43sfiaQHa2RCUu+THTwFJaBOd0qYR7P
I++SIct+OFU9lnwQkjgyiQEcBAEBCgAGBQJVdDmcAAoJEEDIKBSTsBwWBw4H/RBP
40aLWMqRX3imEIg3jCBmtj9fsPn3OM+D8drF1v5vq2cQHGZcwqLnnaxP9KrZA06A
5/o0ofuqY5dg4jukPWjvqx6hsUlUbEpcJVV9eg0XIlmluaUPc6eVopLJOL0bhYi8
2zk4GLZiiGt7asoJ/rjhQg0BR4aajNALw1wF1pk4oQlm68M5PfjDu9voEd6vg6nv
tILBnEGzJjgiOnXHzHcld7+MG1Kut9EmFNTNNgDasLw7HenGTHt9G/rJq5mSwPZY
0Btd7yJ/cbBlCmyC3OIViN2bd+gCeF5HYtVNyMomMaM/0yunqi9ioMxWFaGrmY1d
JJF3TtQUDXrgOoXUlD0=
=4Yho
-----END PGP SIGNATURE-----

Isso for comments

Mon, 01 Jun 2015 12:04:58 +0000

As I said in my latest post, I wasn’t very happy with using Disqus to store my comments, mainly because I do not want my data to be hosted by someone else. Thanks to some commenters, I was made aware of an alternative, called isso.

After reading the online documentation, I decided to set it up with dennogumi.org. It was all a matter of creating a new user called isso, setting a virtualenv to its home dir, and then installing isso itself and uWSGI:

Dynamically static

Sat, 30 May 2015 09:52:40 +0000

Since 26th December 2005, I’ve been runnning this blog with Wordpress. At the time there were little alternatives and finally I had got hold of a host (Dreamhost, at the time) that supported PHP and MySQL without being overly restrictive. 10 years later, things have somehow changed.

The issue
#

The main reason lies in how Wordpress has evolved over time: no, I’m not speaking about the subjective “bloat”, but the fact that it’s been moving towards a full-blown CMS, which is not what I have in mind to run my blog. Also, performance with many plugins had somehow worsened, in particular when accessing things like the administration interface. Not to mention that plugins itself are still somewhat fragile, and upgrade could still cause harm to your whole site. Lastly, the mere fact that I had to use plugins to lessen the performance impact was off-putting.

Plasma 5 live images for openSUSE and on the default openSUSE desktop

Mon, 06 Apr 2015 08:35:43 +0000

A lot has been happening on the KDE side of openSUSE… this post summarizes what’s been going on so far.

Live media for Plasma 5
#

One of the most-often requested ways to test Plasma 5, given it can’t be coinstalled with the 4.x Workspace, is the availability of live images to test either in VM or bare metal without touching existing systems.

Danbooru Client 0.3.0

Mon, 23 Feb 2015 23:27:32 +0000

Following up on yesterday’s release, I’ve released Danbooru Client 0.3.0.

This early new release is mostly due to the fact that the QML view file wasn’t installed (sorry!) so part of the UI would not even load (or even crash).

That said, I’ve managed to get some extra features in:

Fade-in/out animation when posts are being downloaded
Support for tagging is back (EXPERIMENTAL): it is optional, and requires KFileMetaData (not yet a framework, but should be distributed with Plasma 5).

Release details
#

Currently, there is only a source tarball. For security, I have signed it with my public GPG key (6E1A4E79) and I have also provided a SHA-512 hash of the release.

Danbooru Client 0.2.0 released

Sun, 22 Feb 2015 20:38:02 +0000

After my previous post, development went quicker than expected, so I’ve actually managed to get a real version out. ;) So without much ado… here’s Danbooru Client 0.2.0!

This redesigned C++ version brings a few more features compared to the PyKDE4 version, notably:

Infinite scrolling (experimental) - Just scroll down to load the next set of posts
QML-based thumbnail view

Click on the image below to have a demonstration of what’s in this release (warning: 2M GIF file):

Sometimes they come back: Danbooru Client ported to KF5 and C++

Sun, 15 Feb 2015 21:59:37 +0000

Some of you may remember a semi-complex application I wrote back in the days, namely Danbooru Client. Written in PyKDE4, it provided a semi-decent interface to Danbooru-style boards. It mostly worked and received little maintenance (also because I didn’t have that much time for maintenance).

In the mean time, I started learning some C++. No, it’s not that I don’t like Python (in fact I do, I use it a lot in my day job), but I wanted to gain at least some basic skills to be able to contribute directly to KDE software.

Plasma 5.2 for openSUSE? You bet!

Tue, 27 Jan 2015 15:27:08 +0000

The ever-amazing Plasma team from KDEjust put out a new release of Plasma. I won’t spend much describing how big of an improvement it is - the release announcement at KDE has all the details needed to whet your appetite.

And of course, now it’s the turn of distributions to get out packages for the users at large.

This is also the case for openSUSE. The KDE:Frameworks5 repository hosts the new 5.2 goodness for released distributions (13.1 and 13.2) and Tumbleweed. Packages have also been submitted to Tumbleweed proper (pending legal review, so it will take some time).

KDE PIM changes in openSUSE Tumbleweed

Sat, 17 Jan 2015 09:45:00 +0000

Short version: the KDE PIM in openSUSE Tumbleweed is moving from 4.14.x to the KF5 based version. More details below.

Some history
#

As you may know, up to now the default PIM suite for Plasma 5 in openSUSE Tumbleweed was the KDE PIM 4.14, based on kdelibs 4.x. While upstream KDE has offered a KF5-based version since Applications 15.08, it has been originally marked as a technology preview, so we (the openSUSE community KDE team) thought it would be more prudent to stick with the 4.14 version (but offer the KF5 based PIM as an option for the daring).

Policy-based routing for single IPs using EdgeOS

Fri, 02 Jan 2015 20:11:40 +0000

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

KDE Applications and Platform 4.14.2 available for openSUSE

Wed, 15 Oct 2014 16:30:53 +0000

Following up on KDE’s announcement of the latest stable release, we have now packages available for 12.3 and 13.1 (a 13.2 repository will be made available after it is out). You will find them in the KDE:Current repository. Current users of this repository will get the new release automatically once they update.

Why you should upgrade? You can take a look at the list of changes to get an idea. These fixes touch many important KDE applications, including KMail, Okular and Dolphin.

Latest 4.13, newest 4.14 beta and Plasma 5 in openSUSE

Wed, 16 Jul 2014 05:43:49 +0000

Congratulations to KDE (of which I’m proud of being a part of) for the newest release of the Plasma workspace! At the same time, the 4.x series has seen a new beta release, and the stable branch got updated, too.

I’m betting a few people will ask “Are these available for openSUSE?” and of course the answer is yes, thanks to the efforts of the openSUSE community KDE team and the Open Build Service.

Changes in KDE Frameworks 5 and Plasma 5 packaging in openSUSE

Sat, 28 Jun 2014 11:59:23 +0000

Since a couple of weeks the packages offered by openSUSE in the KDE:Unstable:Frameworks repository have undergone a series of changes. In particular, the packages now install to /usr. For the libraries (KDE Frameworks 5) this will mean a transparent change for the userbase as they are expected to be co-installable, but the workspace components (Plasma 5) will confict with the existing Plasma 4.11.x installation.

What does this mean in practice? If you want to use Plasma 5 you will not be able to use a 4.11.x Plasma Workspace. The move was made to ease maintenance and packaging, as it meant dropping a number of hacks, and also to make KF5 + Plasma 5 packages suitable for inclusion in openSUSE Factory. At the same time, the 4.11.x workspace packages were adjusted to reduce the number of components conflicting, so that applications depending on workspace libs (such as KDevelop) would remain on the system also with P5 installed.

New acquisition: ThinkPad X220

Sun, 25 May 2014 19:15:10 +0000

Recently I was looking for a laptop: the previous one I had (an Asus EeePC 900) was almost dead (the fan broke, and the idea of dismantling everything to get to it wasn’t appealing).

When looking around, I had the following requirements:

It needed to run on Linux well. No exceptions.
_Portable: _ at home and at my workplace I have rather powerful machines, so a desktop replacement was not needed.

Notes to self: nginx Piwigo rewrite rules

Sat, 26 Apr 2014 08:31:57 +0000

This was inspired by this forum thread on the Piwigo forums. Set up rewrite rules in nginx where “piwigo” is the path the gallery lies in:

location @rewrite {
    rewrite ^/piwigo/picture((/|$).*)$ /piwigo/picture.php$1 last;
    rewrite ^/piwigo/index((/|$).*)$ /piwigo/index.php$1 last;
    # The following is needed for batch operations which use i.php
    rewrite ^/piwigo/i((/|$).*)$ /piwigo/i.php$1 last;
}

location /piwigo {
    index index.php;
    try_files $uri $uri/ @rewrite;
}

location ~ ^(?<script_name>.+?\.php)(?<path_info>/.*)?$ {
    try_files $script_name = 404;
    fastcgi_pass unix:/var/run/php-fpm/php-fpm.sock;
    fastcgi_param PATH_INFO $path_info;
    fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
    include fastcgi_params;
}

Lastly, add the relevant information to the Piwigo configuration (LocalFiles editor):

Unlocking KWallet with PAM

Fri, 25 Apr 2014 09:02:06 +0000

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

KDE:Current and 4.13 packages for openSUSE

Thu, 24 Apr 2014 20:35:47 +0000

This is a guest post by Raymond “tittiatcoke” Wooninck, with contributions from myself and Hrvoje “shumski” Senjan

In the next hours the KDE:Current repository will publish the latest release from KDE (4.13). As that this release comes with a big change (the new semantic search), we would like some simple steps in order to perform the right upgrade.

Before the upgrade
#

In order to migrate data automatically from the Nepomuk store to the new format, you will need Nepomuk up and running, and just for the time needed for the migration. Ensure that Nepomuk is running before the update (in System Settings > Desktop Search). This is only necessary in case Nepomuk is in use on the system.

Being Current

Mon, 31 Mar 2014 19:00:14 +0000

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

4.13 Beta 1 Workspaces, Platform and Applications for openSUSE: start the testing engines!

Fri, 07 Mar 2014 19:45:27 +0000

Yesterday KDE released their first beta of the upcoming 4.13 version of Workspaces, Applications and Development platform. As usual with the major releases from KDE, it’s packed with a lot of “good stuff”. Giving a list of all the improvements is daunting, however there are some key points that stand out:

Searching: KDE’s next generation semantic search is a prominent feature of this release. It’s several orders of magnitude faster, much leaner on memory and generally is a great improvement from the previous situation (this writer has been testing it for the past months and he’s absolutely delighted about it).

An expedition in the QML realm

Sat, 04 Jan 2014 08:03:18 +0000

Among the different widgets I use on my desktop, there is a small one which tells me my current public IP address. The reason I’m having it is due to the fact that my own ISP uses a NAT for almost all its customers (don’t ask - long story) and so I need to keep tabs on my current IP, because it may have been blacklisted, and so on.

Up to now I was using this plasmoid written in Python, but the code had several issues and used its own way of getting the public IP. However, I knew Plasma has already a way to give you your IP, that is the _geolocation _DataEngine. I thought of adjusting the current widget to use this engine, but then I thought “What if I make one in QML?”.

8 months with KDE and openSUSE - looking back after the 13.1 release

Mon, 25 Nov 2013 18:48:09 +0000

And so, finally openSUSE 13.1 is out of the door (I couldn’t celebrate like I wanted, as I’ve been very busy). This release has lots of improvements, and of course, the latest stable software from KDE. It is time (perhaps?) to look back and see what the team has done during this development cycle.

With regards to the KDE software packaging, the past 8 months have seen quite an increase in the involvement of poeple from the community. Aside the “usual suspects” like Raymond “tittiatcoke” Wooninck and Hrvoje “shumski” Senjan, we’ve seen offers from help from the Cloverleaf community (now folded into openSUSE) and in general an increase of non-SUSE contributions. Relationship with upstream has also improved, as a number of changes present in the packages were submitted directly to KDE (which is always a good thing).

KDE:Unstable:Playground is no more (or: adjustments in KDE repositories)

Sat, 02 Nov 2013 22:42:43 +0000

As you may know, there is an ongoing effort to rearrange and adjust the openSUSE KDE repositories. In line with the previously announced deletions, and more recent adjustments, a number of changes went into the organization and layout of the KDE repositories:

KDE:Distro:Factory and KDE:Release:4xy will now hold the “core” KDE packages: this means the base Development Platform, Workspaces and Applications, and additional applications for a basic desktop experience. Other, non-core packages have been moved to KDE:Extra

KDE in openSUSE: repository and maintainership changes!

Fri, 13 Sep 2013 05:37:09 +0000

Summer is ending soon (at least for those living in the northern hemisphere) and while usually cleaning is done during spring, the KDE team decided to do what I’d call… autumn cleaning of repositories.

You may know that the KDE presence in openSUSE, aside being the default desktop, is quite a long one. In the past years different repositories were created by the members of the openSUSE KDE team (at the time mostly made up by KDE people hired by Novell) in order to review and test packages, like newer Qt versions, KDE software, and so on. Fast forward to the present: nowadays the members of the KDE team are almost completely from the openSUSE community, and quite a number of changes went by the repositories as well. For example, newer releases of KDE software are submitted as maintenance updates for the latest available version of the distribution, and there are the KDE:Release:xy repositories for those who want the latest and greatest KDE software.

Qt5 on openSUSE (including experimental KF5 packages)

Tue, 06 Aug 2013 12:40:19 +0000

In the past few days, the openSUSE KDE team has been working hard, following the footsteps of the nice work done by the Kubuntu and Arch Linux communities, to provide Qt5 packages for the distribution. In fact, work was already done in the past, but the packages were not coinstallable with the existing Qt4 installation.

Thanks to a renewed effort, the OBS holds now Qt5 packages that won’t overwrite the existing Qt4 install: they currently live in the KDE:Qt51 repository (Factory and openSUSE 12.3) and they have been submitted to Factory itself, with the plan of having a full set of Qt5 packages for the next version of the distribution. PyQt5 was also packaged, for those who are interested in using Python with Qt.

Last round of testing: 4.11 RC2 packages for openSUSE

Tue, 30 Jul 2013 05:32:23 +0000

The latest release of the KDE Platform, Workspaces, and Applications (4.11) is around the corner: in fact, the last RC was recently made available. We’re almost there, but it doesn’t mean that testing and reporting should stop: on the contrary, it is needed even more to ensure that no bad bugs crawl up in the final release.

As part of this effort, openSUSE packages for RC2 have been released through the OBS, and are available in the KDE:Distro:Factory repository. Like always, please report upstream bugs to KDE directly, and use Novell’s Bugzilla for packaging or openSUSE specific issues.

KDE releases 4.11 RC1, and openSUSE packages follow!

Tue, 16 Jul 2013 21:30:11 +0000

The latest release from KDE moved from beta to RC stage, thus finding and reporting bugs is more important that ever. At the same time, the distribution packaging teams are also working in polishing their packages.

As far as openSUSE is concerned (not dissing other distros, just mentioning the one I’m involved in ;), you can kill two birds with one stone by installing the packages provided in the KDE:Distro:Factory repository. There are two kinds of issuses you need to report:

4.11 beta 2 openSUSE packages available

Mon, 01 Jul 2013 18:18:12 +0000

KDE released the second beta of the KDE Platform, Workspaces and Applications 4.11, and after the necessary time for the OBS to build packages from the released tarballs, packages are available for openSUSE 12.3 and openSUSE Factory. Like the previous beta, they are available through the KDE:Distro:Factory repository. 4.11.x is is targeted for inclusion in the upcoming openSUSE 13.1.

So far 4.11 has been pretty stable for me, but you should never forget these packages are for testing and bug reporting purposes: don’t use them on production systems. In case you find a bug:

4.11 beta 1 packages available for openSUSE 12.3

Mon, 17 Jun 2013 05:50:55 +0000

As a consequence of the recent changes in the repositories, the openSUSE KDE team is happy to announce the availability of packages containing the first beta of the KDE Platform, Workspaces and Applications 4.11.

Packages are available in the KDE:Distro:Factory repository. As it is beta software, it may have not-yet-discovered bugs, and its use is recommended only if you are willing to test packaging (reporting bugs to Novell’s bugzilla) or the software (reporting bugs directly to KDE). For specific queries on the 4.11 beta not related to specific openSUSE packaging, use the KDE Community Forums 4.11 Beta/RC area.

Upcoming changes to openSUSE KDE repositories

Fri, 14 Jun 2013 06:11:07 +0000

Since KDE has released the first beta of Platform, Workspaces, and Applications 4.11, there will be some changes in the packages offered in the openSUSE repositories.

In short:

KDE:Distro:Factory will now start tracking 4.11 betas and RCs: packages are being worked on. Use this version to test packages and to report bugs upstream.
KDE:Release:410 has been decoupled from KDE:Distro:Factory. If you were using 4.10 packages from KDF, you’re highly encouraged to move to this repository.
KDE:Unstable:SC will keep on carrying snapshots from KDE git repositories.

If you test the 4.11 packages, report bugs in the packaging (or openSUSE-specific functionality) to Novell’s bugzilla, and bugs in the software to bugs.kde.org. Also, please use the dedicated area on the KDE Community Forums to discuss issues.

KDE Platform Workspace, and Applications 4.10.4 for openSUSE

Thu, 06 Jun 2013 05:47:41 +0000

These posts kind of sound like a broken record, right? ;) Anyway, since KDE has released new versions of Platform, Workspaces and Applications as part of the stable release cycle, thanks to the OBS we have packages available for openSUSE 12.2 and 12.3. The 4.10.4 update will also be released as an official update for 12.3 in due time.

Where you can get the packages? Two places, as usual:

KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release;
KDE:Release:410 (openSUSE 12.3 or openSUSE 12.2) in case you just want to upgrade to the latest and greatest version

What to look forward to in this release? More than 50 bugs being fixed, including:

KDE Platform, Workspaces and Applications 4.10.3 for openSUSE

Tue, 07 May 2013 18:46:56 +0000

KDE released 4.10.3 versions of the Platform, Workspaces and Applications yesterday, with more than 70 bugs being fixed. Notably:

Several fixes in handling encrypted mails in KMail
Fixes for KDEPIM syncing and ownCloud
A number of improvements in Dolphin, including crash fixes
Optimizations in the Plasma Workspaces

[The full list](https://bugs.kde.org/buglist.cgi?query_format=advanced&bug_status=RESOLVED&bug_status=VERIFIED&bug_status=CLOSED&bugidtype=include&chfieldfrom=2013-01-01&chfieldto=Now&chfield=cf_versionfixedin&chfieldvalue=4.10.3&order=Bug Number&list_id=638034) has other important changes.

As usual, there are two different repositories from which you can get them:

KDE:Distro:Factory in case you are interested in contributing to packaging for the next openSUSE release;
KDE:Release:410 (openSUSE 12.3 or openSUSE 12.2) in case you just want to upgrade to the latest and greatest version

In case you upgrade now, you should be aware of an issue with KDM that makes it not start: thankfully there’s a workaround available, and updated packages are already being built by the OBS, so it will be solved soon.

Accessing Casio EX-WORD 電子辞書 from Linux

Wed, 01 May 2013 19:33:17 +0000

I’m a (happy!) owner of a Casio EX-WORD Dataplus 5 XD-A4700, a Japanese electronic dictionary. Recently I looked into updating the Japanese-English dictionary (currently the Shogakukan PROGRESSIVE dictionary) installed, because it’s not good enough: too often when looking up odd sentences (like the ones in Fate/Extra CCC) I do not find any matches.

EDICT is adequate, and while I can use it on my phone and tablet, I like the fact that the EX-WORD has a physical keyboard along with the stylus, and a very nice kanji handwriting recognition. After a bit of looking, I found the 5th Edition of the New Kenkyusha dictionary, offered as microSD card, to be what I needed (but a bit pricey, 10,500 yen on Amazon, and that’s heavily discounted!).

KDE Platform, Workspaces and Applications 4.10.2 packages available for openSUSE

Sat, 06 Apr 2013 16:04:13 +0000

KDE has released its monthly update for the 4.10 release, and after a brief wait while the Open Build Service worked over the released tarballs, the openSUSE KDE team is pleased to announce the availability of the 4.10.2 release packages for openSUSE 12.2 and 12.3.

Despite being a minor release, more than 100 bugs were fixed, in particular there were many KDEPIM fixes touching both the low level stack and KMail/KAddressbook/Kontact. Some highlights on the fixed issues:

KDE Platform, Workspaces and Applications 4.10 available for openSUSE

Wed, 06 Feb 2013 06:47:14 +0000

Hot on the heels of the announcement from KDE, the openSUSE KDE team is happy to announce the availability of packages for the latest stable release of the KDE Platform, Workspaces, and Applications.

Packages are available in the KDE:Distro:Factory repository (which is where the packages to land in 12.3 are tested) for openSUSE Factory (soon to be 12.3) and openSUSE 12.2 and soon (when the Open Build Systen finishes rebuilding a number of packages) in the KDE:Release:410 repository for openSUSE 12.2 users.

Package updates in openSUSE 12.3 KDE

Sat, 02 Feb 2013 13:46:30 +0000

During the discussions for the release of openSUSE 12.3, the topic of update notifications and applets was brought up again. Originally openSUSE shipped with a custom update applet, but since it was basically unmaintained, the decision was made to switch to Apper for openSUSE 12.2

The original Apper used in that version had a number of issues, which the upstream developer (Daniel Nicoletti) fixed in a newer version, which also had a lot of other improvments. However we originally couldn’t switch because it depended on a newer, API-incompatible version of PackageKit, meaning that the PK bindings for libzypp (the heart of openSUSE’s package management) needed to be adjusted and ported.

KDE Platform, Workspaces, Applications 4.10 RC3: openSUSE packages available

Sat, 19 Jan 2013 21:03:52 +0000

Following up on the announcement from KDE, the openSUSE KDE team is happy to announce the availability of 4.10 RC3 packages. Remember that they are packages meant for testing and reporting bugs, so that the next release will be as polished as possible.

You will find the packages in the KDE:Distro:Factory repository. An updated live media based on the upcoming openSUSE 12.3 (see previous post) is also available (files named KDE4-4.10.RC3) . The openSUSE 12.2 based version is also available (files named KDE Reloaded) at the same address.

Test the upcoming openSUSE 12.3 and KDE Workspace, Applications and Platform 4.10 RC2

Sun, 13 Jan 2013 13:38:45 +0000

Following up on my previous post, a different type of image has been made by the openSUSE KDE community members. In particular, alin has created images sporting the same software from KDE (4.10 RC2) but using the upcoming openSUSE 12.3 as base.

Download links:

32 bit version
64 bit version
Release directory (in case the above links go 404; the files are named KDE4-.4.10.RC2-Live)

These images are provided not only to test 4.10 in openSUSE, but also to test part of the distribution itself, without touching existing systems. Should you encounter a bug, please report it as follows:

KDE Workspaces and Applications 4.10 on live images courtesy of openSUSE

Thu, 10 Jan 2013 23:24:10 +0000

The 4.10 release for the KDE Development Platform, Workspaces and Applications is drawing nigh… as you may have read, there is now an additional release candidate in order to test some last-minute changes.

Of course, the KDE developers can only do so much: it’s impossible to test all possible combinations. That is, unless the community at large helps by finding and reporting issues the developers can fix. But doing so requires a 4.10 install. You can of course use packages from distributions, but you may not feel comfortable installing a prerelease on your system (and no one would blame you for that). Of course, if you had something to test without touching your own system…

Just finished - Kami Jigen Game Neptune V

Sun, 06 Jan 2013 13:12:14 +0000

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

Testing KScreen packages available for openSUSE

Thu, 27 Dec 2012 09:29:17 +0000

Yesterday Alex Fiestas showed on his blog a video of a recent development version of the KScreen library, created to handle easily multiple monitor setups in KDE, almost in an “automagic” way. As this is a project where configurations and setups are highly heterogeneous, a lot of testing is required to ensure things work reliably.

Of course, you cannot ask a developer to have all sorts of screen combinations, but remember one of the strengths of FOSS: “many eyes make bugs shallow”. And that’s why the KDE team prepared testing packages for KScreen for openSUSE users.

Systemd and KDE Workspaces in openSUSE 12.3

Sat, 15 Dec 2012 14:01:31 +0000

openSUSE is migrating to the use of systemd for the upcoming 12.3 version, given the difficulties that emerged in trying to co-maintain two different init systems (SysV + systemd). While I am not going into the details of this choice (I leave this to more informed people), this has some consequences for software higher in the stack.

As ConsoleKit is deprecated, systemd offers its own daemon to keep track of sessions and assigned seats in a system. However, the KDE Workspaces rely on ConsoleKit to handle user switching, reboot, shutdown and a lot of ther things. Removing ConsoleKit would mean that users would suffer feature loss. On the other hand, with something that’s been deprecated and no longer actively worked on, you have issues with maintenance.

4.10 Beta 2 packages available for openSUSE

Tue, 04 Dec 2012 19:17:48 +0000

The KDE community has just released Beta 2 of the upcoming 4.10 release of the Development Platform, Workspaces, and Applications. Of course, distributions are providing binary packages for the adventurous… and how could the green distro be left out?

In fact, it is not. Beta 2 packages were uploaded and built in the KDE:Distro:Factory repository. Updated packages have also been submitted to the development version of openSUSE (Factory) as the ultimate goal is having 4.10 in openSUSE 12.3.

Making KDE applications Python 3 friendly

Sun, 02 Dec 2012 18:00:57 +0000

When I’m not on forum duty or handling openSUSE-related contributions, I try to improve my code contributions to KDE, even though I’m by no means an experienced programmer (I program all day long in Python, but I’m still a biologist after all). For the upcoming 4.10 release I’ve been polishing up Python 3 support.

As you may know, Python 3 isn’t the standard in many distributions (Arch Linux excluded), but despite the slow start, it is slowly gaining steam. PyKDE4 was built keeping in mind Python 3 support, so theoretically we supported it right from the start.

New theme for KDE openSUSE 12.3 is now in!

Sun, 25 Nov 2012 08:30:30 +0000

Following up my earlier post, the new openSUSE 12.3 theme has finally landed into the official openSUSE repositories and will be part of the upcoming 12.3. A lot of work has gone into the new theme since I last posted about it, so this post will show how things look at the moment.

A few caveats:

The theme targets the 4.10 release of the KDE Workspaces, so it may be not be perfect under 4.9;
The default wallpaper has not been chosen yet.

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

openSUSE KDE Bug Squashing Days

Mon, 12 Nov 2012 19:52:04 +0000

Like everything, openSUSE is not perfect. Bugs crop here and there, or there is missing / quirky functionality that users may run into. Being a distribution of heterogeneous software, this means that bugs fall into these categories:

Upstream bugs in the software shipped by openSUSE
Bugs in the packaging
Bugs in distribution-specific setups or that derive from interactions with these setups (e.g. kernel, low level software stack, etc.)

To improve the distribution and to act like good FOSS citizens, distribution bugs need to be divided from upstream bugs: the former need to be properly fixed by openSUSE, the latter need to be communicated upstream so that everyone would benefit when they are fixed, including our favorite green distro.

What's cooking for KDE in openSUSE 12.3 - theming

Sun, 28 Oct 2012 13:04:20 +0000

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

Another story of a patch, or of bugs, investigation, and fixing

Sat, 29 Sep 2012 21:14:07 +0000

As others, bigger members in the KDE community say, “nobody will do it for you, and therefore they will”. The patch from the title comes from such a story.

Let’s give some background first: I’m really a heavy activity user, especially when working. My home PC has about five activities, my work one 3, and I managed to compartimentalize the various “topics” that each activity does pretty well.

After an update a couple of weeks ago from the latest code from KDE git, I started noticing weird behavior. Activities would not start when stopped, and there was no way of getting an application on a single activity. As I had set up KWin rules, that made things even worse.

Story of a patch, or: united we stand

Sat, 22 Sep 2012 20:26:44 +0000

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

Of Brainstorm, ideas and seeking help

Sun, 27 May 2012 16:01:28 +0000

Many of you know that KDE Brainstorm ideas aren’t posted straight away: they are always pre-screened to avoid repetitions, features that cannot be implemented technically, violations of the Code of Conduct, and so on. This is possible thanks to the work of the Idea Moderators, that patrol Brainstorm and evaluate the new ideas being posted.

Recently, a few of them got too busy and thus we’re experiencing a backlog of ideas staying in the Vault (the staging area for evaluation) for longer times than usual. The existing staff is already quite busy, so despite the efforts some deficencies still remain.

Want to make KDE Brainstorm more useful?

Sat, 31 Mar 2012 07:11:34 +0000

The recent post by Dario on the KDE Workspace Vision raised some concerns on why Brainstorm was not used. One commenter even said _Right now it feels like “Throw an idea over a wall for no-one but end users to discuss until it bitrot’s”. _

_
_

The Brainstorm section is indeed in need of help. To make it more useful, a couple of things are needed:

Statistics to evaluate which ideas are best representative: it can’t be just the number of votes per se as there are things like confirmation bias or controversies that may inflate the numbers
Integration with Bugzilla: a way to automatically (using XML-RPC) send the ideas flagged as representative to a bug report filed under “wishlist”. As it stands, the current forum team has not the time to carry out these tasks. But perhaps someone from the community can. If you thought you could not contribute because KDE was all about C++ and not about web languages, this is your chance to contribute: if you have PHP /HTML/web knowledge and want to help, hop on the #kde-www IRC channel and we’ll be happy to help you.

Some more Nepomuk, please

Sun, 12 Feb 2012 19:57:06 +0000

Recently we’ve seen several blog posts on Planet KDE related to Nepomuk. Reading those I thought that I could add some (little) semantic features to Danbooru Client.

Danbooru Client already makes use of Nepomuk: if enabled, tags extracted from Danbooru items are added as Nepomuk tags. But since at least some Danbooru boards are specialized in certain types of images (e.g., wallpapers only, for examples) I found it would be nice to have Nepomuk show me only the images that come from a specific Danbooru board.

Unexpected Christmas gifts: THE IDOLM@ASTER

Sun, 25 Dec 2011 20:04:26 +0000

Sometimes Christmas presents are really unexpected, and today I found out I was given one such gift: the limited edition of _THE IDOLM@STER 2, _PS3 version. It was quite a bulky box, showing all the main characters from the game (and from the recently-ended anime) (click to enlarge):

Of course, having such a box means that there’s a lot of stuff inside. In fact, once opened, there are two game BDs (one being the actual game, the second being the first volume of Gravure for you! starring Haruka), a soundtrack (no songs, though), a booklet, a number of postcards (mine were showing Iori’s ending from episode 2 of the TV series), a booklet and also the first BD of the anime version:

I'm honestly surprised...

Wed, 07 Dec 2011 20:49:13 +0000

By browsing through sites, I noticed that the Spanish site Akihabara Denno Gumi Universe has posted a translation of an interview the webmaster had with me through email.

Here it is (Spanish language). It feels nice to recall some memories of the past once in a while, especially since I couldn’t still believe that dennogumi.org had been such a resource back in the days…

Screensavers and the KDE Workspaces - your opinion is needed

Sun, 02 Oct 2011 11:26:37 +0000

Recently in the Plasma mailing list, KDE developers have discussed a new screen-locking implementation that could be added to the upcoming 4.8 release of the KDE Workspaces. The first reason to do so was to solve some security constraints of the existing implementation. As an added bonus, screen locking should be also more aestetically pleasing.

There is however a trade-off: such implementation would mean that screensavers that rely on X (also called X screensavers) would not be compatible. The current plan is to have a fallback mechanism if a user has a screen saver configured, and remove the support for X scrensavers entirely by 4.9. It is the intention of the developers to ultimately provide a way to make screensavers with QtQuick (QML) and in a way that they could be shared via GHNS (e.g., places like kde-look.org).

PyKDE4: Queries with Nepomuk

Wed, 29 Jun 2011 19:27:42 +0000

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

Access multiple Google Calendars from KOrganizer

Sat, 11 Jun 2011 10:06:29 +0000

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

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

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

Multiscale bootstrap clustering with Python and R

Sun, 29 May 2011 12:11:40 +0000

While reading the statistics for my blog, I noticed that a number of searches looked for hierarchical clustering with Python, which I covered quite a while ago. Today I’d like to present an updated version which uses more robust techniques.

A retrospective view: Galaxy Angel

Wed, 11 May 2011 20:33:16 +0000

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

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

Moving hosts!

Tue, 03 May 2011 20:48:49 +0000

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

I haven’t moved off a few services yet (including my primary mail), but I’m rather satisfied at the moment.

Taking video snapshots quickly: KDE VLC Snapper

Sun, 10 Apr 2011 12:40:26 +0000

Some of the oldest readers of this blog are well aware of a certain hobby of mine. Over the years I’ve always wanted to write more about that, including the stuff I’m viewing nowadays, but I found a hassle to collect snapshots from videos / DVDs, selecting them, and so on.

Recently I learnt that VLC has some rather complete Python bindings, and I thought, why not make the process automated? Yesterday I had some free time on my hands and a quick session of hacking brought some results already.

Improvements to the Git hooks

Wed, 26 Jan 2011 11:59:04 +0000

As you may already know, recently the KDE sysadmins completely overhauled the commit hooks used with the Git infrastructure. Written in Python, they have already brought significant improvements to the current workflows. These hooks include keywords that when specified trigger particular actions: the most used are to CC specific email addresses (CCMAIL), to CC bug reports (CCBUG) or to close bug reports (BUG).

With the adoption of Review Board to facilitate code reviews, there were also requests for a REVIEW keyword that could close the review requests without asking the submitters to do so manually (which is slow and not always effective). Since the hooks for Git were written in Python, I thought I could give a hand there.

PyKDE4: Retrieve data using KIO

Sat, 01 Jan 2011 21:09:26 +0000

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

In this post I’ll show how to use KIO to retrieve files from network resources using PyKDE4. The whole example is also available in the kdeexamples module.

PyKDE4: Tag and annotate files using Nepomuk

Tue, 26 Oct 2010 19:37:16 +0000

Some time has passed since I last blogged… this was not only due to lack of time but also due to motivation (writing long texts can be discouraging at times). In any case, I’d like to rectify for that. In this post, I’ll talk about Nepomuk, and in particular how to use it to tag and annotate arbitrary files using its API in PyKDE4.

Before starting, let me say that creating this tutorial was only possible thanks to the help of Sebastian Trueg, who helped me by pointing out some mistakes I was doing.

And so, it begins again...

Sat, 04 Sep 2010 04:50:45 +0000

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

What this might ever be?

Tue, 27 Jul 2010 22:41:14 +0000

The rest is up to you to figure out.

OCS and KDE Forums - work continues

Sun, 25 Jul 2010 18:49:22 +0000

With my last entry, I announced the start of the work for an OCS library for the KDE Community Forums. Today I’d like to blog again about the recent developments.

First of all, now there isn’t one, but two Python modules:

_ocslib, _ a pure Python module that can be used to interface with OCS-based forum systems;
ocslibkde, a PyKDE4 based module that can be used to interface with OCS-based forum system in KDE applications.

Currently ocslib supports reading and posting, while ocslibkde only reading (as of now). Both can be retrieved from the kde-forum-mods repository under the ocs-client subdirectory. The Python lib needs unit-testing, then I’ll be able to push a tarball soon for people to test (but you can always check out the Git repository). With regards to the PyKDE4 library, I plan on making a proof-of-concept plasmoid soon that shows how to use the API.

Open Collaboration Services and KDE Forums

Sun, 18 Jul 2010 10:00:39 +0000

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

A dedicated application would be usually much better than a browser, because you can work around the intrinsic limitations of the browser itself. The problem is that you can’t really access a forum with anything else than a browser. That is, it used to be like this, but now things are changing.

What's cooking at the KDE Community Forums?

Sat, 05 Jun 2010 11:56:51 +0000

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

Akademy: my own BoF

Sat, 29 May 2010 19:55:37 +0000

My Akademy talk proposal was not accepted, but the organizers were kind enough to offer me the chance to hold a BoF on the same subject. Now I bet you wonder on what I’m going to discuss, and I think the title already gives you an idea:

KDE and bioinformatics: the missing link

Although in the KDE community we have our fair share of scientists (hey there, Stuart!), my BoF will focus on the adoption of KDE in the field of bioinformatics (my day job, not-so-by-chance) on the “outsiders” front and how to improve the current situation. To elaborate further, bioinformatics is a rather broad field where biological data are treated with computational methods. The oldest and most famous branch of bioinformatics is sequence analysis and related field, where sequences of DNA are analyzed, for example, to find common ancestors among several species, or to reconstruct the genetic code of an organism by comparing it to a related species. Another recent example is related to high-throughput technologies, technologies which produce huge amounts of data from a very small number of experiments ("ultramassive sequencing" and DNA microarrays are examples of such a technology).

PyKDE4: new style signals and slots

Sat, 06 Mar 2010 08:04:48 +0000

Those who use PyQt and PyKDE4 are certainly familiar with the syntax used to connect signals and slots:

[python] from PyQt4 import QtCore from PyQt4 import QtGui from PyKDE4 import kdeui

class MyGUI(QtGui.QWidget):

def __init__(self, parent=None):
    super(MyGUI, self).__init__(parent)
    self.pushbutton = kdeui.KPushButton()
    self.pushbutton.setText("Push me!")
    
    QObject.connect(self.pushbutton, QtCore.SIGNAL("clicked()"), 
                           self.button_pushed)

def button_pushed(self):
    print "Button clicked"

[/python]

The main advantage of this syntax is that it’s very close to the C++ equivalent, and so you can translate easily from C++ to Python. Unfortunately the advantages of this syntax end here. The disadvantages, at least from a Python coding perspective, outweigh the advantages:

The world of KIO metadata - checking the HTTP response from a server

Thu, 18 Feb 2010 21:42:46 +0000

Recently, I investigated how to perform some checks on web addresses using KIO for Danbooru Client. My old code was synchronous, so it blocked the application while checking, thus causing all sort of troubles (UI freezing, etc.). Therefore, making the switch to KIO was the best solution. However, I had one problem: how could I check the HTTP response?

I knew already that the various ioslaves can store metadata, consisting of key-value pairs which are specific on the slave used. Normally you can get the whole map by accessing the metaData function of the job you have used, in the slot connected from the result signal. For some reason, however, in PyKDE4 calling metaData() triggers an assert in SIP, which ends in a crash (at least in my application; I stil need to debug further). KIO jobs have also the queryMetaData function, which returns the value of the key you have queried. Unfortunately, there was no way I could find the name.

Ar Tonelico III

Sat, 06 Feb 2010 21:33:20 +0000

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

Learning by example

Wed, 13 Jan 2010 21:37:38 +0000

With my brand-new SVN account, I just committed some code to kdeexamples, KDE’s example code module. In particular, I committed a simple example which shows how to use KConfigXT via PyKDE4, a simplified version of what I wrote about here.

As most of KDE is C++, and the Python API docs are translated directly from the C++ API docs, it is essential to have good examples to help newcomers learn faster. There are some PyKDE4 examples in the kdebindings module already, but I put mine in kdeexamples for a number of reasons:

Danbooru Client 0.5 is out

Sun, 27 Dec 2009 08:54:54 +0000

Sometimes answering apparently harmless questions on instant messaging can have unexpected results. In particular, I was telling about Danbooru Client to someone and a question popped up “Why don’t you support pages?”. It seemed a nice idea, so I branched off the code (yay for git!) and started working on it.

Well, it took me more than a month to get this thing done… I didn’t spend every day coding, but it was a challenge. Glad it’s over now, which means that Danbooru Client 0.5 is finally available. Grab it at the usual place on kde-apps.org.

Living on the edge

Mon, 07 Dec 2009 20:29:35 +0000

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

After a hiatus, Klassrooms continue!

Sun, 29 Nov 2009 22:25:34 +0000

Do you like KDE? Did you ever find yourself in a position of wanting to help, but you didn’t know what to do, or who to talk to? Do you feel you could use help to get started?

Today, the KDE Community Forums would like to provide the opportunity to answer those questions by annoucing the continuation of the tutorial courses known as Klassrooms.

What are Klassrooms?
#

Klassrooms are tutorial “lessons” held in a specific area of the forum. Held by one or more “mentors”, they are focused in guiding people through helping KDE by tackling a particular problem. Examples of such problems include:

KDE Marketing Sprint - Day 2(?)

Sat, 14 Nov 2009 23:26:28 +0000

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

Danbooru Client - a client for Danbooru based sites

Sun, 25 Oct 2009 20:16:50 +0000

A while ago I presented “danbooru2nepomuk”, a small program to tag images coming from Danbooru-based image boards. Today I want to present the evolution of that program, that is a PyKDE4 client for those boards.

HOWTO: KConfigXT with PyKDE4

Mon, 19 Oct 2009 21:43:10 +0000

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

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

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

danbooru2Nepomuk - a Nepomuk tagger for Danbooru images

Fri, 02 Oct 2009 20:25:00 +0000

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

Introducing KDialogue

Sun, 20 Sep 2009 18:46:22 +0000

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

Interesting plasmoid: Drop2Tag

Tue, 15 Sep 2009 20:06:59 +0000

While browsing around kde-look.org, I’ve stumbled upon a nice little Plasma scripted widget, and I’m publishing this to have it get more exposure.

A good part of the KDE community knows at least little about Nepomuk, and its ability to attach semantic tags to your files - basically words that describe the file, be it an image, a text document, or anything you’d like. For example, you could tag all the photos from your vacation with the name of the place you’ve been. After that, you can recall tagged files by accessing the nepomuksearch://hasTag:TAG_NAME url in Dolphin or Konqueror (there are more advanced uses, but I won’t cover them here), where TAG_NAME is your tag.

KDE Brainstorm Monthly (?) Digest - issue 3

Sun, 06 Sep 2009 19:46:55 +0000

Hello people! Yes, it’s been a while but I haven’t forgotten about it… with the Brainstorm’s new look and most technical issues resolved, I’m able to make Brainstorm Digests more often (hopefully!)

Issue 3 - Special summary issue
#

Since we have skipped a few months, what I’d like to present today (aside the usual data about the past month), is a general overview of the state of Brainstorm since the start of the initiative a while ago. Now we finally have data to draw some conclusions. But I’ll get to that at the end of the digest.

Holidays

Fri, 07 Aug 2009 13:18:08 +0000

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

See you on August 30th!

KDE 4.3 released - thanks to all developers!

Tue, 04 Aug 2009 18:33:40 +0000

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

Scripting languages and KDE

Mon, 03 Aug 2009 18:23:26 +0000

Up to now, the main language in which KDE applications are developed is C++. This is a perfectly valid choice: however, at least for users that don’t have a computing background (I include myself in the list: I do science) C++ can be a rather steep requirement (although Hans, fellow staff member at the KDE Community forums, is doing a nice job in explaining his learning experience).

Scripted language bindings (that have a lower barrier of entry) for KDE exist: on top of my memory I can list Python, Ruby, and C# (and I’ve probably missed a few). Despite that, the only official non-C++ programs that are in KDE’s SVN currently, including only what’s in the official modules, are system-config-printer-kde and printer-applet, which are written in PyKDE. This is quite striking to me, because the language bindings allow full access to the API in kdelibs, and thus allow the creation of applications with (theoretically) less effort on part of the writer. Yet, such applications, despite the bindings being rather mature, are lacking.

KDE Community Forums present the new KDE Brainstorm

Sun, 02 Aug 2009 21:40:17 +0000

The KDE Brainstorm, where users can post and vote for feature requests for KDE, is the most visited area of the KDE Community Forums. In an effort to improve the experience of both users and developers, the KDE Community Forums staff is proud to present a brand new version of the KDE Brainstorm.

The new interface resembles the IdeaTorrent sites, but it is still powered by the forum software (phpBB), a clear example of the flexibility of the platform. Posting new ideas, voting, commenting and filtering the lists is now extremely easy and requires just a few mouse clicks.

Camogli and Portofino

Sun, 19 Jul 2009 17:32:32 +0000

Yesterday I’ve been in Camogli and Portofino, two small towns in the eastern part of Liguria. The weather was nice and warm, and I took the opportunity of taking a few photos:

[singlepic id=328 w=320 h=240 float=]

[singlepic id=331 w=320 h=240 float=]

Those are samples, the rest are available in the gallery.

The next iteration of the Plasma FAQ - call for help

Sat, 11 Jul 2009 19:18:35 +0000

A few may know that I more or less maintain the Plasma FAQ page on KDE’s UserBase. Given the rapid advance of Plasma between KDE versions, each time a new version is out a new FAQ needs to be made, as the content rapidly becomes obsolete. For 4.3, unfortunately, I’m not sure I’ll be able to put a new version up in time for the 4.3 release.

The reason is mostly practical: it takes a bit of work to collect and add information, and currently my free time is limited due to a rather heavy workload and some other commitments. As UserBase is a wiki, I thought I could ask the KDE community at large if I could get some help in having a new version ready before release.

A brand new look for KDE Community forums

Sat, 27 Jun 2009 23:18:47 +0000

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

Tears to Tiara - Blu-Ray volume 1

Fri, 19 Jun 2009 19:57:08 +0000

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

DataMatrix 0.8 is finally out

Sat, 13 Jun 2009 13:29:40 +0000

At last, after months of inactivity, I pushed out a new release of DataMatrix. Although the version bump is small (0.8) there are a lot of changes since last releases. The most notable include:

Ability to apply functions to elements of the matrix
Ability to filter rows by column contents
Ability to transpose rows with columns
An option to load text files produced by R (which are, by design, broken)
Removed the getter for columns, using dictionary-like syntax directly
A lot of bug fixes

The download links on the project page have been updated, along with the documentation. Also, there is another change, because from now on the official Git repository is hosted on gitorious.org, and no longer on github, because gitorious (the software) is also free, while github.com’s is not. It’s mainly a philosophical issue (the same that prompted me to switch from twitter to identi.ca).

KDE Brainstorm Monthly Digest - issue 2

Sat, 30 May 2009 20:18:18 +0000

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

New, refactored System Settings

Fri, 01 May 2009 07:53:14 +0000

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

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

Amarok 2.1 beta in openSUSE

Tue, 28 Apr 2009 14:34:16 +0000

Currently, the openSUSE Build Service contains Amarok 2.1 beta packages only for the KDE:KDE4:UNSTABLE repository (i.e. current trunk, soon-to-be 4.3). However, a quick search identified a repository that contains a RPM of current 2.0.90 compiled for the KDE:KDE4:Factory Desktop (which will change to 4.3 with Beta 1) and another one for the KDE:42 repository. So you can add them using YaST or zypper and download the relevant package. I had to force a repository using zypper, otherwise zypper would complain and try to install amarok 1.4 from Packman…

KDE Brainstorm Monthly Digest - issue 1

Sat, 25 Apr 2009 07:02:01 +0000

Hello, and welcome to the first “issue” of the KDE Brainstorm monthly digest.

First of all, a few words of introduction. There are quite a number of ideas being posted on the KDE Brainstorm, and it would be nice to know how the initiative is faring, and important highlights, like what ideas are more popular, which are more controversial, etc. That is why the idea of a monthly digest was born (in a similar fashion as the fabolous Commit Digest). Our idea is to publish these digests monthly, providing the community (and perhaps even developers) with useful information about the state of the initiative.

First KDE Brainstorm idea implemented!

Sat, 04 Apr 2009 10:06:45 +0000

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

Gene search applet: suggestions and code review needed

Tue, 31 Mar 2009 17:33:09 +0000

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

KDE Brainstorm: after the launch

Sun, 22 Mar 2009 09:55:48 +0000

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

KDE Brainstorm is live!

Fri, 20 Mar 2009 20:02:59 +0000

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

I love poison

Wed, 18 Mar 2009 16:56:33 +0000

No, it’s not_ _a teen-like “I hate my life, I’m going to die tomorrow” post. I’m actually referring to the comments of a person nicknamed “I Love” that are popping up in almost all blogs that are linked to PlanetKDE which deal with Plasma or KDE4 adoption. The name “I Love” contrasts with an attitude that is unconstructive and rather trollish. This wouldn’t be such a big problem, if not for the fact that posts from said individual have had a rather negative effect: for example Aaron was forced to turn comment moderation on on his blog, Jos’ entry on the new Plasma in the upcoming KDE 4.3 was the theatre of a flame-fest in the comments, and now I’ve seen poisonous comments also on Nookie’s and Socceroos’ blogs.

Tears to Tiara in animation - faithful?

Tue, 17 Mar 2009 17:40:58 +0000

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

Bilbo Blogger

Tue, 17 Mar 2009 15:58:07 +0000

Mtux, of choqok fame, along with another person, has written Bilbo Blogger, a blogging utility for Blogger or any blog that supports Blogger1.0, MetaWeblog, and MovableType APIs (EDIT: also GData). It is based on the KDE4 libraries and it includes a WYSIWYG editor, an HTML editor, and a Post Preview function that can even fetch your blog’s CSS to render the entry and see how it looks.

It’s not released yet, but for the daring, you can actually try and compile it. You need to check out and install the blogging library (BlboKBlog) first:

Moving on

Fri, 27 Feb 2009 16:30:57 +0000

Some say that all good things must come to an end. I’m not entirely sure that this is a universal truth, but I can say that at some point in life there are decisions that need to be taken.

In this case I made my own: today was the last day in Dr.Cristina Battaglia’s laboratory, a place where I spent my three-year Ph.D. course and one year as a post-doc research fellow.

Science and KDE: kile

Sun, 22 Feb 2009 20:49:20 +0000

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

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

Science and KDE: rkward

Sat, 07 Feb 2009 18:55:53 +0000

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

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

Fishing for ideas

Sat, 31 Jan 2009 00:16:27 +0000

I have been thinking of doing another Kourse at the KDE Forums, similar to the one that has produced three nice screencasts.

My idea would be to show very brief and focused screencasts, a sort of “how do I…”. I have a few ideas, but I’d like to ask the KDE community at large. I’m mostly interested in showing single features (short videos), preferably of the “eye-opener” kind.

If you have any suggestions, leave a comment.

"The Answer"

Tue, 27 Jan 2009 21:08:49 +0000

Yes, I know I’m a bit late to the party (unfortunately today was one of the busiest days ever where I work), but I thought I’d join the other members of the KDE community, because KDE 4.2 has been released today.

Take a look at the visual guide, or see if your distribution has already packages for you. For your enquiries, the KDE Forums are at your disposal.

Hello Planet KDE

Sun, 25 Jan 2009 16:22:38 +0000

If everything has gone correctly, my blog should be on PlanetKDE now. That means it’s time for an introduction for those readers. My name is Luca Beltrame, I’m a biotechnologist doing bioinformatics in the life sciences areas, and I’m a Free Software user/enthusiast since many years.

I’ve been using KDE since 1.0 or so (if memory serves me well), but only recently, with the 4.x line of development, I’ve been trying to actually contribute a bit back to the project. Since I’m just a Python learner at the moment (I use Python a lot where I work, but it’s just text manipulation), I thought there were other areas I could contribute to. Currently, I maintain the Plasma FAQ, and I’ve been working together with Simon Edwards for some Python Plasma tutorials.

New Plasma with Python tutorials

Sat, 24 Jan 2009 11:09:36 +0000

I just finished writing a new Python tutorial on KDE’s Techbase. This one deals with writing DataEngines in Python (a complement to Simon Edwards’s own Using DataEngines).

Let me know what you think. As it’s a wiki, comments and suggestions are welcome.

Python Plasma tutorials on KDE Techbase

Tue, 20 Jan 2009 22:02:42 +0000

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

For anyone wanting to try these out: you need KDE 4.2 (currently RC 1), PyKDE4 and kdebase compiled with Python support (not the case of openSUSE at the moment).

Kurokami - The Animation - episode 1

Sun, 11 Jan 2009 11:06:13 +0000

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

Last Plasma screencast

Sat, 10 Jan 2009 21:09:17 +0000

It turned out I forgot to add the last screencast produced by the students of Kourse 2, so I’ll fix my mistake right now. Here’s Panel settings, by Kourse student TeaAge:

[blip.tv ?posts_id=1653914&dest=-1]

New theme and 2.7

Sat, 10 Jan 2009 21:02:59 +0000

As you have noticed, I have upgraded FailWordpress to version 2.7, getting also a new theme in the process. The header image is temporary, until I or someone else gets it fixed. The gallery has also changed: I ditched WPG2 and Gallery 2 because they kept on breaking every time I upgraded Wordpress (of course it’s probably Wordpress’s API and schema instability to blame).

Therefore, the gallery had been organized and most likely older posts won’t show images anymore (I’ll get to fix those eventually).

More Plasma screencasts

Thu, 08 Jan 2009 21:03:19 +0000

Students from Kourse 2 fengshaun and Primoz have prepared two nice screencasts, dealing with the Zooming User Interface (ZUI) and desktop settings respectively. Without further ado, here they are:

Zooming User Interface by fengshaun

[blip.tv ?posts_id=1648944&dest=-1]

Desktop settings by Primoz

[blip.tv ?posts_id=1646835&dest=-1]

As usual, both Free and non-Free versions are available. The students are also at work on subtitled versions, without the Notes plasmoid. I’ll be sure to post them once they’re done. Don’t forget to share these!

Published! (and it matters more)

Tue, 06 Jan 2009 17:39:39 +0000

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

It’s a bioinformatics paper;

Kourse 2 - First finished screencast

Mon, 05 Jan 2009 16:33:53 +0000

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

Why Plasma is the best thing since sliced bread

Mon, 29 Dec 2008 14:22:29 +0000

Today I was adjusting a bit the layouts of the Activities (as defined in Plasma) to better suit my workflows. To do so I was using the brand new Activity Bar which is present in KDE 4.2. It’s very neat, but takes up space on the desktop, and while it’s not a big deal on my main PC (1280x1024 resolution), it is an issue on my recently-resuscitated EeePC (1024x600).

It was then that it occured to me that such applets are, in Plasma-speak, PopupApplets, which means they adjust their behavior depending if they are in a panel or “free”. Also, I knew that Plasma had panel auto-hiding. 5 seconds later, I had a solution that fit my tastes, as this screenshot shows:

DataMatrix 0.7 has been released

Sat, 27 Dec 2008 15:33:07 +0000

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

As a nice way to break the hiatus, I’m releasing a new version of DataMatrix, my implementation of R’s data.frame in Python. Although the version bump is small, there are loads of improvements. First of all, there is proper support for file-like objects, as well as support for appending and inserting both rows and columns. writeMatrix has been substantially improved and now writes files correctly, and I have added (experimental) support for a DataMatrix object that does not require files - EmptyMatrix. Also, there is now proper documentation. Last but not least, unit tests have been added, a good way to watch out for regressions in the code.

The plague of cross-database annotations

Sun, 02 Nov 2008 14:15:20 +0000

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

Alternatives to Kubuntu for the Eee PC?

Wed, 22 Oct 2008 20:07:36 +0000

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

DataMatrix page up

Sun, 12 Oct 2008 20:14:14 +0000

Ok, ok… my definition of “tomorrow” is not like what most people use, apparently. Although I took quite a while, now there is a static page on DataMatrix. There you will find a summary of wht I wrote in my other blog posts regarding this module. Of course, it will be kept up-to-date should I release a new version.

Aside that, I put a contact form on this blog. It may be useful for reports that aren’t directly related to the posts.

Posting from KOrganizer

Sat, 20 Sep 2008 03:46:00 +0000

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

DataMatrix 0.5

Fri, 19 Sep 2008 19:54:58 +0000

At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax.

In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).

New PC, at last

Sat, 13 Sep 2008 21:24:35 +0000

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

I installed Linux on it, of course, but instead of Kubuntu I gave openSUSE a try. It’s quite polished, although I had to go through some hoops to enable font hinting, especially in Firefox (not that I use that browser a lot, but I still need it for some things). I’ll be keeping Kubuntu on the Eee, as there’s a larger community for customization.

I'm back

Wed, 27 Aug 2008 19:00:42 +0000

Sadly (for me) I’m back from the holidays. For those of you who wondered why the updates on Japan stopped: when I got back to Tokyo I didn’t have an Internet connection, so I had no means to update. The whole holiday was a blast, though, and we’re considering getting back in two years.

Aside from that, work has picked up a really fast pace immediately (why on Earth journals don’t accept LaTeX-produced PDFs?) and I expect a round of meetings and planning to start soon to plan the next three months. I had a poster accepted at the ECCB 2008 conference, but the steep fees (1200 euro for flight, registration and lodging) made me reconsider. Better luck next time, I guess.

Japan - Day 6

Fri, 08 Aug 2008 11:54:24 +0000

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

Japan - Day 5

Thu, 07 Aug 2008 12:51:28 +0000

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

Japan - Day 3 and 4

Thu, 07 Aug 2008 12:14:28 +0000

I was too tired to write an entry yesterday, so I’ll just sum things up here. Yesterday we went to Nikko, home of the Rinnoji Temple, the Toshogu Shrine and the Futarasan Shrine. We decided to visit it to see the tomb of Ieyasu Tokugawa. We took the Tobu Railways SPACIA train to Nikko then used a special pass I had bought beforehand online (the World Heritage Pass) to see the places. Nice nature and architecture, and I saw three large statues of Buddha (three BIG BUDDHA, right NRK?) in the Rinnoji temple. The Toshogu shrine was also magnificient, although the famous _Nemuri-neko _(sleeping cat) was extremely small, almost unnoticeable. Rain caught us in the afternoon so we went back to Tokyo.

Japan - Day 2

Mon, 04 Aug 2008 12:44:53 +0000

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

After that we moved to the Toshogu Shrine in Ueno Park, a shrine that was dedicated to the shogun Ieyasu Tokugawa. It’s not an “active” shrine anymore, but you can visit it for 200 yen. As the heat was killling us, we went back to Tokyo Station for lunch.

Japan - day 1

Sun, 03 Aug 2008 13:00:33 +0000

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

Once that was settled, we boarded the Japan Rail (JR) Narita Express and arrived in Tokyo. From there it was a matter of finding the right subway line to get to our hotel. Said hotel is pretty clean but rooms are quite small, and for two of us even a double room is small (not mentioning we have large luggages!). After some good sleep (we arrived at around 21.00), we spent the next day going to the East Gardens of the Imperial Palace.

Digital camera

Fri, 18 Jul 2008 18:28:04 +0000

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

Plasma - resizing and moving panels

Sun, 13 Jul 2008 20:34:01 +0000

Today I’m in a posting spree…This clip shows how to resize and move Plasma panels around.

[youtube]http://www.youtube.com/watch?v=Rmpv-S5JJI4[/youtube]

Plasma - creating a sidebar panel

Sun, 13 Jul 2008 12:15:59 +0000

Following up on my previous post, here is another screencast showing off how to create a sidebar panel and add a few plasmoids to it. As usual, the version on Youtube has annotations.

[youtube]http://www.youtube.com/watch?v=WPeFSDdt2PY[/youtube]

Plasma ZUI video

Tue, 08 Jul 2008 22:37:23 +0000

I’ve put together a small video that shows what you can do with zooming in and out with Plasma’s Zooming User Interface (ZUI). Enjoy. (note: the version on Youtube has also annotations that explain better what is going on)

[youtube]http://www.youtube.com/watch?v=EhODrJkoidA[/youtube]

If you can, please spread the link to the video. We need more correct information out there.

Spread the word!

Mon, 07 Jul 2008 19:47:08 +0000

Those of you that follow my Linux-related posts know that I work (along with others) on a FAQ trying to explain some magic behind KDE 4.x’s Plasma. Now, especially since on the Internet, there is the need to spread correct information (most of the naysayers are not quite informed).

So, if you want to help KDE, please spread the word on the Plasma FAQ! If people have questions on Plasma, just direct them to

Slayers Revolution - a comeback

Sun, 06 Jul 2008 09:24:00 +0000

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

Annoying fork talks

Sun, 29 Jun 2008 20:51:50 +0000

Now even the (once respected) Steven J. Vaughan-Nichols is jumping on the bandwagon of Plasma haters. With a rather uninformed and rant-ish entry that just advocates a fork, like some other people said on the kde-devel mailinglist a week or two ago.

The entry is rather dismissive of everything in KDE 4 save Plasma (and a mention on Dolphin’s single click icon), and also gets some facts and links wrong (yes, the Plasma web site is outdated, but since the developers are busy coding, someone else should step up and help). I wanted to point out a link to the Plasma FAQ, but apparently I can’t (I assume it’s because of my ISP, as usual).

data.frames in Python - DataMatrix

Sun, 29 Jun 2008 08:13:55 +0000

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

Commercial applications, public funding

Fri, 27 Jun 2008 20:15:10 +0000

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

Asus Eee PC here!

Sat, 07 Jun 2008 17:28:37 +0000

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

PM6-4 redux

Wed, 21 May 2008 19:31:57 +0000

(Note: I should really start posting more often nowadays)

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

FOSS and research

Sat, 10 May 2008 07:30:48 +0000

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

Wordpress SNAFU

Sun, 04 May 2008 07:35:07 +0000

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

The biggest issue was, however, the mangling of my .htaccess file due to a wrongly-generated permalink rule that was without a trailing slash (/). Such a badly done .htaccess would cause:

More novels

Sun, 04 May 2008 07:26:49 +0000

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

Ookami to koshinryo - DVD 1

Sat, 19 Apr 2008 13:10:47 +0000

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

Performance and R

Sat, 05 Apr 2008 13:12:18 +0000

I’m often wondering why people only resort to R when working with microarrays. I can understand that Bioconductor offers a plethora of different packages and that R’s statistical functions come in handy for many applications, but still, I think people underestimate the impact of performance.

R is not a performing language at all, it doesn’t parallelize well when using HPC (at least from the talks I’ve had with people studying the matter), and in general is a memory and resource hog. For example, it takes much more to perform RMA via R that with RMAExpress (which is a C++ application): the latter works also better with regards to memory utilization. I can understand the complexity of some statistical procedures, but what about ?

Eee PC interest

Sun, 30 Mar 2008 11:05:56 +0000

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

I’d like to get impressions on the Asus Eee, before considering a purchase (€ 300 are still a lot): did you try it? How was it? And if not Eee, are there other interesting alternatives?

Wordpress 2.5

Sun, 30 Mar 2008 09:21:13 +0000

I have upgraded this blog to Wordpress 2.5. As a result, there are some functions, such as the image gallery, that have been disabled due to the annoying habit of the Wordpress developers of making core changes in very little time.

Please report any problems you find, and notice that although the thumbnails look truncated in the new gallery, the full images are actually displayed correctly. I had to fiddle a bit wit the “new media manager”, not only because it’s in Flash, but because at least on Linux it gives odd results (apparently no one from the WP team bothered to check past Win and OSX?).

Back, and movies

Fri, 28 Mar 2008 14:14:45 +0000

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

Let’s resume from the hiatus by writing about my latest Final Fantasy XI session. Given that Square Enix didn’t release a lot of content for the recent Wings of the Goddess update, I did the few (four) quests in total in one day. Although the story was quite interesting, they were far too easy. I could have done them alone, probably. I wonder, what was the point of waiting four months for that? At least some form of challenge would be appreciated.

Follow up on meta-analysis

Thu, 28 Feb 2008 19:42:15 +0000

Fourteen days since my last post. Quite a while, indeed. Mostly I’ve been stumbled with work and some health related issues. Anyway, I thought I’d follow up on the meta analysis matter I discussed in my last post.

It turns out that it’s a fault of both limma and the data sets, because apparently the raw data found in the Stanford Microarray Database have different length, gene-wise (a result of not all spots on the array being good?) and limma itself does need equal length tables to form a single object (I stumbled upon the same problem when doing my thesis, but I used a hack to work around it), and does not perform any checking.

Meta analysis difficulty increasing

Thu, 14 Feb 2008 20:17:09 +0000

Again in the past days I’ve been banging my head thanks to the fact that doing meta-analysis with microarray data is more difficult than what it seems.

The problem sometimes lies in the data, sometimes lies in the analysis software and sometimes in a combination of factors. When doing work on a public data set (Zhao et al., 2005), I had to start analysis from raw data. Now, I tried using both the limma and marray Bioconductor packages, but both of them bail out with cryptic error messages. From what I’ve learnt by googling around, it seems that R doesn’t like batch loading of tables of different length.

people.complain()

Wed, 30 Jan 2008 07:13:11 +0000

To me nowadays reading KDE Dot News is a bother. Not because of the news, which are always high quality, but the comments leave a lot to be desired.

Let’s take for example the recent news about Nokia buying Trolltech: 99% of the comments talk doom and gloom. This is not bad per se, but most of them bring absolutely nothing to the discussion. Truth is, it’s too early to say, so we’ll have to wait and see. It’s not like something like this happens overnight.

Browser-less entries

Sun, 27 Jan 2008 17:27:11 +0000

From today on I’ll try to write posts without a browser, since I’m not that fond of such an approach. As a matter of fact, I’m using kblogger now, a blogging application for KDE 4 (I didn’t mention that I switched to that full time, more on that when I get time).

If you notice something odd in the way the posts are written, please let me know. Thanks.

Okami to Koshinryo, episode 1

Sun, 20 Jan 2008 09:57:28 +0000

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

FFXI-URUSHI-Chaos: 01-02-03

Sun, 20 Jan 2008 09:24:39 +0000

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

Ph.D.!

Mon, 14 Jan 2008 15:07:57 +0000

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

In any case, I’m happy that it’s over, as the past period has been rather hectic. No time to rest now as I’ve got papers to write and more analyses to do!

Be free.

Fri, 11 Jan 2008 18:39:34 +0000

The word is official: KDE 4.0.0 has been released. Make sure to check out the Dot story, or the nicely done visual guide. And if you’re new to Plasma, have a look at the FAQ as well.

Congratulations to all the KDE developers, translators, and coordinators for pushing forward our favorite desktop environment. Rock on!

KDE 4.0.0 tagging

Fri, 04 Jan 2008 20:46:10 +0000

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

QSql vs DB-API?

Fri, 28 Dec 2007 12:58:40 +0000

I’ve recently begun trying to create GUIs for my Python applications with PyQt, and I can say I’m absolutely loving the toolkit, relatively easy to use and featureful. As I’m trying to create a GUI for some module I wrote that deals with databases (using MySQLdb), I also learnt that Qt has a series of classes for dealing with databases, mainly QSql.

My question, directed to whoever has experience with QSql and the Python DB-API, is: what are the advantages of one approach to the other? I’m leaning towards DB-API because like that I can create modules which work also in command line applications.

Brain drain

Sat, 22 Dec 2007 11:53:26 +0000

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

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

Plasma FAQ

Wed, 19 Dec 2007 22:57:50 +0000

I’ve started working on a FAQ related to Plasma, in order to ease the transition for the early adopters of Plasma when KDE 4.0 is released. That, coupled with another idea I had (offering video tutorials of operations) should make the gap smaller.

Currently the FAQ is a work in progress (still a lot of TODOs, I hope to have a look after Friday as I’m really busy now) and resides in KDE’s TechBase until a more suitable solution is found. If you think you can help, feel free to contribute!

Publishing idiocy

Sun, 16 Dec 2007 22:26:34 +0000

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

Wings of the Goddess "opening"

Sat, 15 Dec 2007 12:39:23 +0000

Despite the utter lack of content in Wings of the Goddess my brother has managed to create a movie clip (inspired by the opening of Wild ARMs The Vth Vanguard). You can view it below (streaming) or obtain a higher quality version.

[googlevideo]http://video.google.com/videoplay?docid=8316261647217076877[/googlevideo]

(apologies for the lack of updates. I’ve been quite busy. I will probably post more in during the Christmas holidays)

Dancer... dancing

Sun, 02 Dec 2007 09:09:19 +0000

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

Wings of the Goddess - first impressions

Fri, 30 Nov 2007 20:24:02 +0000

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

Lamestop

Sun, 25 Nov 2007 18:13:42 +0000

The title clearly shows what I think about the aforementioned company. The reason surfaced a few days ago, when I tried to see if they would ship Wings of the Goddess to Italy. I had ordered from them a few times before, and although their customer service left a lot to be desired, I couldn’t complain much.

Two days ago I found that they will no longer ship anything to Italy. I mean, they will to other European countries, but not here. The big question here is why? What has Italy possibly done? I contacted their customer support and I just got a rather uninformative answer such as “we do not ship or take orders from your country”. Very nice, Gamestop.

Cavernous Maws

Tue, 20 Nov 2007 20:25:57 +0000

With the new version update, these strange portals have been appearing throughout Vana’diel. They’re supposedly the gateways to the past, but since I don’t have Wings of the Goddess yet I can’t really see what will they do. Nevertheless, I was curious and went to take a look at them.

They’re **huge. **I estimate at least twice the height of my character. For those curious, here are two photos (one is of my brother’s character, the other is mine):

Final Fantasy XI windowed mode

Tue, 20 Nov 2007 07:45:05 +0000

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

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

Wings of the Goddess - the details emerge

Sat, 17 Nov 2007 07:18:50 +0000

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

Gene identifiers

Thu, 15 Nov 2007 19:57:16 +0000

While working today on an annotation class in Python I stumbled on a problem. Normally I work with lists of genes that are consistent, i.e. all Entrez Gene IDs (or RefSeq IDs, or Genome Browser IDs…), but today I had a list of mixed identifiers.

The subsequent idea was “let’s implement auto-detection of common identifiers in the class”. The problem is… is there any actual documentation on how identifiers are made? So far, using regular expressions, I’ve tracked down a few:

Blast from the past: Akihabara Denno Gumi PataPi!

Sun, 11 Nov 2007 21:30:43 +0000

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

Data clustering with Python

Wed, 07 Nov 2007 18:15:29 +0000

**Notice:**Just now I realized this has been linked to to a Stack Overflow question. I recently wrote a new post that uses a different technique and a combination of R and Python. Check it out!

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

Buggy bioinformatics software

Wed, 07 Nov 2007 14:43:52 +0000

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

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

Opinion on the KDE Krush day

Sun, 04 Nov 2007 18:15:53 +0000

Yesterday I spent some of my free time to help with the KDE 4.0 Krush Day. Unfortunately, I did a lot less than what I was supposed to do, mainly because at some point the home directory ran out of space (I forgot to remove qt-copy object files), then I inadvertently removed some of the directories and I had to re-sync with SVN.

Nevertheless, it was interesting and nice to be able to contribute even if you don’t speak C++. I reported a crash in Gwenview, and some problems regarding the use of authentication with IO-slaves. I also confirmed a few other issues some others raised.

KDE 4.0 bug squashing day!

Thu, 01 Nov 2007 14:14:29 +0000

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

Thesis completed

Sat, 27 Oct 2007 15:24:28 +0000

My supervisor has given me an OK for my thesis (save for a couple of cosmetic changes), therefore now I have just to wait for the verdict of the Ph.D. council then fill in some paperwork: the next step is the defense, sometime in January.

After that I’ll probably put my thesis online and post a few articles on the concept of group testing for microarray data.

New sport, Plasma bashing

Thu, 25 Oct 2007 08:10:30 +0000

First of all let me make some disclaimers :

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

As you may know, KDE 4.0 Beta 3 was released a while ago. With it came the usual number of criticisms, some sensible, a lot of others not. Most of the latter fell into the category of “it’s an alpha, not a beta” and “Plasma sucks”. Well, one can ignore most of them since they rarely provide anything constructive.

My experience with KDE4, part 2

Wed, 24 Oct 2007 19:51:40 +0000

I obviously did not want to stop with a single compile of KDE4, therefore I’m updating more or less randomly my build off the SVN to check what has been changing.

The first and most important change since my last post was the addition of the K-menu in the taskbar: Kickoff was moved from playground (where it resided) to kdebase. Also, kate now works perfectly, and is already usable as a full-blown text editor.

My KDE4 impression

Sat, 20 Oct 2007 21:18:58 +0000

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

Script to make captures of movie files

Tue, 16 Oct 2007 20:44:46 +0000

The other day I was thinking about how to make screencaps for the anime I watch. Windows users often use Media Player Classic, which can create a video contact sheet (i.e., a series of captures) out of a movie file. I had two problems with this:

The biggest is that it runs on Windows, and I don’t use Windows;
The frames needed to be manually cropped every time, which was slow.

Clannad 1

Sun, 14 Oct 2007 13:48:17 +0000

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

Prism Ark 1

Sat, 13 Oct 2007 15:52:34 +0000

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

Blogging scholarships!?

Fri, 12 Oct 2007 20:29:41 +0000

I just read from Weblog Tools Collection that CollegeScholarships.org is hosting a vote for a round of $10,000 blogging scholarships. Now, I may be a little out of the “Web 2.0” trend (actually for me “2.0” does not relate to Tim O’Reilly’s buzzword, but to real and interesting technologies like the Semantic Web), but I find this absurd.

I mean, I have no doubts that the people listed there have made interesting blogs. But I would rather give a scholarship based on merit rather than the mere act of blogging something “interesting”. Don’t get me wrong, blogging can be fun and has its uses (see scientific blogging) but for heaven’s sake, this is a little overboard.

New theme

Thu, 11 Oct 2007 21:13:36 +0000

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

SOFT file woes

Tue, 09 Oct 2007 20:00:23 +0000

Today I started working on a data set published on GEO. As the sample data were somehow inconsistent (they mentioned 23 controls when I found 28), I decided to parse the SOFT file from GEO in order to get the exact sample information.

I did a grave mistake. First of all, Biopython’s SOFT parser is horribly broken (doesn’t work at all) and quite undocumented: I could work around the lack of documentation (API docs) but not with the fact that it wouldn’t work. So I turned to R, which offers a GEO query module through Bioconductor.

Unimpressive management: Wordpress 2.3

Sun, 07 Oct 2007 19:01:33 +0000

I’ve recently upgraded this blog to Wordpress 2.3. While I’m interested in the new changes this release brings (like tagging support) I question the way the transition to the new version was handled.

In particular, I am referring to the (questionable) idea of breaking the database schema three weeks before the release. Given the amount of breakage that brought upon plugins, it should have been announced at the start of the 2.3 development cycle. Right now, heavily customized installations are a pain to update (that’s why The S.T.E.A.L. Saga is staying on 2.2 for now).

Easy RMA: RMAExpress

Thu, 04 Oct 2007 21:17:56 +0000

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

Gutsy Gibbon Beta

Mon, 01 Oct 2007 20:11:58 +0000

After some thought, I’ve joined the fray and installed the beta version of Kubuntu 7.10 (Gutsy Gibbon) on one of my computers. It hasn’t too recent hardware (AMD Thunderbird 2100+, 512 Mb RAM and a motherboard with a Nforce 2 chipset), and it is my test system for distributions.

It ran Feisty Fawn, so I tried to use the upgrader tool, which crashed when removing unsupported packages. Oh well, it was a beta, so nothing to worry about (the only worry was that it didn’t output anything at all). I then tried dist-upgrading and again the process failed due to file ownership conflicts: I solved that with some fiddling, but again nothing to worry about too much.

The Internet lynch mob

Fri, 28 Sep 2007 19:13:39 +0000

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

An update

Wed, 26 Sep 2007 19:40:40 +0000

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

Not all’s lost. I plan writing a few posts in the next days, one regarding the recent release of Wordpress 2.3 and another on the Nanoha StrikerS DVDs.

New Wings of the Goddess trailer

Sat, 22 Sep 2007 07:49:45 +0000

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

The tower of Babel of bioinformatics

Wed, 19 Sep 2007 19:26:22 +0000

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

Idiocy at its maximum

Mon, 17 Sep 2007 18:49:03 +0000

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

Treasures of Aht Urghan Mission 44

Sun, 16 Sep 2007 20:00:43 +0000

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

New office

Tue, 11 Sep 2007 18:30:09 +0000

After little more than a year, I’ve been moved to a new office, because new people needed to be put in the room I was in. The new place is slightly bigger (four desks instead of six) and for now quieter. I spent most of the morning fixing things and setting up network connections. This is how it looks now:

Of course these distractions took time away from my thesis, but I’ve still managed to write a part of the last section, the discussion. I still have a long way to go before finishing, though.

Treasures of Aht Urghan Mission 42

Fri, 07 Sep 2007 19:05:44 +0000

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

Science and Microsoft Word

Sat, 01 Sep 2007 12:45:57 +0000

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

Saber Revoltech figure

Wed, 29 Aug 2007 20:05:26 +0000

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

Holidays

Thu, 02 Aug 2007 06:28:09 +0000

I haven’t been able to post much recently, mostly because I’ve been quite busy regarding my thesis and work and because I’m preparing everything for the holidays. I’ll be leaving on August 3rd for Rome, and after a week’s stay, I’ll go to the sea until August 26th. Unfortunately I’ll have to bring my work with me to do something as I’m a little behind in writing the thesis.

Due to the holidays, I won’t be able to update here regularly (if any), however I’ll try to post one last entry before leaving.

Nanoha StrikerS DVD 1

Fri, 27 Jul 2007 20:00:47 +0000

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

Why KDE?

Sat, 21 Jul 2007 10:08:35 +0000

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

Who said Windows works better?

Fri, 20 Jul 2007 19:36:04 +0000

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

Of course I tried everything I could, of course. It was very frustrating to reboot every time to test (probably due to the large hack called Registry) and of course not being able to get it working. Google searches did not get conclusive information, perhaps a BIOS bug or a firmware bug. On Linux, it’s just a matter of using

New details on WoTG

Sun, 15 Jul 2007 08:56:43 +0000

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

Among the other things mentioned, new jobs (I wonder if the usual people will start already complaining about “they suck for endgame! Boo hoo!”), a global adjustment of all the other classes (I’m hoping on an adjustment of Ninja as a subjob, probably the most abused subjob ever) and eve a hint on Tanaka’s new MMORPG, which is apparently still top secret.

Full speed ahead

Thu, 12 Jul 2007 19:20:55 +0000

After giving in the summary of my thesis today, I also started writing the actual thing. Of course this is not something I will finish in a few days. It’s a long journey that will go on until I deliver it.

Aside that, I’ve been having some problems with R, a language which I really don’t like and I hope to use as less as possible. I was obtaining a list of differentially expressed genes (DEGs) out of some data files with SAM, and of course I had to supply a matrix with expression values for every gene.

/ borked (again)

Sun, 08 Jul 2007 11:03:21 +0000

Looks like my laptop doesn’t really want to keep its data in stable form. Like I have blogged previously, the bus-reset issue apparently trashed my root partition again. I do not know the cause as it seemed a normal shutdown… but the moment I rebooted I had lost a lot of files (thankfully not on /home: I’m glad I keep data separated from the rest).

Reinstalling proved less difficult, thanks to a Kubuntu DVD I burnt with my other computer. However, I still had to tinker manually because of read errors (notice that this seems to be an issue with my DVD-ROM, rather than with the DVD itself). When those were unrecoverable, I manually changed the temporary sources.list to point to Internet mirrors and all was well.

Command line scanning

Wed, 04 Jul 2007 21:26:31 +0000

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

Instead, I found that scanimage sends its results to standard output, and also that ImageMagick can accept standard input as source file, it was easy to convert on the fly:

Nanoha licensed for the USA

Sat, 30 Jun 2007 18:26:00 +0000

According to the Anime News Network, Geneon Entertainment has bought the license for distributing Maho Shojo Lyrical Nanoha and Nanoha A’s in the United States.

Fans rejoice? I think not. Being outside of the USA market, I view things with a different approach. The companies here in Italy have all their problems, but to a certain degree they care about delivering to the user something more than just the episodes. Extras that can also be an incentive over downloading (illegally) over the Internet.

Transformers

Sat, 30 Jun 2007 10:16:20 +0000

Looks like NRK beat me to it, but I’ve seen this film myself yesterday night.

To be frank, I wasn’t really expecting a nice result. That is, because most Hollywood “conversions” from other franchises often end up being terrible (Street Fighter, anyone?). Nevertheless, having watched the animated series when I was little (it was good, despite some shortcomings), I was set on seeing Transformers since its original announcement.

Despite not being related to the TV series, I found it to be rather good. The various CG effects for the robots are really well done, especially since they’re quite integrated with the rest of the scenes. I recognized the most famous robots (Megatron, Starscream, Optimus Prime, Bumblebee) but some others not, mainly because the Italian version used different names.

Publish or perish

Mon, 25 Jun 2007 17:57:45 +0000

The idea to blog about this common phenomenon came after I read a post over at Bioinformatics Zen on the matter of open science. There, Mike describes the situation quite clearly: mostly, you need a middle ground between complete secrecy and absolute openness.

That said, I still think science should be more open, at least in the field of life sciences. Publication should be a way to let others know, benefit and also build upon your work, not just a way to obtain funding or improve one’s career. The last two motives aren’t bad per se, but recently the philosophy of “publish or perish” is getting to an extreme.

A trip to the sea

Sun, 24 Jun 2007 10:18:52 +0000

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

Data handling

Wed, 20 Jun 2007 17:50:39 +0000

As the people who read my science related posts already know, I’m in the middle of doing meta-analysis. That brought up a problem, so to speak, and it’s related to annotations.

ToAU Mission 35 - take 2

Sat, 16 Jun 2007 08:00:35 +0000

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

Einherjar

Thu, 14 Jun 2007 20:56:36 +0000

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

Aht Urghan Mission 35 - take 1

Mon, 11 Jun 2007 19:38:03 +0000

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

A small project

Mon, 04 Jun 2007 19:59:56 +0000

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

Dancougar Nova DVD 1

Sat, 02 Jun 2007 15:46:03 +0000

477

Yesterday I got the first DVD of Dancougar Nova in the mail. As it’s a first press edition, there were two nice postcards inside (one of the Dancougar itself, one of Aoi) and the cover is reversible, again showing either the mech or Aoi (the one shown in this post, which is also available in the gallery).

So what has changed from the TV version? As far as I can tell, not much as the first two episodes were the ones with the best animation (along with episode 12) , though the DVD cover mentions something changed in episode 2. What is noticeable is the huge jump in image quality, the pictures are much better than the TV version, and also the format switched to anamorphic 16:9. UPDATE: The changes aren’t that trivial at all, there is a whole new part that explans how Sakuya gets his communication device to contact the Dragon’s Hive.

Underrated anime: The Skull Man

Sat, 02 Jun 2007 13:49:46 +0000

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

/ borked

Thu, 31 May 2007 19:29:11 +0000

The title will already give an idea of what happened to my laptop two days ago. Due to a bus problem and a forced reboot, my root partition got corrupted. Luckily no data was lost as I keep /usr and /home separated from the rest. However reinstalling proved to be a very difficult task.

First of all, my DVD drive has some problems, and so it wouldn’t read the Kubuntu Feisty install disk I had brought from work. I tried then using a thumb drive but no luck, this buggy BIOS does not allow USB boot. I then copied the disk over to a DVD-RW I had, following my brother’s suggestion. So I was able to boot.

More meta-analysis difficulty

Mon, 28 May 2007 19:27:29 +0000

UPDATE: Today I found out that J Brooks (the corresponding author of Zhao’s paper) has agreed to send the data I needed. Thanks a lot!

When you do bioinformatics, you often test your own procedures not only on your data, but also on datasets provided by other people and publicly available. As I stated previously, that’s what meta-analysis is. I’m doing a bit of that for my thesis and recently I noticed that some datasets, while being public, are far from complete.

Lifeless people

Sat, 26 May 2007 16:27:49 +0000

When starting a run in Dynamis-Beaucedine, some person in charge of my brother’s Dynamis linkshell stated that over a whole Dynamis run (approximately four hours) you should not leave or be away. This statement is misguided at best, and personally I found it rather offensive for a series of reasons:

Not everyone is in the same timezone: if you have other commitments that force you to stay away for a longer period (such as meals with other people) you should not be blamed for it, after all real life takes serious precedence over gaming;

tab2dokuwiki

Thu, 24 May 2007 18:16:18 +0000

Today I made a simple sed script that converts a tab-delimited text file to a format that can be pasted into a DokuWiki wiki. There is a plugin that permits to read CSV files directly, however:

It doesn’t support tab-delimited text files;
It’s incompatible with some plugins (one being DokuTexit, which I need).

Hence the need for this script. To use it, just copy and paste the code (see below) into a new file, make it executable (chmod +x) and then invoke it with

Hardware upgrades

Mon, 21 May 2007 22:07:21 +0000

At work I’ve recently got hold of two nice hardware upgrades: a portable 60 Gb HD (useful for carrying around large data) and an 80 Gb hard disk. The latter was much needed as the 40 Gb HD inside my Acer Veriton 7500G was getting rather small, both on the Windows side (which sadly I still need to use for some things) and on the Linux side (at one point / filled up, resulting in a system that would not log into X at all).I already made backups and moved the data, installing a fresh copy of Kubuntu 7.04 on the new HD. This means I’ll be able to keep my laptop at home and avoid largely nerdish settings such as this:

Thesis work and wikis

Fri, 18 May 2007 20:29:53 +0000

I’ve been able to complete most of the analysis for my Ph.D. thesis work, at last. I need a few runs more but I am arranging to work at a location of one of our research partners, as I don’t have a powerful enough computer to handle the calculations (apparently, 1Gb of RAM isn’t enough). At least the results I have look promising. Now all it’s left (and that’s not an easy task, heh). is to write them down in the “thesis summary” (deadline: June 30th) and then in the thesis itself. I’m already studying a bit on the topic and papers are quickly piling up on my desk.

Final Fantasy XI - Wings of the Goddess

Sat, 12 May 2007 09:38:02 +0000

I did not expect it, but today Square Enix announced a new expansion for Final Fantasy XI, called Wings of the Goddess (but I like the Japanese title - something along the line of The Holy Warriors of Altana - more). There’s also a trailer available on the main PlayOnline page.

From what I can see it looks like a time-warp expansion, set back in time in the Crystal War, but the images are scarce. It’s been announced for Winter 2007, I’ll see how it will be. I hope it’s not like Treasures of Aht Urghan, which was a disappointment all along.

Useful command line tips

Sun, 06 May 2007 08:40:21 +0000

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

Nanoha StrikerS 4-5

Sat, 05 May 2007 07:15:09 +0000

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

Enough with the negativity

Tue, 01 May 2007 11:16:24 +0000

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

I’ll say it again, people had unrealistic expectations. KDE 4 is a big step ahead than previous versions, and first of all a new foundation was needed. A large part of the improvements is under the hood (think about Solid or Phonon, for example). Plasma, as far as I can see, was not immune from that. Solid bases had to be built before moving forward. Thanks to that paradigm, there are already interesting results such as the new krunner. But there’s still (according to a glance on the KDE Techbase) a lot of work on the user-invisible parts to be done.

Databases

Wed, 25 Apr 2007 14:26:07 +0000

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

Nanoha StrikerS 2-3

Sun, 22 Apr 2007 20:44:50 +0000

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

Kubuntu 7.04

Sun, 22 Apr 2007 07:03:09 +0000

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

One man, one lame ideology

Sat, 21 Apr 2007 21:17:24 +0000

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

Python usefulness

Sat, 21 Apr 2007 07:45:05 +0000

I’ve again seen how useful and powerful Python can be. The other day I had to prepare an Excel spreadsheet (sadly) which among other things needed to contain links to the GeneCards database for each gene listed. There were more than 2900 genes listed, so adding links by hand would have been suicidal.

That’s when Python, through its Windows extensions, comes into play. First of all I created a module for COM objects using the makepy utility. Then it was a matter of importing the right modules and initialize the COM object:

Big anime mash-up

Wed, 18 Apr 2007 20:03:14 +0000

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

Bioinformatics != sequence analysis

Sat, 14 Apr 2007 07:55:45 +0000

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

lolTribe

Thu, 12 Apr 2007 16:14:31 +0000

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

Romeo x Juliet 1

Fri, 06 Apr 2007 20:49:06 +0000

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

Idolm@ster XENOGLOSSIA 1

Fri, 06 Apr 2007 15:17:24 +0000

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

Nanoha StrikerS episode 1

Mon, 02 Apr 2007 20:01:53 +0000

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

Playing with Feisty Fawn

Fri, 30 Mar 2007 21:02:15 +0000

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

GenBUGG

Thu, 29 Mar 2007 19:29:42 +0000

This entry already shows what I think of a popular open source pathway analysis and visualization program, GenMAPP. It’s quite used to map gene expression data coming from microarrays to metabolic pathways, and in addition to that you can also evaluate enrichment for both pathways and Gene Ontology terms. Last but not least you can create and contribute new metabolic maps.

So why the title of the post? Because, despite being actively developed and with conscious developers that don’t want to break the software with new features, it’s extremely buggy. Yesterday I spent a whole afternoon trying to get it to work. The program doesn’t work if you use the comma as the decimal separator OS-wide, or some applications crash completely if your regional settings (sadly it’s a Windows only program) aren’t set to USA. What’s worse is that such a “feature” has been reported two years ago. I can understand the limited resources and all, but please, those are really basic bugs. It’s not as bad as software “fit for publication”, but still a massive annoyance…

Treasures of Aht Urghan Missions

Fri, 23 Mar 2007 21:27:23 +0000

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

When you call a GM...

Mon, 19 Mar 2007 21:24:31 +0000

You usually don’t expect them to actually appear. Today, after a call made by my brother, was different…

Relic armor on mannequins is stupid

Sat, 17 Mar 2007 18:46:59 +0000

A lot of times when doing Dynamis it happens that people lot for a particular piece of relic armor then when asking about the stats I see responses like “It’s crap” or something similar. This brings the question: why do you want it in the first place? To put it on a mannequin to show off? There **is no use_ _**for relic armor unless worn. So, next time you make a lot, do the others a favor, save it for pieces you really want and let people who want to use the blasted things go first. At least they want to use it, and not just show off.

Dancougar Nova 4

Wed, 14 Mar 2007 21:47:10 +0000

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

A BED file builder

Tue, 13 Mar 2007 20:00:17 +0000

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

A change

Tue, 13 Mar 2007 18:10:57 +0000

Just something different, for a change. I got up this morning and on one of my windows I saw this:

(for the record, those are my two cats, Minou on the left and Matisse on the right)

Old code

Mon, 12 Mar 2007 20:03:05 +0000

Today I went over my old Python code, back when I first started programming. I’d say that I found what I had written to be largely amusing to say the least. Loads of ugly hacks all over the place, duplicated functions, etc… in short, a real mess.

I’m quite happy of the results I achieved in the past month, since I finally learnt how to code properly and started making my own classes (this book was immensely helpful). I hope I improve enough to be able to make a package for what I’ve made, as there is a distinct lack of annotation tools for microarray data in Python (Bioconductor steals the spotlight for everything, but I can’t stand R).

Oxygen

Fri, 09 Mar 2007 21:46:59 +0000

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

Dancougar Nova 3

Fri, 09 Mar 2007 21:04:16 +0000

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

Fear of change

Mon, 05 Mar 2007 19:51:55 +0000

A recent article on dotKDE caused really a stir and a rather long (more than 430 comments!) debate. What is the reason? The decision to use the [Dolphin file manager](The Road to KDE 4: Dolphin and Konqueror) instead of Konqueror as default file manager.

I found myself rather surprised at such a reaction. After all, Dolphin and Konqueror will share much of the code base (which means that they will improve both) and Konqueror won’t be removed and will be available as default file manager through configuration. It sounds like a safe choice for me, however people didn’t like it that much apparently.

Deadlines and domains

Thu, 01 Mar 2007 21:13:43 +0000

I just learnt today that the paper I’m writing with my colleague has to be in an acceptable state (almost submission ready) by the 20th. Considering I’m still behind with the analysis, it will be certainly challenging to complete the task, considering I also have other duties to attend to. In primis I need to study more and more papers (I add more and more to my TODO list).

Also, probably next week the new infrastructure for authentication (which includes a Primary Domain Controller for Windows clients) will be put in place and I’ll have to make sure that the data handling for our group will be without problems. So far I have used a simple MS-DOS script to copy over data from the Affymetrix scanner to a network drive, but I’ll need something slightly more sophisticated for the new system (since data will have to be copied in two different places), including email notifications for certain events.

Thoughts

Thu, 01 Mar 2007 21:06:32 +0000

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

A lot of work

Sun, 25 Feb 2007 21:57:24 +0000

Work is getting hectic as we’re finally gathering a lot of data for a new publication. This means reading a lot of literature, choosing the figures and planning results and discussion properly. On top of that, I’m starting to study pathway analysis for my thesis, and of course, seeing how I can use that to study our own data.

I also have some other non research duties to attend to, such as being the person repsonsible for data handling of our group in relation to the server that we bought recently, I need to learn more Python and do some more administrative tasks on our computers (such as upgrading a few Windows 2000 installations to Windows XP). In short, everything will become hectic rather soon… I’m sure it will get pretty interesting from now on.

Dancougar Nova 2

Sat, 24 Feb 2007 11:31:12 +0000

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

Richard M. Stallman is disgusting

Sat, 17 Feb 2007 21:08:09 +0000

No, I’m not talking about his looks. I’m talking about him being morally disgusting. The reason? The fact that he went to Cuba and convinced them to switch to FOSS. You may want to know, why is that a bad thing?

Easy answer: Cuba isn’t a democracy. Think what you want, blame the United States for the embargo how much you like, but you won’t be able to hide the fact that it is a totalitarian, oppressive regime. You can get arrested just by expressing dissent, or by promoting ideas that aren’t what the government wants.

Dancougar Nova

Fri, 16 Feb 2007 21:24:01 +0000

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

Two days in Firenze

Sun, 11 Feb 2007 09:05:10 +0000

I’ve just came back from a two days’ trip in Firenze. On the first day we had a long (4.30 hours) meeting on some interesting research topics, such as cellular aging and about oxidative damage in yeast.

On the second day I attended part of a workshop on pathway analysis and related topics. Many speakers were from the NuGO project funded by the European Community, but the talks were still quite general. Several tools were presented, some look interesting (EU.GENE) while others seem less useful at least for a research environment (mostly commercial software, but I think I’ll go into more detail in a separate entry).

A day with an Apple Xserve

Sat, 03 Feb 2007 14:19:18 +0000

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

There are no movies

Tue, 30 Jan 2007 07:37:50 +0000

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

In short, if you have come here to get movies, or music files, you won’t find them. If you want to know the reason, check the About page. I will probably have to put up custom pages to people looking for those files…

Wordpress 2.1

Mon, 29 Jan 2007 07:44:59 +0000

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

At last!

Thu, 25 Jan 2007 20:40:53 +0000

I’m pretty happy. As some of you already know, the book I wrote with my brother is finally out. The preview copies I had ordered arrived yesterday, and I can see it’s pretty impressive to hold the book you have written with your own hands:

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It only needed a couple of adjustments in the drawings’ captions, so I made it available for everyone last night. All I need to do now is to wait and see the reactions…

Playstation 3

Sun, 21 Jan 2007 00:19:27 +0000

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

Editing work

Sun, 14 Jan 2007 15:53:19 +0000

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

Yes, plenty of S.T.E.A.L. related work going on. It’s understandable though, as the release time getting near…

A newbie approach to GUIs

Sat, 06 Jan 2007 10:13:08 +0000

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

Mai-Otome Zwei

Fri, 05 Jan 2007 20:41:24 +0000

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

Checker mark III

Wed, 03 Jan 2007 22:05:47 +0000

Reading Wesley J. Chun’s excellent Core Python Programming I realized I could definitely improve my wallpaper checker, at least internally. That’s what I did today, and aside that, I added an option to view a thumbnail of the images contained in the lists. Note that it is not meant to be an image viewer, just a way to show the images in the list (and I suggest you filter it first if it’s long). The image viewing part is my first try with Tkinter, the Python module to create interfaces using Tk. It’s ugly looking, but at least it works.

Mai-Otome

Mon, 01 Jan 2007 01:09:45 +0000

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

Improved wallpaper checker

Sun, 31 Dec 2006 13:55:25 +0000

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

Nanoha StrikerS... Nanoha?

Fri, 29 Dec 2006 14:29:45 +0000

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

Relic 4/5

Thu, 28 Dec 2006 14:10:03 +0000

On the day after Christmas I went to do Dynamis-Beaucedine with United. I had to be the main assist for this run, and surprisingly everything went well. Not only that, the run had really **loads_ _**of drops (including a 100 currency piece), as the relevant thread says. Most importantly, I finally obtained the Valor Breeches. I had never seen them drop in Beaucedine Glacier, and luckily I was the only one lotting (I managed to lot of the ridicolously low amount of 172). All that’s left now is the super-rare Valor Surcoat, and having a Xarcabard run on 2nd of January I will put all my bets on that one. Of course, there is now the obligatory screenshot:

Wallpaper size checker

Sat, 23 Dec 2006 10:42:21 +0000

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

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

Update disappointment

Sat, 16 Dec 2006 08:35:21 +0000

I noticed recently that Square Enix has announced a new event in FFXI, namely Salvage. Apparently this looks like an Assault with other modifications (such as special conditions forced on the players) thrown in.

To me, this is a huge disappointment, as I expected more integration in the extremely fragmented ToAU landscape. Everything looks incomplete, and adding another incomplete part will not cut it. Not to mention that the only rewards are items… items that can only be used with the “regular” activities. Unlike the other expansions, everything seems loose and without a clear goal. I wish they’d stop adding half-baked features and focus on providing more for each update instead.

Final Fantasy XII

Wed, 13 Dec 2006 21:26:15 +0000

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

Working with Genome Browser data

Wed, 13 Dec 2006 21:13:59 +0000

In the past two days I’ve been tackling an annotation problem. I’m trying to provide annotations for genes found in regions that are significantly altered, DNA copy-number wise (thanks to the STAC method). The idea would be to annotate those regions (that span one megabase) using UCSC Table Browser.

However, the task was impractical, so I decided to automate it a bit. I converted the data into ranges and then used the KnownGene annotation file (downloaded from UCSC) to obtain which genes were in which reagion. The last part wasn’t easy at all (at least in Python), as I had to check for ranges and adjust for consecutive regions. The code is terribly ugly, so I’ll try to clean it up before posting it.

GRUB hell

Sat, 09 Dec 2006 08:57:15 +0000

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

Actually, that part of the installation went fine, but once rebooted I got “error 21”, which meant “disk not found”. Looking around in the Ubuntu bug tracker showed that GRUB did not support the JMicron SATA controller of the motherboard (I put the disk there by mistake, instead that on the ICH8 controller). Well, I wanted to remove GRUB, and that’s where problems started to arise.

Zealotry

Thu, 07 Dec 2006 11:49:58 +0000

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

Probably useless, but...

Fri, 01 Dec 2006 20:07:36 +0000

A post I wrote ended up on the front page of nodalpoint.org. I liked that, even though it may not seem a lot to many: at least it shows that some of my concerns are shared with other people in the scientific community.

Also after viewing some presentations about Web 2.0 at the EMBL, I decided to make a del.icio.us account. I find it quite handy so far to organize bookmarks and such.

Obtained: Gallant surcoat+1.

Mon, 27 Nov 2006 21:23:34 +0000

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

New heading and other stuff

Sat, 25 Nov 2006 09:09:30 +0000

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

A simple annotator

Sat, 25 Nov 2006 09:06:10 +0000

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

Random photos

Fri, 17 Nov 2006 19:06:31 +0000

Since recently (thanks to my brother) I got a new cellular phone with better capabilities, photo-wise, I decided to take a few photos of my workplace. I changed office a while ago, now I’m located on the first floor of the building, sharing the office with 5 other people: Raoul, Michele, Giorgio, Roberta and Alessandro. This photo shows my current computer setup:

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Quant was running a screensaver when I took this photo: the mouse pad and that other black thing next to the keyboard are gel pads to help me with my tendinitis. The other picture I took today shows part of my “study area”:

More studying

Wed, 15 Nov 2006 09:31:20 +0000

EURASIP Journal on Bioinformatics and Systems Biology is having a special issue on text mining for biology. My boss wants to publish something there, and asked if I and a colleague could work on that. I’ll probably focus on evaluation methods, since I’m not an expert in text mining or language processing.

And that’s where the problem comes in: I know almost nothing on text mining. Which means this will add up to the ever growing pile of papers and books I have to study, including but not limited to Python programming, microarray analysis and XML…

The joy of meta-analysis

Fri, 10 Nov 2006 22:04:54 +0000

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

PhD students

Tue, 07 Nov 2006 18:11:48 +0000

After discussing my second PhD year today, and after noticing that not even a single professor from the commitee was there (save my boss and a person that joined later on), I realized that the situation for students like me isn’t really the best.

A PhD program is supposed (at least here) to be a cross between a research job and a student’s position, since you should study but at the same time conduct research and (if you’re lucky) also get paid for it. But actually (and it’s really depressing), professors just “use” the students as cheap labor. Yes, cheap because they don’t pay for them, the ministry does. Who cares if they don’t follow courses, don’t go to conferences, miss presentations… All it matters is that they can do their research, only to be replaced when the three year program ends. It is really lame.

New computer

Fri, 03 Nov 2006 20:25:28 +0000

Wednesday I got around to assemble a replacement for largo, what used to be my old “main” desktop. I also got a new case and power supply for leon, the other desktop I own, but I need to switch things around from the “old” largo to leon and I didn’t have the time yet.

Without any more delay, here are the specifications:

Pentium Core 2 Duo 6600
NVIDIA GeForce 7950GT

Software and biology

Thu, 02 Nov 2006 20:19:16 +0000

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

ToAU Mission 22

Sat, 28 Oct 2006 07:30:23 +0000

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

Text files with Python

Mon, 23 Oct 2006 20:32:58 +0000

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

Kubuntu Edgy

Fri, 20 Oct 2006 20:06:20 +0000

I’ve upgraded both leon (one of my computers at home) and quant (my work machine) to Kubuntu Edgy Eft (now in Release Candidate status, screenshots here). Leon’s upgrade went perfectly, while quant gave me some headaches. First of all there was a conflict between packages, then the nvidia module for legacy hardware wouldn’t load:

$ modprobe nvidia_legacy

FATAL: Module nv not found.

In the end I manually compiled the nvidia module, and had to insert it via insmod or it would give out a cryptic error message (“error running install for module nvidia”). I think most of the headaches are coming out because I was using a custom kernel and because I dist-upgraded to a still unstable distribution. In any case, I’m quite pleased so far with Edgy, and once it becomes official I’ll put it on my laptop as well.

More S.T.E.A.L. related work

Sun, 15 Oct 2006 10:20:27 +0000

I haven’t had much time to write here as I’ve been busy fixing and arranging things for the web page on S.T.E.A.L. It appears that thanks to Too’s deviation posting and subsequent journal entry, hits have skyrocketed. This makes me happy but it also means more work and need for refinement. As a matter of fact, I wrote a little more yesterday, and today I’ll be aiming to complete chapter 4. Since I’ve been working on that for the past 3 years, it would be a nice accomplishment.

My first real Python program

Wed, 11 Oct 2006 20:59:34 +0000

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

S.T.E.A.L. cover!

Mon, 09 Oct 2006 20:41:32 +0000

Just minutes ago I got a MSN message from Too, stating that the cover for the novel had been completed! Of course, I downloaded it eagerly…

Novels! Novels! Novels!

Sun, 08 Oct 2006 19:39:08 +0000

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

Dutch weekend

Wed, 04 Oct 2006 20:03:19 +0000

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.

Valkyrie Profile Silmeria

Wed, 04 Oct 2006 19:51:29 +0000

I recently obtained a copy of Valkyrie Profile Silmeria in a language that I can understand. I’ve been playing it for a while and I can say I like it.

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The graphics look nice, but I don’t understand why tri-Ace made a fake 2D perspective. In my opinion it makes all that 3D look rather useless, since there’s little you can do depth-wise. The same can be said for the battles: while you can move around in 3D, the perspective shifts in 2D when you attack (in a manner similar to the original Valkyrie Profile). The soundtrack by Motoi Sakuraba is nice as always, especially battle music.

A disappointment: Galaxy Angel II

Wed, 04 Oct 2006 19:23:46 +0000

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

Valor Gauntlets!

Mon, 02 Oct 2006 16:18:21 +0000

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

On Free Software and FSF

Thu, 28 Sep 2006 19:36:24 +0000

WARNING: This entry is somewhat political in nature.

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

Cooperation and stupidity

Sun, 24 Sep 2006 08:36:25 +0000

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

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.

Kubuntu Edgy Knot 3 artwork

Thu, 21 Sep 2006 19:03:50 +0000

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

On unrelated news, I still have got some RSI issues, so I’ll have to slow down posting. Bah.

Another S.T.E.A.L. snapshot

Sun, 17 Sep 2006 16:49:22 +0000

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.

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.

S.T.E.A.L. related news

Sat, 16 Sep 2006 16:53:11 +0000

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):

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ATI drivers and Linux

Sat, 16 Sep 2006 07:58:45 +0000

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

Annotations and Linux

Wed, 13 Sep 2006 17:27:58 +0000

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

Kile 1.9.2 for Dapper

Sun, 10 Sep 2006 09:09:29 +0000

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

Dynamis-Buburimu

Thu, 07 Sep 2006 22:05:19 +0000

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

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

The Black Coffin and merits

Mon, 04 Sep 2006 20:22:47 +0000

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).

New kernel

Sun, 03 Sep 2006 15:57:07 +0000

[code]lb@hardin:~$ uname -a Linux hardin 2.6.17-emission7 [/code]

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

S.T.E.A.L. snapshot released

Wed, 30 Aug 2006 21:11:56 +0000

As promised, I put up a new snapshot of S.T.E.A.L. (available here) 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;

I'm back

Tue, 29 Aug 2006 08:52:45 +0000

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 earlier this year). It may be what I need to perform some comparison analysis between different kinds of tumor samples.

Holidays

Fri, 04 Aug 2006 09:43:56 +0000

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

As “parting gift” I uploaded a new snapshot of S.T.E.A.L., which includes Too’s fantastic art. Take a look, I hope you appreciate it. As usual, comments are welcome!

Departure

Wed, 02 Aug 2006 17:54:25 +0000

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.

Computational Biology... biology?

Sat, 29 Jul 2006 08:29:08 +0000

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). The development in this field can be regarded as quite astounding, just a look at journals like BMC Bioinformatics, Bioinformatics or others can give an insight of that.

However, and talks at Bertinoro seemed to confirm this impression, it looks like that many in the computational field forget that we’re talking about biology. 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.

Perspectives

Fri, 28 Jul 2006 17:44:40 +0000

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. 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 for it and so far it’s going OK.

I'm still alive

Thu, 27 Jul 2006 21:15:45 +0000

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.

Clarification

Mon, 24 Jul 2006 12:37:35 +0000

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).

RSI

Fri, 21 Jul 2006 21:36:08 +0000

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.

Under Observation

Mon, 17 Jul 2006 21:42:12 +0000

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.

Additions and changes

Mon, 17 Jul 2006 17:52:35 +0000

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.

Finally!

Fri, 14 Jul 2006 22:50:47 +0000

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, 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, I have the first set of seven pictures I commissioned (out of nine)!

New happenings on Asura

Mon, 10 Jul 2006 19:29:04 +0000

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.

The power of the shell

Sat, 08 Jul 2006 08:16:30 +0000

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.

Image editing using FOSS tools

Sun, 02 Jul 2006 17:07:52 +0000

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.

Widget fun

Sat, 01 Jul 2006 21:11:35 +0000

As you may have noticed the theme and the layout changed slightly. I updated the Regulus theme to the newest version, making it widget-enabled and improving the overall layout. That means I can customize my own sidebar as I please without coding using the so-called Widgets, and that’s why it changed. The only problem is that the gallery now looks a little fuzzy, but it’s ok for my tastes.

Kubuntu Dapper arrived

Sat, 01 Jul 2006 10:17:33 +0000

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Yesterday when I went at work I found an envelope coming from Canonical. Inside, there were the five Kubuntu 6.06 “Dapper Drake” LTS CDs I ordered from Shipit. Those are Live CDs that will run Kubuntu without any needs for installing (though I’d have preferred real install CDs).

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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 are perhaps better suited for this). I plan on testing one of these today or tomorrow, to see how they perform on certain hardware.

Image editing

Sun, 25 Jun 2006 16:44:46 +0000

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.

Implosion

Sun, 25 Jun 2006 11:25:53 +0000

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.

Upgrade

Tue, 20 Jun 2006 17:51:34 +0000

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).

Busy busy busy!

Sat, 17 Jun 2006 14:52:49 +0000

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.

Books

Fri, 16 Jun 2006 16:47:53 +0000

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.

The gods themselves

Thu, 08 Jun 2006 17:21:25 +0000

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:

Classes and meetings

Thu, 08 Jun 2006 17:02:33 +0000

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) 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.

The problem with binary only drivers

Sat, 03 Jun 2006 20:04:38 +0000

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.

Kubuntu 6.06 LTS / Dynamis-Xarcabard

Fri, 02 Jun 2006 08:52:51 +0000

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

dist-upgrade fun, DNS, drama

Sun, 28 May 2006 10:37:09 +0000

Yesterday I updated my laptop to Kubuntu Dapper RC. Overall the (long) process was quite smooth save a couple of problems (the use of NetworkManager for exaple, that caused me headaches to make wireless work) including the fact that the ATI drivers were looking in the wrong location (/usr/X11/lib/modules/dri instead of /usr/lib/dri) so 3D acceleration wasn’t working.

It seems smooth so far, though I think the idea of NetworkManager needs polishing, as some services that are started before it connects will fail (such as autofs).

Biological software and HIG

Thu, 25 May 2006 15:37:18 +0000

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

Xolotl Xtrapolator

Sat, 20 May 2006 11:00:35 +0000

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:

Antispam, or inconvenience?

Sat, 20 May 2006 10:32:36 +0000

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.

Stress

Wed, 17 May 2006 17:54:11 +0000

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.

Security breach

Mon, 08 May 2006 20:17:29 +0000

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).

Continuous analysis

Fri, 05 May 2006 19:33:24 +0000

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.

Ubuntu games

Mon, 01 May 2006 13:42:52 +0000

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).

Treasures of Aht Urghan

Sun, 30 Apr 2006 13:30:50 +0000

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);

Cursing

Mon, 24 Apr 2006 11:52:49 +0000

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).

Sickness

Sat, 22 Apr 2006 07:16:10 +0000

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.

Outage

Mon, 10 Apr 2006 21:32:32 +0000

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.

Orz!

Mon, 10 Apr 2006 21:28:07 +0000

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).

Windows and Missions

Thu, 06 Apr 2006 22:13:28 +0000

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).

Upgrades

Sat, 01 Apr 2006 12:35:12 +0000

I’ve upgraded the theme (now it uses a non-hacked version of Regulus), the image gallery with the new Gallery v2.1, and also the new WPG 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.

Mixed entry (yet again)

Thu, 30 Mar 2006 21:56:31 +0000

I haven’t been writing on this blog as much as I wanted, partly because of tiredness, partly because of my always-present tiredness.

Today I delivered the receipts from the Bertinoro school and also from Trieste: I hope I get a refund fairly quickly (although usually “fairly quickly” means around 3-4 months if I’m lucky). Also, these days I’m working on the DNAcopy package from Bioconductor (a series of add-on packages for R) to see if I can use the data from Affymetrix’s Chromosome Copy Number Analysis Tool to get a genome-wide view on copy number aberrations (CNAT only permits you to see one chromosome at a time). 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.

Bertinoro - Day 4

Wed, 22 Mar 2006 21:03:57 +0000

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.

Bertinoro - Day 3

Tue, 21 Mar 2006 22:06:22 +0000

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.

Bertinoro - Day 2

Mon, 20 Mar 2006 20:33:34 +0000

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.

Bertinoro - Arrival & Day 1

Sun, 19 Mar 2006 17:57:54 +0000

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

Random entry

Thu, 16 Mar 2006 18:17:25 +0000

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 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.

Trento, March 7th-8th

Sat, 11 Mar 2006 11:40:02 +0000

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.

Migrating

Sun, 05 Mar 2006 17:44:51 +0000

I’ve been migrating settings and files from the old router to the new one (check my brother’s blog to understand better what I’m talking about). I noticed the free space already dropped significantly, as you can see from this:

[code]

lb@hari:~$ df -h

Filesystem Size Used Avail Use% Mounted on

/dev/hda1 9,2G 859M 7,9G 10% /

tmpfs 43M 0 43M 0% /dev/shm tmpfs 43M 13M 30M 30%

/lib/modules/2.6.12-10-386/volatile

/dev/hda6 83G 8,5G 70G 11% /home

It lives! (part 2)

Thu, 02 Mar 2006 23:17:38 +0000

I’m very happy to write that I got a second drawing from firekitty! I liked the first one but I like the second one better. Now I’m just waiting for too 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.

Bertinoro di Romagna

Tue, 28 Feb 2006 22:24:05 +0000

After sorting out the bureaucracy, finally I was able to enroll for the 6th Course in Bioinformatics for Molecular Biologists that will take place in Bertinoro di Romagna in three weeks. I’m glad I was able to, the course program looks really interesting and perhaps I’ll be finally able to learn bioinformatics in the right way, since so far I’m entirely self-taught, and sadly, it shows.

On another topic, the ceiling is going to be fixed by tomorrow, I hope, so I’ll be able to get back to my old office at last.

Ceiling

Tue, 21 Feb 2006 23:45:07 +0000

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…

Valor Coronet! Relic armor 1/5

Tue, 21 Feb 2006 23:30:58 +0000

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.

Rain

Sun, 19 Feb 2006 19:19:10 +0000

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

general/desktop.jpg

I also tried to update my old Mandriva 2006.0 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.

Opo-opos and Hyppogriphs

Fri, 17 Feb 2006 23:06:24 +0000

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.

Fate/stay night #06

Wed, 15 Feb 2006 18:30:36 +0000

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.

Wordpress 2.0.1

Mon, 13 Feb 2006 22:05:40 +0000

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.

Webcam on Linux, success!

Sun, 12 Feb 2006 14:10:20 +0000

general/webcam_work.jpg

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

New S.T.E.A.L. snapshot

Sat, 11 Feb 2006 11:52:33 +0000

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.

It lives!

Wed, 08 Feb 2006 17:09:45 +0000

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!

Woes of a scientist

Mon, 06 Feb 2006 22:55:18 +0000

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:

All-in-one entry

Sun, 05 Feb 2006 17:47:05 +0000

First of all, the strangest oddity ever. On Friday once at the laboratory I was contacted by an Affymetrix representative regarding this entry . 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.

Knightly Earring

Wed, 01 Feb 2006 22:27:30 +0000

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 (my target) dropped, and also the Heavy Lance. Heavy Lance will go to one of our dragoons, I’ll inform the linkshell’s council soon.

Clarissa's birthday

Mon, 30 Jan 2006 22:33:48 +0000

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.

More about S.T.E.A.L.

Sun, 29 Jan 2006 15:22:46 +0000

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.

Badly written software, or policy?

Thu, 26 Jan 2006 20:40:09 +0000

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

Of life and pets

Wed, 25 Jan 2006 18:19:20 +0000

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.

The end of Wild ARMs 4

Wed, 25 Jan 2006 18:12:23 +0000

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…

Wild ARMs 4

Sun, 22 Jan 2006 10:37:37 +0000

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.

Office, take 2

Fri, 20 Jan 2006 22:01:36 +0000

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.

Fate/stay night

Mon, 16 Jan 2006 21:25:30 +0000

I just got around to see the first two episodes of this anime, which is an animated version of TYPE-MOON’s H game (without the H aspects, luckily). So far I like it. Despite being from Studio DEEN, the animation quality is good (for now) and the story seems intriguing enough to keep on watching. Music is by Kenji Kawai and is also nice. Also, the opening theme (disillusion by Number 201) is quite catchy, and I’ll be looking forward to the single’s release (22th Jan).

Moved

Mon, 16 Jan 2006 21:15:18 +0000

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).

New S.T.E.A.L. snapshot

Sat, 14 Jan 2006 15:52:06 +0000

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.

Always needed

Wed, 11 Jan 2006 20:44:17 +0000

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.

Moving? Not yet

Mon, 09 Jan 2006 20:16:07 +0000

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

Programming quality

Sun, 08 Jan 2006 14:32:03 +0000

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

Money oddities

Sat, 07 Jan 2006 14:55:57 +0000

Some things strike me as being really odd. Regarding the commission post 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 fame) offering money to help the GIMP project and then being forced to withdraw it, perhaps I shouldn’t be so surprised. Nevertheless, I’ll keep on trying.

Drawing commissions

Thu, 05 Jan 2006 19:15:32 +0000

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

DVD burning

Thu, 05 Jan 2006 19:05:33 +0000

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….

Cats and finances

Wed, 04 Jan 2006 14:52:12 +0000

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

Unfair treatment?

Tue, 03 Jan 2006 10:14:51 +0000

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…

Roc Star... yet again

Mon, 02 Jan 2006 15:58:18 +0000

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.

New Year

Sun, 01 Jan 2006 13:11:24 +0000

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.

New books

Sat, 31 Dec 2005 15:26:37 +0000

I recently got myself a couple of new books, thanks to the folks at Archonia:

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.

Up and running

Mon, 26 Dec 2005 19:23:14 +0000

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 on dennogumi.org

Out with the old, in with the new (??)

Leave of absence? #

An art-challenged individual's perspective on AI (anime) generated art

Translations available for KDE unstable packages

Setting up Let's Encrypt certificates for the 389-ds LDAP server

Setting up OwnTracks Recorder and OAuth2 with nginx, oauth2-proxy and podman

Blast from the past: 超獣機神ダンクーガ (Super Beast Machine God Dancougar)

Partings

DIY KVM over IP with pikvm

Quick tips: Server Name Indication for internal domains with Turris Omnia

Omnia? #

The problem #

Fixed comments

Refreshed look

Why? #

Providing KDE software updates from git for fun and profit in openSUSE

New server: away from Kolab

Hack of the day: extracting comments from Nicovideo

Dolphin and openQA and other assorted bits

Testing the Dolphin file manager #

Hack of the day: downloading VOICEROID実況 from Nicovideo

実況? Is it something edible? #

There can never be enough testing

Danbooru Client 0.6.1 released

What is Danbooru Client? #

Announcing a new project

Killing the redundancy with automation

Some prerequisites #

Testing the untestable

The heroes we deserve

The report #

Two in one

I have a problem...

Step 1: Someone posts a problem #

Danbooru Client 0.6.0 released

What is Danbooru Client? #

Of gases, Qt, and Wayland

I’d like the most recent Qt, please #

Where are my noble gases? I need MORE noble gases!

HOWTO: Configure 389-ds LDAP server on openSUSE Tumbleweed

Danbooru Client 0.5.0 released

What is Danbooru Client? #

Tip: opening and closing ports needed by a systemd service

The Big Forum Cleaning

Danbooru Client 0.4.0

What is Danbooru Client? #

KDE Applications 15.08 RC for openSUSE

GPG transition statement

Isso for comments

Dynamically static

The issue #

Plasma 5 live images for openSUSE and on the default openSUSE desktop

Live media for Plasma 5 #

Danbooru Client 0.3.0

Release details #

Danbooru Client 0.2.0 released

Sometimes they come back: Danbooru Client ported to KF5 and C++

Plasma 5.2 for openSUSE? You bet!

KDE PIM changes in openSUSE Tumbleweed

Some history #

Policy-based routing for single IPs using EdgeOS

KDE Applications and Platform 4.14.2 available for openSUSE

Latest 4.13, newest 4.14 beta and Plasma 5 in openSUSE

Changes in KDE Frameworks 5 and Plasma 5 packaging in openSUSE

New acquisition: ThinkPad X220

Notes to self: nginx Piwigo rewrite rules

Unlocking KWallet with PAM

KDE:Current and 4.13 packages for openSUSE

Before the upgrade #

Being Current

4.13 Beta 1 Workspaces, Platform and Applications for openSUSE: start the testing engines!

An expedition in the QML realm

8 months with KDE and openSUSE - looking back after the 13.1 release

KDE:Unstable:Playground is no more (or: adjustments in KDE repositories)

KDE in openSUSE: repository and maintainership changes!

Qt5 on openSUSE (including experimental KF5 packages)

Last round of testing: 4.11 RC2 packages for openSUSE

KDE releases 4.11 RC1, and openSUSE packages follow!

4.11 beta 2 openSUSE packages available

Leave of absence?
#

Omnia?
#

The problem
#

Why?
#

Testing the Dolphin file manager
#

実況? Is it something edible?
#

What is Danbooru Client?
#

Some prerequisites
#

The report
#

Step 1: Someone posts a problem
#

What is Danbooru Client?
#

I’d like the most recent Qt, please
#

What is Danbooru Client?
#

What is Danbooru Client?
#

The issue
#

Live media for Plasma 5
#

Release details
#

Some history
#

Before the upgrade
#

What are Klassrooms?
#

Issue 3 - Special summary issue
#