I love Debian, too.

Though I prefer ‘testing’ (which is currently codenamed Lenny) over ’stable’ (aka Etch).

There’s a how-to on the topic at howtoforge.com.

Note, that for the suggested solution to work, NAT/firewall should be “transparent” for outgoing ssh connections.

I’ve tried it already under Windows, but as my main OS is Debian, I can’t use it

You can sign up for updates on Linux version.

After reading the Google Chrome book, it is a long time waiting for it to be released for Linux….

Also, I’m looking forward for the plugins to enhance Chrome. Although it did import my settings/passwords(?!)/bookmarks from Firefox, but it has no Foxmarks, AdBlock and some other goodies I’m now used to on all the computers I regularly use.

These are the addresses for those who would like to travel lightly, meet new people, get new friends, hang out with interesting people, or just find a shelter for a night in the foreign country.

I’m now registered in both systems (and getting “verified” in CS), and so far I stayed with three people (at two places) found via HC and CS. Both experiences were highly positive. Actually, my world outlook changed quite a bit after my first stay: I heard from someone that

it’s better to trust wrong person once, than always distrust all the people

But building trust, despite being central to HC ans CS, is only one - basic - component. Cultural exchange and knowledge sharing are also important, though so far I was unable to comprehend these components sufficiently to write on them.

At the CouchSurfing.com website, it appears to be popular to put some test/quiz results into profiles. These are the tests:
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There’s a Debian-Med project, aiming to

develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research

Debian-Med has several web sites/pages: one at Debian.org (descriptive), and the actual project’s website at debian-med.alioth.debian.org. There’s also debian-med wiki (for developers).

As of nowadays, Debian-Med has released a number of Debian packages, which are grouped into respective Debian Med Tasks. The Biology-dev task, for example, contains MCL and libsbml packages (among many others).

Check this project out - you might find that the software you need is already available as Debian package.

This post was stimulated by Steffen’s comment.

There’s a troubleshooter for Ubuntu, which (expectedly) works quite the same for Debian (lenny in my case).

I’m installing libsbml to make the iBioSim tool work under Debian GNU/Linux. First thing I had to do was to make Sun’s java interpreter do all the java interpretation work instead of gcj: sudo update-java-alternatives -s java-6-sun (this assumes you do have java-6-sun installed).

Installing libsbml moved me one step further, now I’m getting another error from iBioSim:

Exception in thread "main" java.lang.NoClassDefFoundError: biomodelsim/BioSim
Caused by: java.lang.ClassNotFoundException: biomodelsim.BioSim
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

This yet has to be fixed somehow.

If Zhou Xin’s blog becomes for any reason inaccessible (or moves to his own domain), below is the extract of the instructions from his post on how to install libsbml on Debian/Ubuntu Linux:
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http://debian.org.ua/ and ftp://debian.org.ua/

What is on offer (mirrors):

• backports.org
• cygwin
• deb.opera.com
• debian - stable, testing, sid
• debian-archive (starting from 1.1!)
• debian-multimedia
• installation media (CDs/DVDs)
• debian-security
• even debian-volatile is here!

All this goodness is only 3 hops away from my DSL modem…. (ISP UkrTelecom)

Gone editing /etc/apt/sources.list

P.S. For non-ukrainian IPs, access might be slow/bandwidth-limited; for Ukrainian IPs, speed might be up to 100MBit/sec.

Update: some time after publishing this post, debian.org.ua was down for some reason. When it was up, it was serving me packages with a mere 3 kb/sec . I found that ftp2.debian.org.ua mirror is faster at the moment.

IEs4Linux provides a convenient package of Internet Explorer 5.0, 5.5, 6.0, and (partially supported) 7.0 for Linux.

It installed and runs fine under Debian Etch:

However, as you could notice from the screenshot above, CPU use is almost 100% while IE6Linux is running. It is better illustrated by the next screen:

I didn’t yet bother finding out what’s wrong, but that must have some kind of a fix, as running at 100% CPU on a laptop is … hot.

Debian HOW-TO: CPU power management / frequency scaling

Simplest way to develop your custom Drupal theme is to start with some skeleton/wireframe theme.

In this post, I’m briefly reviewing 4 themes (atck, blueprint, framework, and zen), made specifically to serve as theme developer’s starting point. All 4 are listed with their features (as per Drupal project page of each one), with my personal “impressions” (not based on actual use experience, yet). There’s also my choice and order of preference for the 4 candidates at the end.
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When either consulting on a new website design, or actually designing one, keep in mind Ad Unit Guidelines if the website is going to use advertising. The list is far not exhaustive, but sufficiently standard.

100 legal sources for free stock images (via maxon’s delicious bookmark)

Personal communication resulted in a link to slicehost, who provide VDS/VPS services at prices as low as 20$/mo, which is comparable in price to good shared hosting plans, and is cheaper than Dedicated plans.

I’m considering a move from shared hosting, and found Slicehost attractive. For 20$/mo, you get guaranteed 256MiB RAM, 10GiB disk and 100GiB traffic, which is sufficient to host several under-1k-per-day sites.

The only thing which isn’t spoken aloud is the guaranteed CPU speed. Based on the numbers provided: 16GiB total RAM per server, quad-core CPU, and CPU quotas set equivalently to RAM quotas, I came to a conclusion that 20$-plan guarantees ~125MHz of CPU (take 16 GiB, multiply by 4 20$-plans - you get 64 “slices” - virtual servers; quad core CPUs were quoted as 8+GHz - I assume that’s the sum of the core frequencies, thus 8GHz divided by 64 slices gives as little as 125MHz guaranteed per slice).

The better slice you buy - the more CPU is guaranteed, so for 1024-RAM slice you’d have a minimum of 500MHz of CPU.

However, slicehost describes their CPU-clamping system as the one allowing “bursted” performance, if others aren’t actively using their CPU shares. So it must be much better than what I’m calculating here. And even if it’s not, then for some applications it’s better to have a 125MHz-clamp on CPU, than have a 20-seconds maximal CPU time limit.

Still, I’m looking for reasonably-priced collocation services in Ukraine - e.g. those (currently unavailable) from Volia, starting at 40$/mo for the rented physical VIA C7-based server with enough traffic included.

A year, maybe two ago, I came across the news that someone’s constructing a “building printer”, in the sense that it is first filled with liquid concrete, and then - given the schematics of the building - “prints” concrete, producing almost-any-complexity architectural forms. Unfortunately, the names and links to that instance of object printing was lost and forgotten.

However, I have just stumbled upon the news item about RepRap, which is claimed to be “self-reproducing”. Clearly, this isn’t true, but RepRap - replicating rapid prototyper - is able to produce (some?) of the components necessary to build another RepRap.

I’d like to point out that

“Think of RepRap as a China on your desktop.”

by Chris DiBona, Open Source Programs Manager, Google Inc., is an offensive and unacceptable phrase, which shouldn’t have been put at the top of the quotes. I’d hack down that RepRap website for this single quotation, and would feel vende vindictive towards Chris, if I were Chinese. But that’s not a long time to wait to see China rising and this kind of jokes vanishing.

That was a side note.

Continuing on RepRap, I do find it’s uses intriguing. For the best of everybody, there’s a how-to build reprap page.

First uses which came to my mind were… a new plastic cup, and a custom notebook/PC body/case, to put standard components into and enjoy the benefits of the perfect custom design

Apart from simple things like cups and actually “fast prototyping” (which does depend on the precision of RepRap), there aren’t that much uses for the SOHO owner of RepRap. But as soon as some small-scale silicon-growing/cutting machines become available, that would definitely open up the whole new world of custom gadgeteering and home-brewed electronic wonders. Also, the level of global and local espionage activities will explode, and Big Brothers will grow like mushrooms after raining cats and dogs.

The title of this post is my current - “forthcome”, as in “done” - field of interest.

First article on topic: Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data.

Another one, on combining different high-throughput data sources to get higher-quality results: Uncovering signal transduction networks from high-throughput data by integer linear programming.

I’m especially interested in time-series network reconstruction algorithms. If you have a good advice to share with a newcomer to the networks field - don’t hesitate

With this post, I’m finally announcing the opening of the (mostly) functional COTRASIF web-tool, created for the genome-wide identification of promoter regulatory sequences (transcription factor binding sits, TFBS). You can learn more from the About and Help pages. For an example of use, see the Supplement page (article is currently being prepared; as soon as it’s ready, I’ll make it available).

If you are interested - have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row - see e.g. the most recent Eukaryotic transcription factor binding sites - modelling and integrative search methods.

Note, that under Gnome I only had to use a single system-wide utility to bind volume buttons to volume control. Under KDE things were a tad tougher.

First, you may want to look for kmilo (if you don’t have it yet). It has several plugins e.g. for ThinkPad and Vaio laptops, as well as “generic” plugin. I didn’t try this solution, though.

If you need more than kmilo can offer: keyTouch could help. keyTouch should be good also for non-laptop multimedia keyboards. However, this also wasn’t the solution I used.

If you want to know how to map your special keys to functions yourself - then read on.
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Some things to be aware of when enhancing Drupal site with FLV video playing/conversion features.

• Setup wizard for the free JW FLV Media Player (and the JW FLV Media Player itself)
• Flash Video in Drupal 5: A complete multimedia tutorial to the flashvideo module
• actual flashvideo module page on drupal.org

If you had some programming experience - read it here. Otherwise ignore, it’s targeted for a narrow group.

NicEdit - lightweight inline configurable rich-text editor for the web. Can fit where both FCKEditor and TinyMCE are too clunky and monstrous.