Autarchy of the Private Cave

It has been quite a time since my last serious and long post. On the one hand, summer is vacations time – so I’ve been to one in Turkey; on the other hand – the long-awaited ICSB-2008 conference finally took place in Gothenburg, Sweden, on August 23-27 (or 22-28, counting in tutorials and workshops).

Update: it appears that conference domain name http://www.icsb-2008.org/ was not maintained after the conference, so I had to remove all the links to that website (which now appears to be owned by someone not related to ICSB). However, there seems to be a mirror of ICSB-2008 at http://www.gmm.gu.se/groups/icsb08test/.

Synopsis: in this post I present a personal-perspective report on the 9th ICSB (with a condensed ICSB-2008 photo-report in my gallery).

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One of the benefits, offered exclusively by the Windows Vista Ultimate (not even by the Windows Vista Business), is

running UNIX applications (via SUA, Subsystem for UNIX Applications) , which provides higher flexibility for Windows workstations.

Where is the world going?

And how soon will all the Windows users (not only Ultimate Users) benefit from the higher flexibility by running UNIX applications?

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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Update: as of FireFox/IceWeasel 3.0.14, this bug appears to be fixed.

When right-clicking many links in FF3/IW3, it quite often happens so that a random action is performed instead of opening the context menu (bug report).

One of the solutions work-arounds (suggested by Andre Pirard) is to slow-right-click, that is to hold the right mouse button down until the menu actually appears, then – and only then – release it. Or, you can even slow-right-click, move the pointer over the desired menu item, and then release – that will perform the desired action in a single long right click (instead of more common single right click with a following single left click.)

Alternative workaround (found at the bug report page): install the mouse gestures add-on, and restart firefox. Tested: works for me.

This bug/behaviour is otherwise unsolved.