chem-bla-ics

Today I setup a blog planet for Blue Obelisk members. First I tried Chumpologica but it did not read Atom feeds.

Next in line was Planet, which turned out to be used by many big planet sites, like Planet Debian. It also works with Atom feeds in general, but not well with Atom 1.0 feeds, like that of Carsten. After some googling I found a patched version which did the job.

The result is at http://www.woc.science.ru.nl/planetbo/, but I hope that someone can arrange a http://planet.blueobelisk.org/.

Where I was able to mention earlier that JChemPaint now runs with free (as in open source) Java virtual machines, I just tried to run the core Jmol renderer, using the Integration.java which comes as an example:

The screenshot was made with jamvm 1.3.3 and classpath 0.19.

It is very slow, however. I have not tried it with other free virtual machines, which are supposedly faster.

Don't happen often, but my machine crashed two hours ago. Not a big deal, because I have my important files in SVN. Oh wait, SVN had a commit in progress during the crash. So, svn recover. Mmmm... doesn't work either. OK, SVN FAQ: try db_recover. That worked. No, it did not: svn commit still not working for the files I was trying to commit. Fortunately, I make regular SVN db backups so I created a brand new SVN repository from scratch and recovered the back up. That worked. Really.

Some weeks back there was the CDK5AW, the CDK 5th anniversiry workshop. A small group of international open source chemo-, bioinformatics software developers met, among which two from Sweden. It was then decided to generalize their work resulting in Bioclipse:

http://www.bioclipse.net/

It's heavily using the Eclipse Rich Client Platform, making additional plugins trivial. OK, if this does not convinve you: check the screenshots on the Bioclipse website.

Thanx to Mark's encouragements, I tried to run Jmol and JChemPaint with jamvm.

This evening I have been looking at with the KNOPPIX customization howto, and ran many of the interesting commands. I've setup a environment with Kalzium, OpenBabel, CDK, jython, PyMOL, and for development I included gcj and Eclipse. At some later point I will include kfile_chemical too, but I want to make a deb package first.

Moreover, I also wanted it to include JChemPaint, Jmol and Taverna (with the CDK extension).

OK, just back from the first German Chemoinformatics Conference, which I enjoyed very much. A rather interesting program, and lots of interesting posters too. You can read the programme online, and will not spend too many words on that (at least not now). But what I will do is point out some interesting posters here.

One poster was on the Molecular Query Language (MQL) by Ewgenij Proschak from Frankfurt. You can read more on this in the latest CDK News as it is implemented for the CDK too.

This sunday starts the first German Chemoinformatics Conference in Goslar. It's an interesting programme, with presentations on the InChI, PubChem, 25 years of chemoinformatics, the chemical semantic web, and much more.

Among these presentations is mine, on comparing crystal structures (PDF) and deducing cell parameters. But I'm having a poster on QSAR too.

Not so long ago, it was decided that KDE 4.0 will use SCons as a configuration and building tool, instead of the autotools and make: the common ./configure && make && make install which has served the open source community very well for so long.

SCons is different in several ways. One of these is that the tar.gz packages it produces are some 500kB smaller, which makes a huge difference for kfile_chemical which is now 121kB instead of 635kB.

The great thing about open source is that... it's open.

When I was browsing the internet just now, I dropped in on KDE Dot News. In the rightside column, there is a feed of new KDE software from KDE-apps.org. A new version of my favoriate music player,

amarok, lured me to the KDE-apps website, where I saw rkward is latest announcement.