chem-bla-ics: July 2010

CDK 1.2.6: the changes and the authors

Like all release in the 1.2 series after CDK 1.2.0, release 1.2.6 is a bug fix release. Anyone running a CDK 1.2 version is advised to upgrade. New in this release is the availability of a torrent for the cdk-1.2.6.jar (see BitTorrents for Science). Please find below the changes and the authors that contributed to this release.

The changes

Updated the DebugBond unit test too now: new DebugBond() has zero atoms 6ef1fb1 Backport patch, to make the patches compile with cdk-1.2.x ce9b1bd Additional patch to reduce atom count on setAtom(null, int) and unit tests for the setAtom(IAtom, int) behavior. 6cf95db Also fix the new NNBond() == 0 atoms for the nonotify module 23d9685 Fixed Bond() constructor to create a bond with zero atoms.

Jul

An Ubuntu Blue Obelisk meta package

There was some talk recently about Blue Obelisk software available as Ubuntu / Debian packages. This morning I had trouble waking up, so hacked up a metapackage, so that you can now do:

sudo add-apt-repository ppa:egonw sudo aptitude install blueobelisk Currently, it installs BODR, Kalzium, Gnome Chemistry Utils, Chemical-MIME, OpenBabel, and the CDK. Ideas, feature requests, patches, etc, welcome via GitHub.

Jul

My worst cited paper: supervised self-organizing maps

Amazing! It actually is the paper (doi:10.1021/cg060872y) with the best graphics! Is it really then, that scientists do not care about looks?! Or is this just the curse of Closed Access publishing?

Ping me if you have a nice data set with multiple dependent variables and need some statistics advice!

Jul

Script logs as HTML+RDFa: mix free text reporting with CSV

Richard (Talis) wrote up a three-step tutorial on how to publish your data. I think I would be more than happy if scientists reached step 1. Related, Ola asked me a while ago if I was interested in using the computing facilities of UPPMAX, and I was. But until this weekend I did not have the time or energy to give it a spin. If you are puzzled how the heck I see those two items related, read on :)

Two days later, today, I ran my first analysis.

Jul

Amazon, the Kindle edition is more expensive than the paperback??

I am writing some more educational material on cheminformatics, and wanted to link to some of the handbooks already around. I need the book details in BibTex format, so CiteULike is my primary tool to create such content. One of those books is the book An Introduction to Chemoinformatics by Leach and Gillet.

Jul

Setting up a local Semantic MediaWiki with RDFIO and SPARQL support

My now former student Samuel is doing a really cool Google Summer of Code project on import and export of RDF from a Semantic MediaWiki server.

Jul

RDFaDev: HTML+RDFa development with FireFox

Celso informed me in this old post about an alternative to Operator for RDFa handling in browsers, or Firefox in this case: the RDFaDev add-on.

Jul

A new CDK default fingerprinter?

The current default fingerprinter in the CDK depends on aromaticity, but that concept is algorithmically difficult to define, and even experimentally there are multiple dimensions to this concept. Moreover, calculating aromaticity is not cheap, as it requires detecting of ring systems. The purpose why aromaticity is actually included is this: people expect a ethenol moiety to match phenol.

Jul

Cb: New Blogs #13

The Cb software is still holding... I jettinsoned the old post cache, which speeded up the processing of blogs considerably, but the system just doesn't scale right.

Jul

Aggregating my blogs on this blog using labels

I am reorganizing my blogs, and will now take advantage of the labels concept of Blogger. The new URLs are:

Chemical blogspace becomes http://chem-bla-ics.blogspot.com/search/label/chemicalblogspace A Chemical RCP Adventure becomes http://chem-bla-ics.blogspot.com/search/label/planeteclipse Kemistry Desktop Environment becomes http://chem-bla-ics.blogspot.com/search/label/kemistry And likewise for one or two other blogs.