November last year, I reported my plans to develop a live CD with all our favorite chemo- and bioinformatics software. Bioclipse requires Java5 and sort of still depends on the Sun JVM (I will experiment with classpath-generics later), but is now distributable with operating systems.

Classpath 0.91 is released with 1.45 million lines of code and with 98.96% coverage of Java 1.4.2, and 99.82% of java.swing. Or, as Dave calls it: 0.91 rocks! JChemPaint runs again (they fixed the XML parsing problem), and Jmol still runs <i class=”fa-solid fa-recycle fa-xs”, but slow.

BioMed Central is setting up a new peer-reviewed, open access journal Source Code for Biology and Medicine. It will “encompass all aspects of workflow for information systems, decision support systems, client user networks, database management, and data mining”. Basically, anything that fits into chem-bla-ics.

Timo Hannay blogged in Nature’s Nascent blog about the Open Text Mining Interface (OTMI), which is “a suggestion from Nature about how we might achieve text-mining and indexing purposes”. The idea is that each article has a link pointing to a machine readable file containing raw data about (and from?) the article.

Joerg Wegner mentioned in his blog the graph mining program ParMol which integrates four mining algorithms: MoSS (aka MoFa) and Gaston, which I mentioned in November last year , and FFSM and gSpan, which I did not know about yet. ParMol provides a common interface to the four different algorithms and is, like the four mining modules, licensed GPL. An interesting aspect is that Gaston was originally written in C++.

Rajarshi Guha has set a nightly build service for the Chemistry Development Kit (CDK). The output is pretty, but information rich: it includes results for the JUnit test, DocCheck, and PMD. The compiled jar and the corresponding JavaDoc can be downloaded, offering a cutting edge distribution for users.

Here are some quick download statistics for some of the chemblaics components. First Jmol.

I have not blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript, my new job at the CUBIC where I continued the work on proper protein support in Bioclipse using the CDK and Jmol:

Conference season is nearing. And just in time, Postgenomic.com added a conferences map showing locations of upcoming and recently finished conferences. Oh boy, do I want to set this up for chemoinformatics too!

The data classes of the Chemistry Development Kit are mutable, unlike those of Octet. This means that other classes may need to respond when the content updates. For example, a render class. CDK’s ChemObject provides a notifyChanged() and addListener() methods for this.

Bioclipse 1.0 is to be released in May, and the cartoon on script command is still not working in the Jmol viewer. For those who do not know yet, Bioclipse is a cool Eclipse RCP based Java chemo-and bioinformatics workbench. To have a better idea what goes on inside Bioclipse, I wrote a new BioPolymer tree to show me the strands in the protein.