chem-bla-ics: April 2012

UML diagrams from the command line

I think I found a nice tool for my Groovy Cheminformatics book! And for Java documentation in general :) There are various tools to draw UML diagrams, such as umbrello, but the XMI format it uses is not easily edited from the command line, or included in books as source...

But I recently ran into UMLGraph on StackOverflow. I gave it a quick try but could not figure out how to get interfaces to show up.

Apr

My #NBIC2012 slides on the CDK in NL

CDK development in NL View more presentations from Egon Willighagen

Apr

#NBIC2012: the Chemistry Development Kit in NL

The demos of Bioclipse-OpenTox went well today (tomorrow more opportunity to drop by). Yesterday I installed Ambit2 and the ontology server, and created a plugin with DS-OpenTox configuration for the localhost.

Apr

#NBIC2012: Bioclipse-OpenTox

Tomorrow and Wednesday at the #NBIC2012 meeting (add your twitter account if your speaking or attending), I will demo Bioclipse-OpenTox during the Application Showcase sessions (all abstracts) (Tue: 10:00-11:15 and 14:50-15:50, Wed: 10:30-11:30 and 14:50-15:50). If you cannot attend (or just do not like Lunteren), watch these screencasts.

Apr

Working against CDK interfaces instead of implementations

For quite some time now, we have been working on factoring out the data module implementation of the interfaces. These classes were originally all we had, even before interfaces were introduced. Since then, the CDK adopted other implementations, like silent and datadebug. In time, more and more code became independent of implementations, and I just finished another set of eight patches so that even qsarmolecular is independent from the implementations.

Apr

Dereferencable InChIs: OpenMolecules RDF

About four and a half years ago, I started OpenMolecules RDF, a spin off from Chemical blogspace (Cb, which is still up and running thanks to Peter Maas!) where I started using InChIs in URIs. My interest came from the dereferencability, the ability to take an InChI and find information about the chemical structure representated by it. Because information about anything is scattered around the internet, and we need something decentralized.

Apr

CDK regressions in master

A short note about the state of CDK master. As you may have heard, the master has now forked beyond the cdk-1.4.x branch to such an extend that blindly merging even in a git world no longer works; I now have to manually do this, and am experiencing merge conflicts frequently.

Obviously, this forking is for the better of the CDK and master has a number of API improvements.

Apr

"Emerging practices for mapping and linking life sciences data using RDF"

The "Emerging practices for mapping and linking life sciences data using RDF" (doi:10.1016/j.websem.2012.02.003) is now available online, where I contributed a section on the original workflow for creating ChEMBL triples, and contributed to the section about open licensing, referring to CCZero and the Panton Principles.

Apr

Lördags goodies #1: a Chemical Identifier Resolver plugin for Bioclipse

Saturdays is day where I am normally so tired, but my important inbox has gone down sufficiently, that I treated myself with some lördags goodies. So, I hacked up a Bioclipse plugin to interact with Markus Sitzmann's Chemical Identifier Resolver (here are his recent ACS slides). I'll post the code to my GitHub account shortly, and here's the obligatory screenshot:

The matching BSL script:

ui.open(cir.getByName("morphine"))

Also note the script log just above, where I searched for name.

Apr

A typical QSAR study (cito:citesAsAuthority)

I use CiTO to keep track of how the CDK is cited and used, and just looked at a typical QSAR paper. Here are my comments on "Study of indole derivative inhibitors of Cytosolic phospholipase A2α based on Quantitative Structure Activity Relationship", by Lu et al (doi:10.1016/j.chemolab.2011.11.011). Normally, I am fairly short in these reviews which I publish via the CDK Google+ page, briefly describing what CDK functionality is being used.