CDK 1.2.4: the changes

Here is the changelog of CDK 1.2.4 which I am about to upload to SourceForge:

6 minute read

BlueObelisk StackExchange (.com)

Oh no, not another communication channel?! We already have Google Wave! (BTW, I have quite some new invites…)

less than 1 minute read

Call for Collaboration: JavaDoc validation with OpenJavaDocCheck

I reported recently about my efforts to write an Open Source DocCheck replacement. I received the first patches (from Rajarshi), and brought it online in a CDK branch (see this Nightly page).

1 minute read

New Bioclipse Features: Kabsch Alignment, RMSD Distance and Tanimoto Simarlity Matrices

We recently submitted a second paper on Bioclipse, and have worked hard in the past two weeks on addressing the reviewers’ questions (and we love these feature requests! See also these two blogs). One reviewer seemed very interested in seeing docking available in Bioclipse. While we do not have a full docking feature set up for Bioclipse, we do have functionality to deal with 3D structures, though our researched urged us to focus on the 2D side of cheminformatics so far.

3 minute read

Milestones...

While I am still looking around for a assisting/associate professor position, there are two milestones around my scientific work I want to briefly mention here. This blog is the 500th blog on chem-bla-ics, and the two CDK papers have combined reached 100+ citations as counted by Web-of-Science, as can be seen on my ResearcherID profile.

less than 1 minute read

Bioclipse Manager for MyExperiment.org

Some time ago I wrote about using Bioclipse to query to MyExperiment.org SPARQL end point. I think I had not mentioned that I have also written a manager to download MyExperiment Bioclipse Scripting Language scripts (though there are no GUI elements yet):

less than 1 minute read

Maintaining patches is fixing patches

Today I had a question about having to fix patches against upstream changes because those patches were not included upstream yet is not very productive.

2 minute read