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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.
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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.
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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):
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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.
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CrossRef writes up RSS usage recommendations
CrossTech announced that a CrossRef working group has written a best practices for the use of RSS feeds by publishers. Nice introduction for anyone who is creating RSS feeds. Only comment I could make, is the lack of other modules. For example, a Chemistry module has been proposed by us 5 years ago already (DOI:10.1021/ci034244p) and about which I blogged on several occasions.
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Work in Progress: an Open DocCheck replacement
While it is still very much in progress, I have already made more progress than I had hoped for. The JavaDoc Doclet API is actually not too difficult to use, though my use will very likely improve more later. The CDK has been using Sun’s DocCheck utility for testing the library’s JavaDoc quality, but the reports never really satisfied me. Moreover, the most recent version is ancient and because it is closed source, no one can continue on those efforts. DocCheck is MIA.
