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JChemPaint-Primary moving to Git
I knew it was going to be painful, but making the jchempaint-primary branch a proper patch to the CDK master branch is painful. I am working my way towards setting up a git repository (IMPORTANT: these patches are not final yet, and their history will change, as I am rebasing regularly to make cleaner patches! Making copies is save, but please hold of any forking and/or branching on top of it until it is final. Thanx.) for the patch, with split ups of the various parts into reviewable blobs:
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Bioclipse-JChemPaint #2
Recently, I blogged about Bioclipse-JChemPaint of the imminent Bioclipse 2.0.0 release, a complete rewrite of the Bioclipse application as published in doi:10.1186/1471-2105-8-59. I also blogged about the feature to browse large MDL SF files (Bioclipse 2.1 will have support one or more CML conventions for chemical tables). Ola did some profiling on processing SD files, but also notes that such may be more suitable for the StructureDB
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Knowledge Management - Ontologies
Chemistry has a bit of background in ontologies, and ChemAxiom is certainly not the first (though I think it is rather promising…). Three years ago I gave a presentation at the CUBIC (now existing as LinkedIn Alumni Group), which is not so extensive, but does have a few interesting citations on the use of ontologies in chemistry on slide 16:
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Bioclipse for CDK Developers #2
I reported earlier how Bioclipse allows you to use a script to perceive atom types for the content of the JChemPaint RCP editor. This functionality is now available in the outline, and indicates directly if Bioclipse (and the underlying CDK) understands the chemistry you are drawing. In a future Bioclipse release, these problems will be visualized more prominently, likely using the Errors/Problems Views available from Eclipse, or otherwise.
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Making patches; Attribution; Copyright and License.
I have discussed this in the past on mailing lists, but realized yesterday that I need to strengthen the message a bit more. Just to remove confusion. The below is extracted from an email I sent this morning to the cdk-user mailing list, but I’m sure you can apply this to any other open source project. (Disclaimer: I have not studied international law, and the below cannot be used as legal advice. Like you would have! Hahahaha! Let it be pointers :)
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Michel Dumontier at Uppsala University
Michel visits our group this week and gave a very exciting talk yesterday on the role of ontologies in drug discover. This being ongoing research in our group too, the talk was well received by the audience (which was not too large, because after mid-summer, Uppsala has holiday). First the first time, I microblogged a talk on my twitter account (using the #dumontieratuppsala tag). I have not got a XSLT ready to convert the relevant items into a nice HTML snippet for embedding in this blog, but will try to do that later. Meanwhile, I also made a few bookmarks here and there, which are available from Delicious.
