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Updating my bioclipse.qsar fork with Ola's main branch
GitHub makes forking cheap, and I have a fork of the bioclipse.qsar repository (see Bioclipse moving to GitHub: CIA hooks enabled), so that I can easily share my patches with Ola for review. Ola can review them and apply them back into his main version.
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ELN vendor: "The Open Source stuff just works better"
Simon Coles is CTO of Amphora Research Systems (a company I do not know) and in the business of Electronic Lab Notebooks. I know nothing about their products but would like to propagate the statements he just made on Open Source in reply to a question on LinkedIn (btw, my LinkedIn account):
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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.
