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VR.se funded research to be OA as of 2010
Happy news from the Swedish Vetenskapsradet (via Coturnix): as of next 2010 all peer reviewed journal papers must be Open Access. I am not yet VR funded, but involved in a few VR grant applications. Not that that really matters, as I am happily publishing OA already.
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Keeping my Bioclipse repositories in sync with upstream
Bioclipse is now split up over several Git repositories (and some additional stuff in even more repositories). This has all to do with each repository now having one person acting as point-of-access. This means that I have several repositories checked out, which I need to keep synchronized. Now, I am pretty sure there are many solutions (and suggestions very welcome!), but this is the Bash script I have just written to give me an overview of the state of my repositories, hoping it may be useful to others too:
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CDK Molecules in RDF
Yesterday, I finally got around to starting a branch on adding RDF support to the CDK; in particular, write the CDK data model ontology in OWL and serialization to and from RDF using the ontology. The framework is now set up, but I have yet to formalize all bits and pieces of the CDK data model in classes and properties. Just as a preview, here is what a very basic bit of CDK model in RDF looks like (N3 format):
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Google Wave Invite: but you need to work on the CDK and the CDKitty robot
I just posted to below email to the cdk-user mailing list. Next Monday, I’ll decide.
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Processing the ChEBI MDL SD file with the CDK
Bioclipse has a bug report about browsing the ChEBI SD file in its moltable editor. Some entries make Bioclipse crash (as reported), or just very sluggish as with my Dell superlapcomputer :)
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Extension point for running JUnit tests in a RCP Application instance?
One thing that has been on my wishlist is to be able to run the unit tests we have for Bioclipse from inside a running Bioclipse instance. That is, we have a Bioclipse Test Suite features on the update site, matching the functional features we have there. Each such test suite would run all JUnit tests we have for that feature.
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JChemPaint update: merging of patches and CDK statistics
With the JChemPaint workshop just passed, there is much work from UU and the EBI to be integrated. Moreover, Rajarshi just merged a lot of fixes from CDK 1.2.x into the master branch, which will be a big rebase too. That said, I need to do this to recalculate source code statistics for the CDK.
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