• Oct 16, 2009

    PMD 2.4.5 installed in the CDK 1.2.x branch

    Today I installed PMD 4.2.5 in the CDK 1.2.x branch which contains mostly bug fixes compared to the 4.2.2 version we had earlier. Several of these include false positives: warnings which were not really problems, but tests going bad.

    less than 1 minute read
  • Oct 15, 2009

    SPARQL end points, Jena and bif:contains

    I have been having fun with SPARQL in Bioclipse for a while now, and blogged at several occasions:

    less than 1 minute read
  • Oct 9, 2009

    NMRShiftDB RDF #3: Bio2RDF

    My might have seen my efforts to convert the NMRShiftDB data into RDF:

    less than 1 minute read
  • Oct 8, 2009

    Where are the CDK 1.3.1 and 1.2.4 releases ?!?

    You might be wondering what is keeping the CDK 1.3.1 and 1.2.4 releases. And right you are. When we look at Supernightly, we get a clue (BTW, I hope the EBI nodes will join soon too):

    less than 1 minute read
  • Oct 7, 2009

    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.

    less than 1 minute read
  • Oct 7, 2009

    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:

    less than 1 minute read
  • Oct 6, 2009

    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):

    less than 1 minute read