• Development of the new JChemPaint

    A quick screenshot, after some work on the JChemPaint code based on CDK trunk/. Nothing much to see, but a rather small code base, which is good. Today, I have set up cdk/cdk/trunk/ and cdk/jchempaint/trunk as Eclipse plugins, allowing the second to depend on the first. So, no more use of svn:externals. This is what it now looks like, and basically formalizes the end result of Niels’ work of last year:
  • Metware Status Report

    Following many, many others, I finally got myself a SlideShare account and uploaded a recent presentation on MetWare, our metabolomics data warehouse project. Some spoilers: SQL, RDF/SKOS, JSF.
  • John Wilbanks replies to the ChemSpider/OpenData discussion

    Not long after I posted my view on things, John posted his reply on the ChemSpider/OpenData discussion. His comment was merely to illustrate an internal advice to some organization, which got accidentally leaked. Anyway, a must read, with two good links to further reading on open data licensing.
  • Does ChemSpider really violate Open Data with CC SA?

    ChemSpider is afraid they are doing something bad because they release their data as CC-BY-SA. Because, John Wilbanks says in Peter’s blog:
  • Re: What should a Nature Chemistry paper look like?

    Neil wondered “what a Nature Chemistry paper should look like”, and asked the following questions. Below are my answers.
  • Wicked chemistry and unit testing

    After a discussion on starting development releases for CDK on cdk-devel, the discussion continued on the state of the CDK atom typer . Dan and Rajarshi have done tests in the past against PubChem and its DTP/NCI subset. Rajarshi made his analysis part of CDK Nightly, and provides but a summary (which seems broken: zero fails) and a detailed list.
  • Comparing JUnit test results between CDK trunk/ and a branch #2

    I reported earlier on how to compare unit test results between CDK trunk and a branch . Later, I noted that the diff typically overestimates the fail count, when unit tests had been moved to a different module. Therefore, a sort has to be added. The code is also updated for the SVN directory restructuring: