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. less than 1 minute read

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. 1 minute read

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: 3 minute read

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. 3 minute read

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. 3 minute read

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: 1 minute read

MetWare, SKOS and Java Server Faces

The MetWare components are slowly coming together. The RAW data upload facility prototype went into beta stage, while the SKOS has proven really useful for various things. 2 minute read