One aspect not covered in detail by the ongoing discussion on unit testing quality control for scientific software, is detecting regressions. This is the most important reason why unit testing is superior to random testing. Putting someone behind a keyboard to tests things is nice, but this process has to be repeated, as the testing has to be repeated over and over again.
Define good. Let me say that up front. Good scientists, that is, if you say successful researchers are good scientists, secure good funding. Getting good funding requires doing the most relevant research (define relevant). Or, to put it bluntly, being a successful researcher requires to pimp your research. Doing boring research is nice for you, good for a Nobel prize if it turns out to have a cool spin off, but doesn’t buy you research success.
CDK QSAR descriptors are not allowed to change the input [molecule|atom|bond], and I recently added a unit tests (rev 11138) for that to the abstract class AtomicDescriptorTest.
CDK trunk is getting into shape, thanx to the many people who contribute to this, and special thanx to Miguel for cleaning up his code related to charge, resonance, and ionization potential calculations!
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.
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.
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:
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.
Neil wondered “what a Nature Chemistry paper should look like”, and asked the following questions. Below are my answers.
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.
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.