Recovering full mass spectra from GC-MS data

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. Just to make sure it works for whatever new input, for whatever refactoring, for whatever new cool feature. 5 minute read

Good Scientists Pimp there Research (was: Damn, I'm boring...)

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. 2 minute read

Finding differences between IChemObjects #2

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. 1 minute read

Finding differences between IChemObjects

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! 1 minute read

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: less than 1 minute read

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