Yesterday’s blog about Who says Java is not fast?!? caused quite some feedback (thanx to all commenters!) with several good points. Of course, a table like that in the cinfony paper (see also the comments in the blogs by Noel (the author) and Rich). Many things determine why the CDK might be fastest in that table for SDF iterating. Suggestions have been that OpenBabel and RDKit may be doing much more than simple reading;

While performance tests actually show that for even core numerical calculations Java is at par with C in terms of speeds, and sometimes even hits Fortran-like speeds, people keep think that Java is not fast. I only invite you to test that yourself.

… a source code reviewer nightmare. The must-read lwn.net ran a nice open letter to a Linux kernel developer.

Some time ago, I added parallel building targets for CDK’s Ant build.xml. Now that I am setting up a Nightly for the jchempaint-primary branch, and really only want to report on the CDK modules control and render, I need the build system to use a properties files to define which modules should be compiled.

it provides a recipe to approach (scientific) questions let’s you cook up a (scientific) answer you can use it as a black box (like an orbitrap) you can refine existing methods (well, some can, others don’t) it has an error (but I do not believe it is normally distributed)

Today and tomorrow, Stefan, Gilleain, Arvid and I are having a JChemPaint Developers Workshop in Uppsala, to sprint the development of JChemPaint3, for which Niels layed out the foundation already a long time ago.

I am working on converting Jean-Claude’s Solubility data to RDF (after Pierre’s model, see here, here, and here, here for first data exploration), so that I can integrate it with data from DBPedia, Freebase, rdf.openmolecules.net, etc. Bioclipse will be the workbench in which this will be visualized, and just got graph depiction online using Zest.

Andrew has an interesting thread on the content of a slide of a recent presentation. In the comments you can read the back and forth on things;

CDK 1.1.x releases are well in progress, but a recent commit broke a number of unit tests. Here comes git-bisect.

The Blue Obelisk mantra ODOSOS, Open Data, Open Source, Open Standards, is well known, and much cited too. Jean-Claude Bradley popularized the Open Notebook Science (ONS). This has always been nagging me a bit, because the CDK, Jmol, JChemPaint and other chemistry projects have done that for much longer, though we did not use notebooks as much, so called it just an open source project.

Getting back to some webservice stuff (see part #1 of this series )… actually, I’ll use cloud service from now on, since web service is reserved for SOAP/WSDL (see my EMBRACE presentation ). Let me present this bit of JavaScript I just ran in Bioclipse2: