Cheminformatics Benchmark Project #1

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; Java might actually take advantage of the second core for caching file content.

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Who says Java is not fast?!?

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.

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Short variables and lack of comments...

… a source code reviewer nightmare. The must-read lwn.net ran a nice open letter to a Linux kernel developer. I’d like to cite this bit about code review (see also Re: Open Source != peer review):

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Parallel building the CDK

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.

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Software is a Method (Meme)

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

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Scripting JChemPaint

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.

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Solubility Data in Bioclipse #1

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. The screenshot does not show the RDF yet, but that will follow soon:

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