chem-bla-ics: 2008

Editing and Validation of CML documents in Bioclipse

One advantage of using XML is that one can rely on good support in libraries for functionality. When parsing XML, one does not have to take care of the syntax, and focus on the data and its semantics. This comes at the expense of verbosity, though, but having the ability to express semantics explicitly is a huge benefit for flexibility.

So, when Peter and Henry put their first documents online about the Chemical Markup Language (CML), I was thrilled, even though is actually was still SGML when I encountered it. The work predates the XML recommendation. As I recently blogged, in '99 I wrote patches for Jmol and JChemPaint to support CML, which were published as preprint in the Chemical Preprint Server in a paper in 2000 in the Internet Journal of Chemistry. Neither of the two has survived.

Dec

11 Years of Debian

11 years ago, a day more or less, I bought an the special issue of CHIP which shipped Debian 1.3.1. I think I've tried SuSe and RedHat earlier that year, but this Debian release made me switch away from proprietary products 98% (taxes I still had to do with Windows98). Right now, I am mostly running Ubuntu, which leans heavily on the work of the Debian project.

Dec

State of CDK 1.2.0...

The reason why I have not blogged in more than two weeks, was that I was hoping to blog about the CDK 1.2.0 release. This was originally aimed at September, slipped into October, November and then December. There were only three show stoppers (see this wiki page), one of which the IChemObject interfaces were not properly tested.

The problem was that the unit tests for the methods in superinterfaces were not applied to implementations of subinterfaces.

Dec

Peer reviewed Cheminformatics #2: Code review for the Chemistry Development Kit

Peer review is an important component of open source development, and recently there was the discussion the other way around, if open source is required for peer review.

Dec

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.

Dec

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.

Dec

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):[Andrew Morton] had a number of concrete requests - such as documenting the user-space ABI and the network protocol - which have not been satisfied. He also asked for better code documentation in general:So please. Go through all the code and make it tell a story.

Nov

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.

Nov

Software is a Method (Meme)

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)

Now, to me it's trivial to work put how Open Source supports this.

Nov

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.

Gilleain and Arvid are merging their branches into a single code base, while Stefan is working on the Swing application and applet. The Bioclipse SWT-based widget is being developed for Bioclipse2.