Sunday, June 21, 2009

The Dr Who's of Life Sciences

Peter recently wrote up a model of how several Blue Obelisk (please contribute to the page!) projects changed in history: The Doctor Who Model of Open Source. This was later picked up by Glyn and then by Slashdot (second time Peter got that fame; that's one of the advantages of working at a well-known institute, instead of something like Uppsala University. Beside Bioclipse, GROMACS and the CDK, MySQL AB actually has a headquarters here.) Thanx to Chris who pointed me to the Slashdot coverage.

Now, the several blogs and the Slashdot item contain interesting discussions on whether the 'Dr Who' model is the best model of how open source projects can evolve. Fact is, at least, that the model does not describe a new phenomenon; Peter merely describes a how the Blue Obelisk deals with the limited resources we have in cheminformatics, and that the succession of project leaders ensures both the scientists interest (who are generally not payed for development or, $Foo forbid, maintenance of scientific data analysis methods) as well as the project itself. This makes life science open source different from most pure-IT projects: open source academic software is always something on the side.

So, when Miguel Howard turned to Jmol, he had seemingly unlimited resources to work on Jmol and he had great ideas and made them work: Miguel is the father of the now so popular Jmol applet with scripting functionality. It did mean that the integration with the CDK I worked on, as planned by the original Jmol author Dan Gezelter, Christoph and me in 2000: the CDK data model was too slow (it is amazing how fast Jmol is, without using accelerated graphics! See this Nature Preceedings paper: DOI:10.1038/npre.2007.50.1). My attention was better spend on the CDK.

Now, if the need arises, and the current Jmol head Bob looses interest or time, I'll be available to take over again. That is less likely to happen for an older Dr. Who actor. Several Slashdot commenters also pointed out that the model also matches the 'drummer-in-a-band' model. I guess, or lead-singer... This moved the discussion of what the model exactly models. Peter writes:
    "Instead the Blue Obelisk community seems to have evolved a “Doctor Who” model. You’ll recall that every few years something fatal happens to the Doctor and you think he is going to die and there will never be another series. Then he regenerates. The new Doctor has a different personality, a different philosophy (though always on the side of good). It is never clear how long any Doctor will remain unregenerated or who will come after him. And this is a common theme in the Blue Obelisk."

This brings me back to the earlier observation I wrote down: science is different, and Peter is right when he says you think he is going to die and there will never be another series. This thought is justified for many open source science projects; in Glyn's blog there is the remark of lack of data, but I think if someone would count of the number of dead open source science projects, I think the outcome will be that the fear is highly justified.

This is likely also the power of the Blue Obelisk: it creates a lively and rewarding community with equally minded people, forming an eco-system where the individual projects can flourish. Maybe someone can come of with a good metaphore for the Blue Obelisk, matching the Dr Who model? BBC comes to mind: is the BBC an eco-system where small TV series can survive?

Anyways, my father used to watch Dr Who, and being compared to Dr Who is much more rewarding than being compared to a drummer in some band.