Cow chewing on GillespieSSA

August 22, 2007
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(This article was first published on Mario's Entangled Bank » R, and kindly contributed to R-bloggers)

Sorry blog for the long silence. Lately I have been juggling several time critical projects and there hardly seems to be time for such mundane activities such as sleeping, eating, never mind shaving (someone pointed out that I am starting to resemble a real Canadian, which of course is rather fitting since I recently became one).

After a brief breather and regrouping following the initial release of my R package, GillespieSSA, it was time to hit the supersonic lane again. The initial incentive for making this package was to simplify and streamline the process of setting up stochastic simulation models of continuous time rate equations (coupled ODE models) and to enable me to rapidly prototype and run large scale stochastic simulations. Ultimatelly the goal is, of course, to speed up the process of going from an idea, to results, and a paper product. So now that the package is “finished” I have “enrolled” it in several projects. For example, I just submitted 70000 runs to our in-house cluster, the Cow (remember this is Davis, the home of the fistulated cow). That should keep her busy chewing for a while. These runs are part of a paper I am writing on using stochastic simulation algorithms and GillespieSSA for ecological, epidemiological and evolutionary models.

Of course throwing various novel models at the package has also unraveled a few bugs along the way – so all those of you that are just itching to take the package for a spin might want to consider holding your horses (or cows) a tad longer. The next version, GillespieSSA 0.1-1, will be posted by the end of this month and will, in addition to a bunch of bug fixes, have a ton of new features, e.g. improved plotting utilities, management of large data sets (how large still remains to be seen), better handling of systems with a very large number of states and/or reaction channels, more model templates (just finished a very cool daisy chain SIRS model giving you a diagonal state-transition matrix [more on this in a later post, in the meantime please do not overwhelm me with request :-) ]), etc…. Somewhere along the way I am also supposed to write a manuscript, attempt to resuscitate (or cremate) one that got rejected, review two papers, prepare a lab meeting, analyze the results from another project and send it back to my collaborator, and revise the manual for the package. Oh, someone hinted to me that I should also consider providing a package for Windows (?). When did I say all of this would be done…? Right – I should get back to work, like, right now, it’s not past midnight just yet… Gad I love the academic life (no irony intended).


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