sorgerlab/pysb — Issue #18: Type descriptor (e.g. fwd, rev, cat) for rate parameters
Author: jablists
Created: 2012-02-27 14:07:39+00:00
State: open

If rate parameters are given a type descriptor (as a shortcut, this could even be automatic based on their names, e.g. myrate_kf) then it would be simpler to assign default values to them during rapid model prototyping. Similarly, it would be easier to assign prior distributions when performing parameter estimation. Hoda's code, for example, divides parameters along these lines.

I'm imagining that there could be at least four types: unimolecular forward (e.g., for a state transition that occurs spontaneously for a single species, i.e., A <-> A*, bimolecular forward (typical on-rate for a rxn), reverse (unbinding reaction, could be based on a typical binding in the 100nM range) and catalytic.

This could be achieved by adding a rate_type field to the Parameter class and initializing appropriately when the parameter is created.