|Prof Darren Wilkinson||Professor of Stochastic Modelling|
|School of Mathematics, Statistics and Physics|
This page describes a "shorthand" version of SBML that is much easier to read and write by hand than real SBML, together with a software tool that translates the shorthand model description to real SBML.
It isn't really meant as a complete alternative to GUI model-building tools. It is just a useful tool for rapid building of essential model structure. Once the basics are defined, you can translate to SBML and load up in the GUI tool of your choice.
@model:2.3.1=MichaelisMentenKinetics "Michaelis-Menten Kinetics" @compartments cell=1 @species cell:Substrate=1000 cell:Enzyme=100 cell:Complex=0 cell:Product=0 @parameters k1=1 k1r=2 @reactions @rr=SubstrateEnzymeBinding "Substrate-enzyme binding" Substrate+Enzyme -> Complex k1*Substrate*Enzyme-k1r*Complex @r=Conversion Complex -> Product + Enzyme k2*Complex : k2=3You can download this example: mm.mod. Using the translation tool below, this model translates to this SBML.
Obviously, as the shorthand specification does not contain all SBML features, there is likely to be loss involved. However, there should be no semantic loss in the round-trip SBML-sh -> SBML -> SBML-sh. ie. doing a mod2sbml.py conversion followed by a sbml2mod.py conversion should get back to a shorthand file that is semantically equivalent to the original. sbml2mod.py works very similarly to mod2sbml.py, so no separate documentation should be necessary.