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From 2011.igem.org

SimBiology is a modeling gui very similar to COPASI. Its added advantage is the intergration with the matlab enviorment. This means that you can use scripts functions and other methods produced in matlab to extend the existing functionalety.

Although it looks nice on first glance, it's bugs and quircks are numerous. A horrendously broken unit system combined with a user interface that is not al that friendly to work with make producing something in simbiolegy a challange that migth not be worth taking.

SimBiology also enforces the markov asumtion: every next timestep can be calculated using only the previous timestep. This gives some problems when modeling transcription and translation acurately. Although we where able to produce a workaround we would not reccomend trying this to unexperienced matlab users.