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Looking around at some models, they seem to be like state machines to describe specific subsystems of different organisms. The seem to be using a markup format
by azeemba 4y ago
Looking around at some models, they seem to be like state machines to describe specific subsystems of different organisms.
The seem to be using a markup format called [SBML](https://synonym.caltech.edu/ https://synonym.caltech.edu/).
> Many software tools and databases support SBML directly. You don’t write in SBML yourself—your software does it for you.
So its likely that you aren't supposed to parse/write the SBML directly. The BioModels website also provides PNGs so you can look at the state machines visually.
- bglazer 4y agoThese models are not exactly state machines, they’re usually expressed as systems of differential equations. They’re sometimes expressed as stochastic equations, which are like random state machines, I think. But yeah, SBML is the standard and there are a number of tools that let you express reactions between bio molecules in easy to read formats. These then output SBML, which is easier to share. Kind of impressive that academics were able to settle on some real standardization for this field
- amelius 4y agoPerhaps they should be expressed as (analog) electrical circuits. Then you get differential equations in a format that is common and relatively easy to read.
- sampo 4y agoI don't know. I find the differential equations much easier to read than this corresponding electrical circuit. http://seti.harvard.edu/unusual_stuff/misc/lorenz.htm http://seti.harvard.edu/unusual_stuff/misc/lorenz.htm