Interesting to see Biomodels on HN. This kind of computational modeling is still fairly niche in biology but I think it’s going to play a much larger role in the future in understanding biology. If you look at a graph of all the interactions between proteins in a cell, it’s pretty clear that everything influences everything else, but we still just don’t understand the details of those interactions. It’s also clear that those atomistic level details can matter quite a lot. Tools like AlphaFold are going to be really important for that, but model repositories like biomodels will help us integrate those details into the networks that actually give rise to the larger scale behavior of cells.<p>Happy to answer any questions about computational modeling in biology. I’m just a phd student but I’m writing a review about this at the moment so I’ve been thinking about it quite a bit
Looking around at some models, they seem to be like state machines to describe specific subsystems of different organisms.<p>The seem to be using a markup format called [SBML](<a href="https://synonym.caltech.edu/" rel="nofollow">https://synonym.caltech.edu/</a>).<p>> Many software tools and databases support SBML directly. You don’t write in SBML yourself—your software does it for you.<p>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.