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BioModels
- azeemba 4y agoLooking 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
- bglazer 4y agoInteresting 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. 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
- dr_kiszonka 4y agoRecommendations for good intro textbooks? : - ) Do folks mostly use MatLab or is Python more popular? (IIRC, MatLab used to have a nice GUI for things like system dynamics.)
- melony 4y agoBe very very good at differential equations. Systems/synthetic biology primarily rely on dynamics to model behavior and side effects. AlphaFold is actually pretty different from the biomodel type of modeling. This is a good intro to (non deep learning based) computational/synthetic biology. ML in biology is somewhat orthogonal but it is rapidly growing. http://be150.caltech.edu/2020/content/index.html http://be150.caltech.edu/2020/content/index.html Traditional bioinformatics is mostly text mining and string processing. Modern bioinformatics is heavily dominated by ML.
- dr_kiszonka 4y agoGreat course - thanks for sharing! Regarding being very good at differential equations: if I remember correctly, one way to approach solving them is to convert them to difference equations and solve them numerically (and not analytically). Is this true? As you can probably tell, I am not good at differential equations at all, so I was thinking about using difference equations as a crutch.