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SciML / Catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
https://docs.sciml.ai/Catalyst/stable/
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Moment Equations #22

Open ChrisRackauckas opened 6 years ago

ChrisRackauckas commented 6 years ago

It would be nice to automatically be able to get out the moment equations according to some moment-closure scheme.

https://ifisc.uib-csic.es/users/raul/CURSOS/SP/Introduction_to_master_equations.pdf http://web.mit.edu/biophysics/sbio/PDFs/stochastics.pdf https://www-liphy.ujf-grenoble.fr/pagesperso/bahram/Master_Eq/master.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176737/pdf/nihms252393.pdf https://www.omicsonline.org/open-access/chemical-master-equation-empirical-moment-closure-2329-6577-1000155.pdf http://www.pnas.org/content/110/35/14261 https://www.sciencedirect.com/science/article/pii/S0096300306000117 https://arxiv.org/pdf/1608.06582.pdf

ChrisRackauckas commented 6 years ago

Special methods for first-order reactions: https://www.sciencedirect.com/science/article/pii/S0092824004001247

TorkelE commented 1 year ago

Can this be considered solved by https://github.com/augustinas1/MomentClosure.jl?

Possibly we could add a tutorial in Catalyst as well.

isaacsas commented 1 year ago

I'm not sure MomentClosure.jl covers the full complement of methods we'd want, but it is probably the right place for adding new methods (though it would be good if it got put under SciML or some other organization to try to ensure it is maintained longer-term).

TorkelE commented 1 year ago

Got it, sounds good. We can keep this open until we've figured it out.