Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Hi all, this summer I'm planning on adding a lot of graph/network analysis features relevant for chemical reaction networks to Catalyst. A smattering of things this might include:
Adding a "network summary" that tells you about relevant features at-a-glance
Let me know if people have other suggestions - I would like to focus on functionality that would be useful for practicing chemists/systems biologists, but am not super familiar with this literature. My focus over the next few weeks will be adding algorithms for different properties, rather than the summary/UI side, but if people have suggestions for the latter I'm also happy to hear them.
Detect the set of minimal siphons in the reaction network, following Shiu et al., 2009
Check necessary and sufficient conditions for persistence outlined in Angeli et al., 2007: a network is persistent iff it is consistent (S-matrix has right null eigenvector), conservative (S-matrix has left null eigenvector), and all of its siphons are not critical (i.e. they contain the support of a conservation law)
Hi all, this summer I'm planning on adding a lot of graph/network analysis features relevant for chemical reaction networks to Catalyst. A smattering of things this might include:
Let me know if people have other suggestions - I would like to focus on functionality that would be useful for practicing chemists/systems biologists, but am not super familiar with this literature. My focus over the next few weeks will be adding algorithms for different properties, rather than the summary/UI side, but if people have suggestions for the latter I'm also happy to hear them.