Build and simulate jump equations like Gillespie simulations and jump diffusions with constant and state-dependent rates and mix with differential equations and scientific machine learning (SciML)
@TorkelE pointed out that on a multisite phosphorylation benchmark where species can have many phosphorylation states, we are starting to lose performance relative to network-free methods as the number of sites increases (NF methods track individual molecules and their states). It would be worth thinking about how to include such solvers / representations here too, especially in ways that can exploit our current SSA infrastructure.
@TorkelE when you are able to share, could you link the network files and sources?
@TorkelE pointed out that on a multisite phosphorylation benchmark where species can have many phosphorylation states, we are starting to lose performance relative to network-free methods as the number of sites increases (NF methods track individual molecules and their states). It would be worth thinking about how to include such solvers / representations here too, especially in ways that can exploit our current SSA infrastructure.
@TorkelE when you are able to share, could you link the network files and sources?