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metrumresearchgroup / mrgsolve

Simulate from ODE-based population PK/PD and QSP models in R
https://mrgsolve.org
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Feature Consideration: Stochastic Integrators #575

Closed billdenney closed 4 years ago

billdenney commented 4 years ago

Note that I'm not even calling this to the level of a feature request.

The Gillespie algorithm is used to simulate stochastic, countable chemical reactions (and similar): https://en.wikipedia.org/wiki/Gillespie_algorithm

I'm trying to implement a CAR-T model which includes a stochastic probability of cure: https://www.biorxiv.org/content/10.1101/717074v2

It would be interesting to me if mrgsolve also included a hybrid deterministic/stochastic integrator that could combine typical ODE solutions with the Gillespie algorithm (perhaps simplifying life using the Tau-leap version of the algorithm so that an explicit algorithm switch would not be required: https://en.wikipedia.org/wiki/Tau-leaping).

This would be a massive change, I understand, but it would open up a new class of problems that is not possible today with mrgsolve.

kylebaron commented 4 years ago

Closing this. Maybe is is something that would be doable in the julia package.