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lanl / PyBNF

An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.
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CVODE options #87

Open emitra17 opened 6 years ago

emitra17 commented 6 years ago

Roadrunner allows setting some CVODE options to reduce errors or increase speed https://sys-bio.github.io/roadrunner/python_docs/integration.html

It even lets you switch to other simulators (which are incompatible with events, unfortunately).

Could implement some of these as config options

ryants commented 6 years ago

we could definitely do abs_tol and rel_tol as config options. They'd be relevant for BNGL ode simulations too

emitra17 commented 6 years ago

Have you had experience with changing these settings and having it improve things? Is it worth the effort?