Wrong roadrunner simulations only when running in PyBNF

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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Wrong roadrunner simulations only when running in PyBNF #219

Closed emitra17 closed 5 years ago

emitra17 commented 5 years ago

Boehm_wrong_sim.zip

emitra17 commented 5 years ago

Looks like if a species is in a "compartment" with a volume not equal to 1, libroadrunner within PyBNF multiplies the initial concentration of the species by that volume.

emitra17 commented 5 years ago

Minimal example. Should fit with an error of 0. easy_compartment.zip