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.
A libroadrunner feature is under development (see https://github.com/sys-bio/roadrunner/issues/550) that allows saving and reloading a libroadrunner object. This would let us avoid the slow XML load that currently occurs for every simulation. I've tested a pre-release libroadrunner with this feature, and it is working well.
When this feature is released, PyBNF should use this workflow to gain a significant speedup in SBML fitting.
A libroadrunner feature is under development (see https://github.com/sys-bio/roadrunner/issues/550) that allows saving and reloading a libroadrunner object. This would let us avoid the slow XML load that currently occurs for every simulation. I've tested a pre-release libroadrunner with this feature, and it is working well.
When this feature is released, PyBNF should use this workflow to gain a significant speedup in SBML fitting.