Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories
Fig 3
Software pipeline for realistic cell geometry simulations.
Geometries are learned from images by CellOrganizer. Chemical reaction networks are generated from rule-based models in BioNetGen. Geometries and reaction networks are imported to MCell via the CellBlender visual editor. The spatial stochastic model is then simulated in MCell, with WESTPA managing a weighted ensemble of MCell trajectories.