BiPSim: a flexible and generic stochastic simulator for polymerization processes

Stephan Fischer (1) , Marc Dinh (1) , Vincent Henry (1) , Philippe Robert (2) , Anne Goelzer (1) , Vincent Fromion (1)

1 MaIAGE - Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas]
2 MAMBA - Modelling and Analysis for Medical and Biological Applications

Detailed whole-cell modeling requires an integration of heterogeneous cell processes having different modeling formalisms, for which whole-cell simulation could remain tractable. Here, we introduce BiPSim, an open-source stochastic simulator of template-based polymerization processes, such as replication, transcription and translation. BiPSim combines an efficient abstract representation of reactions and a constant-time implementation of the Gillespie’s Stochastic Simulation Algorithm (SSA) with respect to reactions, which makes it highly efficient to simulate large-scale polymerization processes stochastically. Moreover, multi-level descriptions of polymerization processes can be handled simultaneously, allowing the user to tune a trade-off between simulation speed and model granularity. We evaluated the performance of BiPSim by simulating genome-wide gene expression in bacteria for multiple levels of granularity. Finally, since no cell-type specific information is hard-coded in the simulator, models can easily be adapted to other organismal species. We expect that BiPSim should open new perspectives for the genome-wide simulation of stochastic phenomena in biology.

Mots clés: mathematical biology

Domaines: Probabilités [math.PR]

Stephan Fischer, Marc Dinh, Vincent Henry, Philippe Robert, Anne Goelzer, et al.. BiPSim: a flexible and generic stochastic simulator for polymerization processes. Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-92833-5⟩. ⟨hal-03288602⟩