BiPSim: a flexible and generic stochastic simulator for polymerization processes.

ABSTRACT: 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.

SUBMITTER: Fischer S 

PROVIDER: S-EPMC8266833 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature