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BiPSim: a flexible and generic stochastic simulator for polymerization processes

Abstract : 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. 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.
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https://hal.inria.fr/hal-03288602
Contributor : Philippe Robert Connect in order to contact the contributor
Submitted on : Friday, July 16, 2021 - 1:37:57 PM
Last modification on : Wednesday, June 8, 2022 - 12:50:08 PM

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Distributed under a Creative Commons Attribution 4.0 International License

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

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