Abstract
AbstractSummaryLarge-scale and whole-cell modeling has multiple challenges, including scalable model building and module communication bottlenecks (e.g. between metabolism, gene expression, signaling, etc). We previously developed an open-source, scalable format for a large-scale mechanistic model of proliferation and death signaling dynamics, but communication bottlenecks between gene expression and protein biochemistry modules remained. Here, we developed two solutions to communication bottlenecks that speed up simulation by ~4-fold for hybrid stochastic-deterministic simulations and by over 100-fold for fully deterministic simulations.Availability and ImplementationSource code is freely available athttps://github.com/birtwistlelab/SPARCED/releases/tag/v1.1.0implemented in python, and supported on Linux, Windows, and MacOS (via Docker).ContactMarc Birtwistlembirtwi@clemson.eduSupplementary informationN/A
Publisher
Cold Spring Harbor Laboratory