Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Neumann, Jacob; Mallela, Abhishek; Miller, Ely F.; Colvin, Joshua; Duprat1, Abell T.; Chen, Ye; Hlavacek, William S.; Posner, Richard G.

doi:10.48550/arxiv.2109.14445

Cited by 1 publication

(1 citation statement)

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“…or developing new computational approaches such as detecting bistable switches (Reyes et al, 2022) (more???). Tool developers on the other hand use libRoadRunner as a core SBML handling component in their modular software design (Choi et al, 2018), runBiosimulations (Shaikh et al, 2021), MASSPy (Haiman et al, 2021), SBMLUtils (Watanabe et al, 2018), Compucell3D (Swat et al, 2012), PhysiCell (Ghaffarizadeh et al, 2018), pyBioNetFit (Neumann et al, 2021) and DIVIPAC (Nguyen et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library

Sauro¹,

Xu²,

Smith³

et al. 2022

Preprint

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Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML).Results: libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python or Julia interface. libRoadRunner uses a custom Just-In-Time (JIT ) compiler built on the widely-used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a large variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and nonlinear algebraic equations) and including several SBML extensions such as composition and distributions. It offers multiple deterministic and stochastic integrators, as well as tools for steady-state, sensitivity, stability analysis and structural analysis of the stoichiometric matrix.Availability: libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under the Apache License Version 2.0. libRoadRunner is also available for ARM based computers such as the Raspberry Pi and can in principle be compiled on any system supported by LLVM-13. http://sys-bio.github.io/roadrunner/index.html provides online documentation, full build instructions, binaries and a git source repository.

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