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libRoadRunner specifications

Information


Unique identifier OMICS_09368
Name libRoadRunner
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Python
License Apache License version 2.0
Computer skills Advanced
Version 1.3.2
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Endre T. Somogyi

Publication for libRoadRunner

libRoadRunner citations

 (7)
library_books

PhysiCell: An open source physics based cell simulator for 3 D multicellular systems

2018
PLoS Comput Biol
PMCID: 5841829
PMID: 29474446
DOI: 10.1371/journal.pcbi.1005991

[…] des, and tutorials, we do not provide templates for such functions beyond the documentation. We are currently testing methods to support SBML specification of ODE models in the cell agents (e.g., via libRoadrunner []), but until SBML is supported, we do not provide templates to integrate ODE models into PhysiCell functions to alter cell phenotype.PhysiCell does not currently provide direct methods […]

library_books

Modelling the molecular mechanisms of aging

2017
Biosci Rep
PMCID: 5322748
PMID: 28096317
DOI: 10.1042/BSR20160177

[…] he challenge of multi-scale modelling. Sütterlin et al. [] developed a novel software workflow (EPISIM) for the semantic integration of SBML-encased models. More recently, Somogyi et al. [] developed libRoadRunner – a Python-based application which supports large-scale problems for SBML-encoded models, including multi-module modelling. Continued progress of this nature in the field of computationa […]

library_books

A Liver Centric Multiscale Modeling Framework for Xenobiotics

2016
PLoS One
PMCID: 5026379
PMID: 27636091
DOI: 10.1371/journal.pone.0162428

[…] sub-cellular SBML and whole body PBPK/SBML models, and transfers quantities between scales. We choose the blood concentration of APAP as a scale-insensitive variable to connect the models. We use the LibRoadRunner [] package, a cross-platform, open-source, high performance C++ library for running SBML-compliant models. LibRoadRunner’s Python API allows the CC3D Python script to load the SBML model […]

library_books

Toward community standards and software for whole cell modeling

2016
IEEE Trans Biomed Eng
PMCID: 5451320
PMID: 27305665
DOI: 10.1109/TBME.2016.2560762

[…] CellDesigner [] and VANTED [], and (3) writing scripts to generate SBML from the diagrams. Other groups used model design tools such as Antimony [], BioUML [], COBRApy [], COPASI [], iBioSim [], and libRoadRunner [] to recode submodels based on the original documentation. A few of the groups encoded submodels by converting the MATLAB code to SBML. As an example, and File S1 illustrate how we rec […]

call_split

Probabilistic adaptation in changing microbial environments

2016
PeerJ
PMCID: 5160922
PMID: 27994963
DOI: 10.7717/peerj.2716
call_split See protocol

[…] The nutrient transition counter model was drawn in CellDesigner (version 4.4) (), serialized as an SBML file, and simulated in Python using libRoadRunner. The SBML file for the model is available at 10.6084/m9.figshare.3493994. A detailed report of the chemical reactions and rate parameters was generated by SBML2 () and is available at 1 […]

library_books

DYVIPAC: an integrated analysis and visualisation framework to probe multi dimensional biological networks

2015
Sci Rep
PMCID: 4518224
PMID: 26220783
DOI: 10.1038/srep12569

[…] ynSig.To enable parallel processing and allow users to utilise the power of high-performance computing, we have also implemented the dynamical analysis steps of DYVIPAC in Python using the API of the libRoadRunner 1.3.1 library (libroadrunner.org) (). Importantly, this implementation allows the users to load models in Systems Biology Markup Language (SBML) format, the most widely used standard for […]

Citations

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libRoadRunner institution(s)
Biocomplexity Institute and Department of Physics, Indiana University, Bloomington, IN, USA; Biomedical Engineering Department, University of Southern California, Los Angeles, CA, USA; Department of Computational Systems Biochemistry, University Medicine Charité Berlin, Berlin, Germany; Department of Bioengineering, University of Washington, Seattle, WA, USA

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