LibSBMLSim: A reference implementation of fully functional SBML simulator

Hiromu Takizawa; Kazushige Nakamura; Akito Tabira; Yoichi Chikahara; Tatsuhiro Matsui; Noriko Hiroi; Akira Funahashi

doi:10.1093/bioinformatics/btt157

LibSBMLSim: A reference implementation of fully functional SBML simulator

Hiromu Takizawa, Kazushige Nakamura, Akito Tabira, Yoichi Chikahara, Tatsuhiro Matsui, Noriko Hiroi, Akira Funahashi

Department of Biosciences and Informatics

Research output: Contribution to journal › Article › peer-review

12 Citations (Scopus)

Abstract

Motivation: The Systems Biology Markup Language (SBML) is currently supported by >230 software tools, among which 160 support numerical integration of ordinary differential equation (ODE) models. Although SBML is a widely accepted standard within this field, there is still no language-neutral library that supports all features of SBML for simulating ODE models. Therefore, a demand exists for a simple portable implementation of a numerical integrator that supports SBML to enhance the development of a computational platform for systems biology.Results: We implemented a library called libSBMLSim, which supports all the features of SBML and confirmed that the library passes all tests in the SBML test suite including those for SBML Events, AlgebraicRules, 'fast' attribute on Reactions and Delay. LibSBMLSim is implemented in the C programming language and does not depend on any third-party library except libSBML, which is a library to handle SBML documents. For the numerical integrator, both explicit and implicit methods are written from scratch to support all the functionality of SBML features in a straightforward implementation. We succeeded in implementing libSBMLSim as a platform-independent library that can run on most common operating systems (Windows, MacOSX and Linux) and also provides several language bindings (Java, C#, Python and Ruby).

Original language	English
Pages (from-to)	1474-1476
Number of pages	3
Journal	Bioinformatics
Volume	29
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btt157
Publication status	Published - 2013 Jun 1

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btt157

Cite this

@article{8829002edc7e4d249c6b7ae5975781ec,

title = "LibSBMLSim: A reference implementation of fully functional SBML simulator",

abstract = "Motivation: The Systems Biology Markup Language (SBML) is currently supported by >230 software tools, among which 160 support numerical integration of ordinary differential equation (ODE) models. Although SBML is a widely accepted standard within this field, there is still no language-neutral library that supports all features of SBML for simulating ODE models. Therefore, a demand exists for a simple portable implementation of a numerical integrator that supports SBML to enhance the development of a computational platform for systems biology.Results: We implemented a library called libSBMLSim, which supports all the features of SBML and confirmed that the library passes all tests in the SBML test suite including those for SBML Events, AlgebraicRules, 'fast' attribute on Reactions and Delay. LibSBMLSim is implemented in the C programming language and does not depend on any third-party library except libSBML, which is a library to handle SBML documents. For the numerical integrator, both explicit and implicit methods are written from scratch to support all the functionality of SBML features in a straightforward implementation. We succeeded in implementing libSBMLSim as a platform-independent library that can run on most common operating systems (Windows, MacOSX and Linux) and also provides several language bindings (Java, C#, Python and Ruby).",

author = "Hiromu Takizawa and Kazushige Nakamura and Akito Tabira and Yoichi Chikahara and Tatsuhiro Matsui and Noriko Hiroi and Akira Funahashi",

year = "2013",

month = jun,

day = "1",

doi = "10.1093/bioinformatics/btt157",

language = "English",

volume = "29",

pages = "1474--1476",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "11",

}

TY - JOUR

T1 - LibSBMLSim

T2 - A reference implementation of fully functional SBML simulator

AU - Takizawa, Hiromu

AU - Nakamura, Kazushige

AU - Tabira, Akito

AU - Chikahara, Yoichi

AU - Matsui, Tatsuhiro

AU - Hiroi, Noriko

AU - Funahashi, Akira

PY - 2013/6/1

Y1 - 2013/6/1

N2 - Motivation: The Systems Biology Markup Language (SBML) is currently supported by >230 software tools, among which 160 support numerical integration of ordinary differential equation (ODE) models. Although SBML is a widely accepted standard within this field, there is still no language-neutral library that supports all features of SBML for simulating ODE models. Therefore, a demand exists for a simple portable implementation of a numerical integrator that supports SBML to enhance the development of a computational platform for systems biology.Results: We implemented a library called libSBMLSim, which supports all the features of SBML and confirmed that the library passes all tests in the SBML test suite including those for SBML Events, AlgebraicRules, 'fast' attribute on Reactions and Delay. LibSBMLSim is implemented in the C programming language and does not depend on any third-party library except libSBML, which is a library to handle SBML documents. For the numerical integrator, both explicit and implicit methods are written from scratch to support all the functionality of SBML features in a straightforward implementation. We succeeded in implementing libSBMLSim as a platform-independent library that can run on most common operating systems (Windows, MacOSX and Linux) and also provides several language bindings (Java, C#, Python and Ruby).

AB - Motivation: The Systems Biology Markup Language (SBML) is currently supported by >230 software tools, among which 160 support numerical integration of ordinary differential equation (ODE) models. Although SBML is a widely accepted standard within this field, there is still no language-neutral library that supports all features of SBML for simulating ODE models. Therefore, a demand exists for a simple portable implementation of a numerical integrator that supports SBML to enhance the development of a computational platform for systems biology.Results: We implemented a library called libSBMLSim, which supports all the features of SBML and confirmed that the library passes all tests in the SBML test suite including those for SBML Events, AlgebraicRules, 'fast' attribute on Reactions and Delay. LibSBMLSim is implemented in the C programming language and does not depend on any third-party library except libSBML, which is a library to handle SBML documents. For the numerical integrator, both explicit and implicit methods are written from scratch to support all the functionality of SBML features in a straightforward implementation. We succeeded in implementing libSBMLSim as a platform-independent library that can run on most common operating systems (Windows, MacOSX and Linux) and also provides several language bindings (Java, C#, Python and Ruby).

UR - http://www.scopus.com/inward/record.url?scp=84878290340&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84878290340&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btt157

DO - 10.1093/bioinformatics/btt157

M3 - Article

C2 - 23564843

AN - SCOPUS:84878290340

SN - 1367-4803

VL - 29

SP - 1474

EP - 1476

JO - Bioinformatics

JF - Bioinformatics

IS - 11

ER -

LibSBMLSim: A reference implementation of fully functional SBML simulator

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this