CellDesigner: A graphical biological network editor and workbench interfacing simulator

Akira Funahashi; Mineo Morohashi; Yukiko Matsuoka; Akiya Jouraku; Hiroaki Kitano

doi:10.1007/978-1-59745-531-2_21

CellDesigner: A graphical biological network editor and workbench interfacing simulator

Akira Funahashi, Mineo Morohashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano

Research output: Chapter in Book/Report/Conference proceeding › Chapter

8 Citations (Scopus)

Abstract

Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/.

Original language	English
Title of host publication	Introduction to Systems Biology
Publisher	Humana Press
Pages	422-434
Number of pages	13
ISBN (Print)	9781588297068
DOIs	https://doi.org/10.1007/978-1-59745-531-2_21
Publication status	Published - 2007
Externally published	Yes

Keywords

Pathway editor
SBGN
SBML
SBW
XML
biochemical simulation
systems biology

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)

Access to Document

10.1007/978-1-59745-531-2_21

Cite this

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abstract = "Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/.",

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author = "Akira Funahashi and Mineo Morohashi and Yukiko Matsuoka and Akiya Jouraku and Hiroaki Kitano",

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AU - Morohashi, Mineo

AU - Matsuoka, Yukiko

AU - Jouraku, Akiya

AU - Kitano, Hiroaki

PY - 2007

Y1 - 2007

N2 - Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/.

AB - Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/.

KW - Pathway editor

KW - SBGN

KW - SBML

KW - SBW

KW - XML

KW - biochemical simulation

KW - systems biology

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BT - Introduction to Systems Biology

PB - Humana Press

ER -

CellDesigner: A graphical biological network editor and workbench interfacing simulator

Abstract

Keywords

ASJC Scopus subject areas

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