Paper Info
Title
CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML.
Abstract
CSML and SBML are XML-based model definition standards which are developed with the aim of creating exchange formats for modeling, visualizing and simulating biological pathways. In this article we report a release of a format convertor for quantitative pathway models, namely CSML2SBML. It translates models encoded by CSML into SBML without loss of structural and kinetic information. The simulation and parameter estimation of the resulting SBML model can be carried out with compliant tool CellDesigner for further analysis. The convertor is based on the standards CSML version 3.0 and SBML Level 2 Version 4. In our experiments, 11 out of 15 pathway models in CSML model repository and 228 models in Macrophage Pathway Knowledgebase (MACPAK) are successfully converted to SBML models. The consistency of the resulting model is validated by libSBML Consistency Check of CellDesigner. Furthermore, the converted SBML model assigned with the kinetic parameters translated from CSML model can reproduce the same dynamics with CellDesigner as CSML one running on Cell Illustrator. CSML2SBML, along with its instructions and examples for use are available at http://csml2sbml.csml.org
Year
DOI
Venue
2014
10.1016/j.biosystems.2014.05.004
Biosystems
Keywords
Field
DocType
CSML,SBML,Quantitative biological pathways,Modeling,Simulation
Programming language,XML,Computer science,Systems Biology Ontology,Theoretical computer science,Artificial intelligence,Machine learning,SBML
Journal
Volume
ISSN
Citations 
121
0303-2647
0
PageRank 
References 
Authors
0.34
12
5
Name
Order
Citations
PageRank
Lingen Chen121.35
Masao Nagasaki236826.22
Emi Ikeda3282.62
Yayoi Sekiya421.06
Satoru Miyano52406250.71