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.
authors.affiliation: Center for Genetic and Genomic Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China,. Electronic address: chenli2012@zju.edu.cn.
authors.forename: Chen
authors.initials: C
authors.lastname: Li
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan. Electronic address: nagasaki@megabank.tohoku.ac.jp.
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan. Electronic address: pond@hgc.jp.
authors.forename: Emi
authors.initials: E
authors.lastname: Ikeda
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan. Electronic address: sekiya@hgc.jp.
authors.forename: Yayoi
authors.initials: Y
authors.lastname: Sekiya
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan. Electronic address: miyano@hgc.jp.
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D003198:Computer Simulation; D053858:Metabolic Networks and Pathways / Q000502:physiology*; D008954:Models, Biological; D011381:Programming Languages; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
keywords: CSML; Modeling; Quantitative biological pathways; SBML; Simulation