Overview

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CSML and SBML are popular used XML-based model definition standards for biological pathways in systems biology. We develope a release of a format convertor for quantitative biological pathways, CSML2SBML, converting models expressed in CSML into SBML, enabling simulations or parameter estimation with compliant tools such as CellDesigner and COPASI. The converter is based on the versions of the standards CSML version 3.0 and SBML Level 2 Version 4 (L2V4).

In our experiment, 11 out of 15 pathway models in the CSML repository and 228 models in the Macrophage Pathway Knowledgebase (MACPAK) are automatically converted into SBML. In addition, converted SBML models with the accurate kinetic parameters mapped from CSML models can reproduce the same dynamics.