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Published June 15, 2016 | Published
Journal Article Open

MOCCASIN: converting MATLAB ODE models to SBML

Gómez, Harold F. ORCID icon
Hucka, Michael ORCID icon
Keating, Sarah M. ORCID icon
Nudelman, German ORCID icon
Iber, Dagmar ORCID icon
Sealfon, Stuart C. ORCID icon

Abstract

MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging—especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format.

Additional Information

© The Author 2016. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received November 11, 2015. Revision received January 19, 2016. Accepted January 25, 2016. First published online: February 9, 2016. The authors thank Thomas B. Kepler, Franz-Josef Elmer, Bernd Rinn and Jannik Vollmer for helpful discussions and implementation ideas. Availability and implementation: MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin. Funding: Modeling Immunity for Biodefense contracts HHSN266200500021C (M.H., G.N., S.C.S.), U19AI117873 (G.N., S.C.S.) and HHSN272201000053C (H.F.G., Thomas B. Kepler), and by the Swiss Institute of Bioinformatics. Conflict of Interest: none declared.

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September 15, 2023
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October 23, 2023