MOCCASIN: Converting MATLAB ODE models to SBML

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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 SBML (Systems Biology Markup Language) 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.<br /><br />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.<br /><br />SUPPLEMENTARY INFORMATION: More information is available at https://github.com/sbmlteam/moccasin.<br /><br />CONTACT: moccasin-dev@googlegroups.com.

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APA

Gómez, H. F., Hucka, M., Keating, S. M., Nudelman, G., Iber, D., & Sealfon, S. C. (2016). MOCCASIN: Converting MATLAB ODE models to SBML. Bioinformatics, 32(12), 1905–1906. https://doi.org/10.1093/bioinformatics/btw056

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