title: MOCCASIN: converting MATLAB ODE models to SBML.
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.
  
  
  
  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
  
  
  
  : mhucka@caltech.edu
  
  
  
  More information is available at https://github.com/sbmlteam/moccasin.
authors: Department of Biosystems Science and Engineering, ETH Zürich, Basel CH 4058, Switzerland.
authors: Harold F
authors: HF
authors: Gómez
authors: Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
authors: Michael
authors: M
authors: Hucka
authors: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, UK and.
authors: Sarah M
authors: SM
authors: Keating
authors: Department of Neurology, Icahn School of Medicine at Mount Sinai, Mount Sinai Medical Center and School of Medicine, New York, NY 10029, USA.
authors: German
authors: G
authors: Nudelman
authors: Department of Biosystems Science and Engineering, ETH Zürich, Basel CH 4058, Switzerland.
authors: Dagmar
authors: D
authors: Iber
authors: Department of Neurology, Icahn School of Medicine at Mount Sinai, Mount Sinai Medical Center and School of Medicine, New York, NY 10029, USA.
authors: Stuart C
authors: SC
authors: Sealfon
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D012984:Software; D049490:Systems Biology