Abstract

Summary: 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.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.Contact: mhucka@caltech.eduSupplementary information: More information is available at https://github.com/sbmlteam/moccasin.

Highlights

  • MATLAB is a general-purpose numerical computing environment whose powerful features have attracted many researchers

  • Supplementary information: More information is available at https://github.com/sbmlteam/ moccasin

  • There are reasons why MATLAB programs are not themselves a desirable format for exchanging, publishing or archiving computational models in biology. These include the lack of biological semantics in MATLAB programs, which makes clear interpretation of programs as models of biological processes more difficult; the fact that MATLAB is proprietary and expensive, which makes it unsuitable as a universal format for open scientific exchange; and the fact that model details are often intertwined with program implementation details, which makes it difficult to determine which parts constitute the essence of a model

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Summary

Introduction

MATLAB is a general-purpose numerical computing environment whose powerful features have attracted many researchers It has been the substrate for countless models as well as software tools written in its object-oriented programming language. These issues led us to develop Model ODE Converter for Creating Automated SBML Interoperability (MOCCASIN), a standalone tool that can take ODE models written in MATLAB and export them as SBML files. The result allows for richer SBML that can be used for qualitative analyses where knowledge of the reaction network behind a system of ODEs is required

Implementation
Parsing module
Converter module
BIOCHAM module
Graphical user interface
Future work

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