LibSBMLSim 1.4.0 – The library for Simulating SBML models

LibSBMLSim 1.4.0

:: DESCRIPTION

LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs). LibSBMLSim provides simple command-line tool and several APIs to load an SBML model, perform numerical integration (simulate) and export its results. Both explicit and implicit methods are supported on libSBMLSim.

::DEVELOPER

Funahashi Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
libSBML
CMake

:: DOWNLOAD

LibSBMLSim

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1474-6. doi: 10.1093/bioinformatics/btt157.
LibSBMLSim: A reference implementation of fully functional SBML simulator.
Takizawa H, Nakamura K, Tabira A, Chikahara Y, Matsui T, Hiroi N, Funahashi A.

SBML Reaction Finder 1.2.1 – Extracts Chemical Reactions from SBML models

SBML Reaction Finder 1.2.1

:: DESCRIPTION

The SBML Reaction Finder retrieves and extracts individual chemical reactions from curated SBML models.

::DEVELOPER

SBML Reaction Finder Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux / Mac OsX
JAVA

:: DOWNLOAD

SBML Reaction Finder

:: MORE INFORMATION

SBMLToolbox 4.1.0 – SBML models toolbox for MATLAB users

SBMLToolbox 4.1.0

:: DESCRIPTION

SBMLToolbox is built on top of libSBML and provides a set of basic functions allowing SBML models to be used in MATLAB. SBMLToolbox provides functions for reading, writing, and validating SBML models; viewing model structures in a simple GUI; converting models into a symbolic form suitable for use with MATLAB’s Symbolic Math Toolbox; and simulate models using MATLAB’s ordinary differential equation solvers.

SBMLToolbox works by translating SBML models to/from a MATLAB structure calledMATLAB_SBML. It provides facilities for manipulating this and its substructures within MATLAB, as well as functions for saving and loading MATLAB_SBML structures to/from MATLAB data files.

::DEVELOPER

Sarah Keating

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux / Mac OsX
MATLAB

:: DOWNLOAD

SBMLToolbox ; Manual

:: MORE INFORMATION

Citation:

Keating, S. M., Bornstein, B. J., Finney, A., and Hucka M. (2006) SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics, 22(10):1275–1277.

SBMLToolbox License