SBML-PET-MPI 1.2 – Parallel Parameter Estimation Tool for SBML based Models

SBML-PET-MPI 1.2

:: DESCRIPTION

SBML-PET-MPI is a parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models. The tool allows the user to perform parameter estimation, parameter uncertainty and identifiability analysis by collectively fitting multiple experimental data sets.

::DEVELOPER

Zhike Zi

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows with Cygwin/ Linux / Mac OsX

:: DOWNLOAD

 SBML-PET-MPI

:: MORE INFORMATION

Citation:

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.
Zi Z. (2011)
Bioinformatics. 2011 Apr 1;27(7):1028-9.

MOCCASIN 1.0.3 – Converting MATLAB ODE models to SBML

MOCCASIN 1.0.3

:: DESCRIPTION

MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) is designed to convert certain basic forms of ODE simulation models written in MATLAB or Octave and translate them into SBML format

::DEVELOPER

MOCCASIN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab

:: DOWNLOAD

 MOCCASIN

:: MORE INFORMATION

Citation

MOCCASIN: converting MATLAB ODE models to SBML.
Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC.
Bioinformatics. 2016 Feb 9. pii: btw056.

JSBML 1.1 beta1 – Java library for SBML

JSBML 1.1 beta1

:: DESCRIPTION

JSBML is a free, open-source, pure-Java library for working with SBML. It emulates libSBML’s API, with more Java idioms and without native object code.

JSBML is the library for reading, writing, and manipulating SBML files and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.

::DEVELOPER

Andreas Dräger and Nicolas Rodriguez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java SE

:: DOWNLOAD

JSBML

:: MORE INFORMATION

Citation

JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A.
Bioinformatics. 2015 Jun 16. pii: btv341

Bioinformatics. 2011 Aug 1;27(15):2167-8. doi: 10.1093/bioinformatics/btr361. Epub 2011 Jun 22.
JSBML: a flexible Java library for working with SBML.
Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M.

LibSBML 5.12.0 – API Library for SBML

LibSBML 5.12.0

:: DESCRIPTION

LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications.

LibSBML understands all Levels and Versions of SBML, as well as the SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It’s written in ISO C and C++ but can be used from all the languages listed in the right-hand box.

::DEVELOPER

The SBML Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

LibSBML

:: MORE INFORMATION

Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
LibSBML: An API Library for SBML.
Bioinformatics, 24(6):880–881, doi:10.1093/bioinformatics/btn051.

Convert2Sbml / Convert2Matlab – Convert Metabolic Network Source files into SBML / MATLAB files

Convert2Sbml / Convert2Matlab

:: DESCRIPTION

Convert2Sbml / Convert2Matlab is the Java tool to convert various metabolic network source files into SBML / MATLAB files.

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

Convert2Sbml / Convert2Matlab

:: MORE INFORMATION

CySBML 1.4.0 – Cytoscape Plugin for SBML

CySBML 1.4.0

:: DESCRIPTION

CySBML is a Cytoscape plugin for the import and work with SBML files in Cytoscape providing the visualisation of SBML network annotations within the network context. SBML models can be imported from BioModels.net or via file or urls. One click access to the annotation resources is provided. SBML validation information about the imported files is available.

::DEVELOPER

Matthias König

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CySBML

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2402-3. doi: 10.1093/bioinformatics/bts432. Epub 2012 Jul 5.
CySBML: a Cytoscape plugin for SBML.
König M, Dräger A, Holzhütter HG.

SBML2TikZ – Converts SBML files to graphical form in LaTeX and PDF using PGF/TikZ

SBML2TikZ

:: DESCRIPTION

SBML2TikZ provides automatic generation of PGF/TikZ TeX Macros to illustrate SBML graphs. The rendering is dependent on the SBML Render Extension proposed by Gauges et al. and the rendering library is built on the existing SBML Layout Library.

::DEVELOPER

SBML2TikZ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX

:: DOWNLOAD

 SBML2TikZ

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 1;26(21):2794-5. doi: 10.1093/bioinformatics/btq512. Epub 2010 Sep 9.
SBML2TikZ: supporting the SBML render extension in LaTeX.
Shen SY1, Bergmann F, Sauro HM.

libRoadRunner 1.3.4 – High performance SBML JIT Compiler & Simulation Engine

libRoadRunner 1.3.4

:: DESCRIPTION

libRoadRunner is an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML).

::DEVELOPER

libRoadRunner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Python

:: DOWNLOAD

 libRoadRunner

:: MORE INFORMATION

Citation

libRoadRunner: A High Performance SBML Simulation and Analysis Library.
Somogyi ET, Bouteiller JM, Glazier JA, König M, Medley JK, Swat MH, Sauro HM.
Bioinformatics. 2015 Jun 17. pii: btv363.

SBMLsimulator 1.2.1 – Java Solver Implementation for SBML

SBMLsimulator 1.2.1

:: DESCRIPTION

SBMLsimulator is a fast, accurate, and easily usable program for dynamic model simulation and heuristic parameter optimization of models encoded in the Systems Biology Markup Language (SBML). In order to ensure a high reliability of this software, it has been benchmarked against the entire SBML Test Suite and all models from the Biomodels.net database. It includes a large collection of nature-inspired heuristic optimization procedures for efficient model calibration.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

  SBMLsimulator

:: MORE INFORMATION

Citation

Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, and Andreas Dräger.
The systems biology simulation core algorithm.
BMC Systems Biology, 7:55, July 2013

MathSBML 2.10.1 – working with SBML in Mathematica

MathSBML 2.10.1

:: DESCRIPTION

MathSBML is an open-source package for working with SBML models in Mathematica. It provides facilities for reading SBML models, converting them to systems of ordinary differential equations for simulation and plotting in Mathematica, and translating the models to other formats.

::DEVELOPER

Bruce E. Shapiro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MathSBML

:: MORE INFORMATION

MathSBML: A Package for Manipulating SBML-Based Biological Models
B. E. Shapiro, M. Hucka, A. Finney and J. C. Doyle.
Bioinformatics 2004 20(16):2829-2831; doi:10.1093