Tag: SBML

CSML2SBML – Converting Quantitative Biological Pathway Models from CSML into SBML

CSML2SBML

:: DESCRIPTION

CSML2SBML is a format convertor for quantitative biological pathways,  converting models expressed in CSML into SBML, enabling simulations or parameter estimation with compliant tools such as CellDesigner and COPASI

::DEVELOPER

CSML2SBML team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 CSML2SBML

:: MORE INFORMATION

Citation

CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML.
Li C, Nagasaki M, Ikeda E, Sekiya Y, Miyano S.
Biosystems. 2014 Jul;121:22-8. doi: 10.1016/j.biosystems.2014.05.004.

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.

MetNetMaker 1.6.2 – Creation of Novel Metabolic Networks in SBML format

MetNetMaker 1.6.2

:: DESCRIPTION

MetNetMaker is the only free software designed solely to create metabolic networks based on the KEGG LIGAND database ready for Flux-Balance Analysis in the COBRA toolbox.MetNetMaker helps with creating a Metabolic Network by keeping track of the details, like naming conventions, cellular compartments and network subdivisions so that FBA-ready networks in SBML format can be created by anyone familiar basic concepts of metabolism.

::DEVELOPER

Tom Forth.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MetNetMaker

:: MORE INFORMATION

Citation

Forth,T. et al. (2010)
MetNetMaker: A free and open-source tool for the creation of novel metabolic networks in SBML format.
Bioinformatics (2010) 26 (18): 2352-2353.

SBMLeditor 2.0-b1 – SBML File Editor

SBMLeditor 2.0-b1

:: DESCRIPTION

SBMLeditor is a portable (written in Java), low-level, tree-structured editor for SBML. It supports annotations and validation.

Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file. SBMLeditor provides the ability to use the annotation framework, based on RDF and dublin core elements and now part of SBML since SBML Level 2 Version 2. Some functions provided by libSBML are available if the library is setup properly on the system.

::DEVELOPER

Computational Systems Neurobiology Group, EBI

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java JRE 1.5 or higher

:: DOWNLOAD

SBMLeditor

:: MORE INFORMATION

Citations

Rodriguez N, Donizelli M, Le Novère N (2007)
SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML).
BMC Bioinformatics, 8:79
[PMID: 17341299] [doi:10.1186/1471-2105-8-79]

SOSlib 1.7.0 – ODE Solver for SBML

SOSlib 1.7.0

:: DESCRIPTION

SOSlib (The SBML ODE Solver Library) is a high pecision ODE solver for SBML.SOSlib is both a programming library and a command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML).

::DEVELOPER

Rainer Machné

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

  SOSlib

:: MORE INFORMATION

Citation:

Bioinformatics. 2006 Jun 1;22(11):1406-7. Epub 2006 Mar 9.
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.
Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C.

SimPheny to SBML l2v1 – Convert SimPheny output to SBML

SimPheny to SBML l2v1

:: DESCRIPTION

SimPheny to SBML is a perl program that converts SimPheny output to SBML.

::DEVELOPER

Bernhard Palsson

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • Perl

:: DOWNLOAD

SimPheny to SBML

:: MORE INFORMATION

N/A

SBML Converters 20100413 – Conversions to & from SBML

SBML Converters 20100413

:: DESCRIPTION

SBML Converters are several converters which transfer SBML to BioPax 2 and 3, SBML to XPP and SBML to Octave, etc.

Converters list:

  • SBML to Octave  (GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.)
  • SBML to XPP (XPP-Aut is a numerical analysis software. It permits to solve differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.)
  • SBML to SciLab (SciLab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.)
  • SBML to CellML & CellML to SBML (CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.)
  • SBML to BioPax (The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.)
  • SBML to Dot (GraphViz is an open source graph visualization software. The language used to encode the graphics processed by GraphViz is called DOT. Note that a “dot” file can be used with other graphical software.)
  • SBML to SVG (Scalable Vector Graphics (SVG) is a language for describing two-dimensional graphics and graphical applications in XML. It is an open standard created by the World Wide Web Consortium.)

SBML Converters also have an online version.

::DEVELOPER

Computational Systems Neurobiology Group, EBI

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SBML Converters

:: MORE INFORMATION

Please send any help requests or bug reports to : biomodels-net-support at lists.sourceforge.net

KEGG2SBML 1.5.0 – Convert KEGG Pathway Database to SBML

KEGG2SBML 1.5.0

:: DESCRIPTION

KEGG2SBML can convert KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway database files to SBML using the KEGG LIGAND database. KEGG2SBML’s capabilities are currently limited to converting only KEGG Metabolic Pathway files and not other types of KEGG files.

::DEVELOPER

Akiya Jouraku, Nobuyuki Ohta and Akira Funahashi , Dept. of Biosciences and Informatics at Keio University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

KEGG2SBML

:: MORE INFORMATION

Citations

  1. Converting KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004).
  2. Converting the KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    5th International Conference on Systems Biology (ICSB 2004), October, 2004.

KEGG2SBML License