Generating kinetic equations for biochemical networks

Short description: SBMLsqueezer generates kinetic equations for biochemical networks according to context of each reaction. When used as a plug-in for CellDesigner it uses the information from the SBGN representation of all network components. In the stand-alone mode, SBMLsqueezer evaluates the Systems Biology Ontology (SBO) annotations to extract this information. An online version of SBMLsqueezer is available that runs without instally any software on the local machine. The rate laws that can be produced by SBMLsqueezer include several types of generalized mass action; detailed and generalized enzyme kinetics, various types of Hill equations, S- and H-systems, and additive models for gene regulation. User defined settings specify which equation to apply for any type of reaction and how to ensure unit consistency of the model. Equations can be created using contextual menus. All newly created parameters are equipped with the derived unit and annotated with SBO terms if available and meaningful textual names. MathML is inserted directly into the SBML file. LaTeX or text export of ordinary differential equations is provided.

Please cite:
[1] Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O. Palsson, and Andreas Zell. SBMLsqueezer 2: Context-sensitive creation of kinetic equations in biochemical networks. BMC Systems Biology, 9(1):1-17, September 2015. [ DOI | details | link | pdf ]
[2] Andreas Dräger. Computational Modeling of Biochemical Networks. PhD thesis, University of Tuebingen, Tübingen, Germany, January 2011. [ details | link ]
[3] Andreas Dräger, Adrian Schröder, and Andreas Zell. Systems Biology for Signaling Networks, volume 1 of Systems Biology, chapter Automating mathematical modeling of biochemical reaction networks, pages 159-205. Springer-Verlag, July 2010. [ DOI | details | link ]
[4] Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, and Andreas Zell. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Systems Biology, 2(1):39, April 2008. [ DOI | details | link | pdf ]

Version 2.1 released: SBMLsqueezer can now deal with Level 2 Version 5 and Level 3 Version 1 including all current extension packages. The plug-in version has been adopted for CellDesigner 4.4. The JSBML and Garuda backend have been updated, too. A new Users' Guide is available explaining the new features. See the Release Notes for details.   -   (draeger - 2015-08-10 16:20)

Version 2.0.1 released: This package includes an updated version of JSBML and Garuda backend. See the Release Notes
for details.   -   (draeger - 2014-10-24 17:50)

Version 2.0 available: Multiple new features have been implemented and the application has become much more stable, better adapted to various operating systems, and versatile. See the Release Notes for details.   -   (draeger - 2014-06-30 11:15)

This project is promoted by:

European Commission Systems Biology Research Group BMBF Virtual Liver
Marie Curie IOF Systems Biology Research Group Federal Ministry for Education and Research Virtual Liver Network