Generating kinetic equations for biochemical networks

Documentation

Main program features

Figure 1 | SBMLsqueezer reaction context menu on Biomodel No. 390

Generates kinetic equations for all reactions in your model, or only for those reactions that are currently lacking a rate law with a large variety of generic and specific rate laws for several standard cases
Allows you to create all rate laws in a reversible manner.
Can detect reactive species, whose annotation indicates that these are genes.
Can assume that all reactions in your network are enzymatically catalyzed and hence change the selection of rate laws.
Defines the units of all species and compartments if necessary and derive the units for all newly created local and global parameters and numbers in order to ensure unit consistency of the entire model.
Can check the model for global and local parameters as well as unit definitions that are never used and addressed. SBMLsqueezer can automatically remove these from the model.
Imports experimentally determined rate equations from SABIO-RK and include them into your model.
Equips your model with default values where no values are defined.
Summarizes all features of the model in an exhaustive LaTeX-based model report.

Users' guide and kinetic laws

Requirements: Acrobat Reader (available from Adobe).

Document (pdf)	Size	Version
SBMLsqueezer 2.1 Users' Guide	4.2 MB	2015-08-10
SBMLsqueezer 2 Users' Guide	4.2 MB	2014-06-29
Revised Kinetic Laws	729 kB	2010-03-31
User Guide	960 kB	2008-04-28
Kinetic Laws	375 kB	2008-04-28

Application Programming Interface Documentation

For software developers, the source code of SBMLsqueezer is freely available (see the download section). Here we also offer the documentation of all methods and classes of all versions of SBMLsqueezer. Have a lot of fun when programing applications using SBMLsqueezer.

Publications

[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 ]

Posters and diploma theses

Nadine Hassis (2007): Automatische Generierung kinetischer Gleichungen aus Stöchiometrien, Diplomarbeit, Universät Tübingen
Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, Andreas Zell (2007): SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks, poster (HepatoSys conference).