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: Dräger A, Hassis N, Supper J, Schröder A, Zell A. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks, BMC Systems Biology 2008, 2:39 (30 April 2008).
Presentation on the COMBINE workshop: You can download the slides from
the presentation of SBMLsqueezer 1.3 on the COMBINE workshop from
(draeger - 2010-10-20 9:05)
New convenient start script: To ease using SBMLsqueezer in stand-alone mode, you can download the example start-script run.sh, which demonstrate how to set environment variables correctly. It may be necessary to costumize this script for your particular environment. - (draeger - 2010-09-22 9:06)
Version 1.3 available: For the first time, SBMLsqueezer can now be used as a stand-alone application independent from CellDesigner. It is based on a completely new data structure, JSBML, and now even creates units for all elements in the model. Furthermore, SBMLsqueezer now contains a plethora of additional rate laws, in particular for gene-regulatory networks. The documentation Kinetic Laws has been completely revised and now covers detailed descriptions of all these new rate laws. An online version that does not require a local installation can now be used. See the download page. and the release notes for details. - (draeger - 2010-04-02 0:49)
Version 1.2.1 available: Bugs were corrected in the thermodynamically independent convenience kinetics and also in the Hill equation. You can download the new version of SBMLsqueezer at the download page. Please see the release notes for details. - (draeger - 2009-08-07 16:35)
Version 1.2 available: Many new features were introduced, SBMLsqueezer was better adjusted to CellDesigner 4.0.1, its data structure was improved and bugs were fixed. See the download page and the release notes for details. - (draeger - 2009-07-31 19:20)
SBML2LaTeX available: This convenient web service allows you to generate a PDF report file from your SBML file. - (draeger - 2009-02-28 19:11)
Version 1.1 available: Many improvments were introduced and bugs were fixed. See the download page and the release notes for details. - (draeger - 2009-02-09 18:07)
First Release: Launch the download link. Note that CellDesigner 4.0 α or higher is required for this program. - (draeger - 2008-04-28 09:23)
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