A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, and Andreas Zell


Short description: SBMLsqueezer is a plug-in for CellDesigner that generates rate equations for biochemical networks according to SBGN and the context of the reaction. Rate laws include generalized mass action; detailed enzyme kinetics (Michaelis-Menten) for up to two substrates or products; Hill equations; or the approximative convenience rate law. User defined settings specify which equation to apply for any type of reaction. Equations can be created using contextual menus. 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).


info
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)

This project is promoted by:

NGFN BMBF ZBIT HepatoSys