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

doi:10.1186/1752-0509-2-39

BMC Systems Biology

Volume 2

Viewing options:

Abstract
Full text
PDF (1.4MB)
Additional files

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Dräger A
Hassis N
Supper J
Schröder A
Zell A

on PubMed

Dräger A
Hassis N
Supper J
Schröder A
Zell A
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Twitter

Software

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

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

Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Sand 1, 72076 Tübingen, Germany

author email corresponding author email

BMC Systems Biology 2008, 2:39doi:10.1186/1752-0509-2-39


Published:	30 April 2008

Additional files

Additional file 1:

SBMLsqueezer: Kinetic Laws. This supplement provides a complete list of all currently supported kinetic laws together with conventions according to the graphical notation of CellDesigner and points out all special cases that are considered for an automatic equation generation including all available SBO terms for mathematical expressions. The derivation of the formula for the rapid equilibrium random order ternary-complex mechanism with one product as well as the ordered ternary-complex bi-uni mechanism can also be found in this document.

Format: PDF Size: 375KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 2:

SBMLsqueezer: Tutorial. This tutorial provides installation instructions and guides the user through a real-world example of a T-cell signaling network. It highlights the modeling capabilities and the application of SBMLsqueezer to create a quantitative biochemical model. Finally it is shown how to apply CellDesigner's simulation module to the network to produce a dynamic simulation of the temporal changes of the species' concentrations.

Format: PDF Size: 960KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 3:

SBMLsqueezer.jar. This is the current version (1.0) of the SBMLsqueezer plug-in for CellDesigner.

Format: JAR Size: 362KB Download file