SBMLsqueezer

SBMLsqueezer is a tool to produce kinetic equations for biological networks given a context of each reaction. The SBMLsqueezer algorithm utilizes various types of mass action, such as many types of Hill equations, S- and H-systems, detailed and generalized enzyme kinetic models, and additive models for gene regulation. SBMLsqueezer also considers the Systems Biology Ontology (SBO). Note, SBMLsqueezer also works as a plug-in for CellDesigner, included in the package.

Topic

Systems biology;Enzymes;Biochemistry;Molecular interactions, pathways and networks

Detail

  • Operation: Enzyme kinetics calculation

  • Software interface: Web user interface

  • Language: Java

  • License: GNU General Public License v3.0

  • Cost: Free

  • Version name: 2.2

  • Credit: The Federal Ministry of Education and Research (BMBF, Germany); the Virtual Liver Network, to the 7th EU Framework Program for Research and Technological Development for AD’s Marie Curie International Outgoing Fellowship, National Institute of Health, the German Research Foundation (DFG), the Open Access Publishing Fund of the University of Tuebingen.

  • Input: -

  • Output: -

  • Contact: Andreas Dräger andraeger@eng.ucsd.edu

  • Collection: -

  • Maturity: -

Publications

  • SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks.
  • Dräger A, Hassis N, Supper J, Schröder A, Zell A. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39. PMID: 18447902; PMCID: PMC2412839.
  • https://doi.org/10.1186/1752-0509-2-39
  • PMID: 18447902
  • PMC: PMC2412839
  • SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.
  • Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol. 2015 Oct 9;9:68. doi: 10.1186/s12918-015-0212-9. PMID: 26452770; PMCID: PMC4600286.
  • https://doi.org/10.1186/s12918-015-0212-9
  • PMID: 26452770
  • PMC: PMC4600286

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