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

ABSTRACT:

Background

The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language). This effort is accompanied by the ongoing development of the human-readable diagrammatic representation SBGN (Systems Biology Graphical Notation). The graphical SBML editor CellDesigner allows direct translation of SBGN into SBML, and vice versa. For the assignment of kinetic rate laws, however, this process is not straightforward, as it often requires manual assembly and specific knowledge of kinetic equations.

Results

SBMLsqueezer facilitates exactly this modeling step via automated equation generation, overcoming the highly error-prone and cumbersome process of manually assigning kinetic

SUBMITTER: Drager A 

PROVIDER: S-EPMC2412839 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature