Monday, October 01, 2007

Sept 2007 CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation

Brendan Sheehan MSc, one of the PhD scholars I supervise is off to The Eighth International Conference on Systems Biology, Long Beach California Oct 1-6, 2007. He is attending various tutorials and presenting a poster on his research, namely: "CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation"

ICSB 2007

Rule-based models provide a declarative means to construct a computational model of biological systems. Rules specify how the model can evolve over time by transforming the underlying data or model into its next state. Most rule-based systems operate on strings. Graph transformation systems (GTS) can provide a more direct and intuitive description of many kinds of biological data such as protein-interaction data and data relating to cell-signalling pathways. Here we implement the GTS based formalism defined by Blinov et al to help generate molecular reactions based on rules that describe interactions between protein domains. We use the GTS tool AGG to implement the tool as a plugin for the forthcoming version of CellDesigner.
by Sheehan and Quigley.

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