Modeling biochemical transformation processes and information processing with Narrator

Background: Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Results: Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transpo...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Johannes J. Mandel, Hendrik Fuß, Niall M. Palfreyman, Werner Dubitzky
• Keywords: Biological Information Processing, BMCBI 2007, Graphical Notation, Tool