Modeling biochemical transformation processes and information processing with Narrator.

Full Abstract

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 transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development.

CONCLUSION:
Narrator is a flexible and intuitive systems biology tool. It is specifically intended for users aiming to construct and simulate dynamic models of biology without recourse to extensive mathematical detail. Its design facilitates mappings to different formal languages and frameworks. The combined set of features makes Narrator unique among tools of its kind. Narrator is implemented as Java software program and available as open-source from http://www.narrator-tool.org.

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Author information

Author/s: Mandel, Johannes J (JJ); Fuss, Hendrik (H); Palfreyman, Niall M (NM); Dubitzky, Werner (W);

Affiliation: Dept, of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, 85350 Freising, Germany. johannes.mandel(-atsign-)fh-weihenstephan.de

Journal and publication information

Publication Type: Journal Article

Journal: BMC bioinformatics (BMC Bioinformatics), published in England. (Language: eng)

Reference: 2007-; vol 8 (issue ) : pp 103

Dates: Created 2007/04/04; Completed 2007/04/23; Revised 2008/11/20;

PMID: 17389034, status: MEDLINE (last retrieval date: 12/26/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Algorithms
Biochemistry - methods
Computer Graphics
Computer Simulation
Information Storage and Retrieval - methods
Information Theory

Associated Chemicals: Proteome (0)

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