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NetBuilder

A graphical tool for building logical representations of genetic regulatory networks

NetBuilder is an interactive graphical tool for representing and simulating genetic regulatory networks in multicellular organisms. Although the diagrams created in NetBuilder represent biological processes, the underlying concepts have their roots in electronic engineering.

Conventional models are based on detailed descriptions of the individual chemical reactions that form a biochemical pathway. A major drawback of the conventional approach is that the number of parameters that need to be specified tends to proliferate as models get larger. Simplifying models whilst retaining their main characteristics is often extremely difficult. As a result, the gap between experimentalists and modellers is large and increasing. Modellers create and analyse ever more complex mathematical systems that won't or cannot be experimentally verified or refuted. Experimentalists, on the other hand, produce their own models of biological control structures, often in the form of diagrams (which look very much like the ones that can be built in NetBuilder). However, making qualitative, let alone quantitative predictions on the basis of these drawings is fraught with difficulties.

In NetBuilder – as in many electronic circuit design packages – pathways are represented as series of linked modules. Each module has specific input-output characteristics. As long as these characteristics conform to experimental observations, the exact transformations occurring ‘inside’ the modules can be safely neglected. The result is a significant reduction in the number of parameters. Thus, NetBuilder aims to provide a way of quantifying intuitively drawn diagrams, and making experimentalists hypotheses testable.

NetBuilder Development team

 

Katja Wegner  K. Wegner at herts. ac. uk

Mark Robinson 

 M.1. Robinson at herts. ac. uk

Attila Egri-Nagy  Attila at Egri-Nagy. hu
Johannes Knabe  J. F. Knabe at herts. ac. uk

Chrystopher Nehaniv 

 C. L. Nehaniv at herts. ac. uk

Maria Schilstra  M. J.1. Schilstra at herts. ac. uk

 

NetBuilder is written in Microsoft Visual C++ 6.0, using Rogue Wave's Stingray Studio (Views 7.1 library).

A completely overhauled version, NetBuilder', is being developed in Python

 

 

 

last modified Monday, 27 November 2006