software

September 18th, 2009

This page primarily contains some software that I implemented during my PhD, although it will be updated as and when new tools are developed.

GNaPN

GNaPN (Genetic Networks as Petri Nets) represents the first tool to provide an automated and optimised mapping from logical regulatory network (an abstraction of a genetic regulatory network) to a Petri net. Written in pure Java, GNaPN takes as input a logical regulatory network specified as a set of multi-valued state transition tables and automates the construction of a Petri net by offering the following key features:

  • a choice between the synchronous and asynchronous network update semantics;
  • systematic multi-valued logic minimisation techniques to massively reduce the size of the resulting Petri net;
  • handling of non-determinism manifested through an incomplete and/or inconsistent knowledge of the underlying regulatory network;
  • construction of low-level and high-level Petri nets, as well as signal transition graphs;
  • rapid mutant model construction;
  • smart initial marking selection to aid model checking;
  • a range of Petri net export formats.

GNaPN has proven essential in a number of case studies at Newcastle University, and has been downloaded by researchers from a wide range of international institutions.

Note GNaPN makes use of a third party binary compiled for Windows and Linux platforms. Download GNaPN.

ModelCreator

ModelCreator is a simple Java utility for creating logical regulatory networks to be used by GNaPN. Writing or deriving the state transition tables manually is very cumbersome, as it requires an exponential number of states to be considered. This tool addresses this by allowing network entities, regulatory interactions and behaviours to be specified using the well-known approach discussed by Rene Thomas.

Download ModelCreator.

STGRefiner

STGRefiner is a Java tool for automatically identifying and interactively resolving dynamic conflicts in signal transition graphs. Biologically, these conflicts represent key points in the model where there is uncertainty as to the outcome of a chemical reaction, and thus prove essential to the modeller who can pinpoint precisely where more information is required. STGRefiner enables the modeller to resolve conflicts interactively, to backtrack through a history of resolutions and to export the model at any time for analysis using external tools such as Petrify. STGRefiner represents the first application of signal transition graphs to biological modelling, and the first tool of its kind to enable rapid conflict resolution, thus supporting the incremental development of realistic biological models.

Download STGRefiner.

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