GRiP (Gene Regulation in Prokaryotes)

GRiP (Gene Regulation in Prokaryotes) is an asynchronous, event driven, hybrid model of the facilitated diffusion mechanism in prokaryotic systems. This software is implemented in Sun Java 1.6, which makes it widely available. There are only two system requirements: (i) the operating system must have Java Runtime Environment 1.6, or later versions, installed and (ii) the system has at least 3GB of RAM available.

Contact details

For software related queries please email n.r.zabet@gen.cam.ac.uk.

Publications

The software is described in:

GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Nicolae Radu Zabet and Boris Adryan. Bioinformatics, 28 (9): 1287-1289, 2012, doi:10.1093/bioinformatics/bts132. (link)

The model, implementation strategy and parameter estimation methods are described in:

A comprehensive computational model of facilitated diffusion in prokaryotes. Nicolae Radu Zabet and Boris Adryan. Bioinformatics, 28 (11): 1517-1524, 2012, doi:10.1093/bioinformatics/bts178. (link)