Journal article

PATHLOGIC-S: A Scalable Boolean Framework for Modelling Cellular Signalling

Liam G Fearnley, Lars K Nielsen

PLOS ONE | PUBLIC LIBRARY SCIENCE | Published : 2012

Abstract

Curated databases of signal transduction have grown to describe several thousand reactions, and efficient use of these data requires the development of modelling tools to elucidate and explore system properties. We present PATHLOGIC-S, a Boolean specification for a signalling model, with its associated GPL-licensed implementation using integer programming techniques. The PATHLOGIC-S specification has been designed to function on current desktop workstations, and is capable of providing analyses on some of the largest currently available datasets through use of Boolean modelling techniques to generate predictions of stable and semi-stable network states from data in community file formats. PA..

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University of Melbourne Researchers

Grants

Awarded by Australian Research Council


Funding Acknowledgements

LGF was funded by an Australian Postgraduate Award from the Department of Industry, Innovation, Science, Research and Tertiary Education of the Australian Government, and through Australian Research Council Discovery Grant DP110103384. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.