research-article

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli

Authors:

Dominique SchneiderAuthors Info & Claims

Bioinformatics, Volume 21, Issue 1

Pages 19 - 28

https://doi.org/10.1093/bioinformatics/bti1048

Published: 01 January 2005 Publication History

Abstract

Motivation: The modeling and simulation of genetic regulatory networks have created the need for tools for model validation. The main challenges of model validation are the achievement of a match between the precision of model predictions and experimental data, as well as the efficient and reliable comparison of the predictions and observations.

Results: We present an approach towards the validation of models of genetic regulatory networks addressing the above challenges. It combines a method for qualitative modeling and simulation with techniques for model checking, and is supported by a new version of the computer tool Genetic Network Analyzer (GNA). The model-validation approach has been applied to the analysis of the network controlling the nutritional stress response in Escherichia coli .

Availability: GNA and the model of the stress response network are available at http://www-helix.inrialpes.fr/gna

Contact: [email protected]

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Ironi LLanzarone E(2018)A Model-Based Tool for the Analysis and Design of Gene Regulatory NetworksIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2017.271694215:4(1301-1314)Online publication date: 1-Jul-2018
https://dl.acm.org/doi/10.1109/TCBB.2017.2716942
Fisman DKugler H(2018)Temporal Reasoning on Incomplete PathsLeveraging Applications of Formal Methods, Verification and Validation. Verification10.1007/978-3-030-03421-4_3(28-52)Online publication date: 5-Nov-2018
https://dl.acm.org/doi/10.1007/978-3-030-03421-4_3
Konur SGheorghe M(2015)A property-driven methodology for formal analysis of synthetic biology systemsIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2014.236253112:2(360-371)Online publication date: 1-Mar-2015
https://dl.acm.org/doi/10.1109/TCBB.2014.2362531
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Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli

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Published In

Bioinformatics Volume 21, Issue 1

January 2005

641 pages

ISSN:1367-4803

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Publisher

Oxford University Press, Inc.

United States

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Published: 01 January 2005

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Ironi LLanzarone E(2018)A Model-Based Tool for the Analysis and Design of Gene Regulatory NetworksIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2017.271694215:4(1301-1314)Online publication date: 1-Jul-2018
https://dl.acm.org/doi/10.1109/TCBB.2017.2716942
Fisman DKugler H(2018)Temporal Reasoning on Incomplete PathsLeveraging Applications of Formal Methods, Verification and Validation. Verification10.1007/978-3-030-03421-4_3(28-52)Online publication date: 5-Nov-2018
https://dl.acm.org/doi/10.1007/978-3-030-03421-4_3
Konur SGheorghe M(2015)A property-driven methodology for formal analysis of synthetic biology systemsIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2014.236253112:2(360-371)Online publication date: 1-Mar-2015
https://dl.acm.org/doi/10.1109/TCBB.2014.2362531
Ito SIchinose TShimakawa MIzumi NHagihara SYonezaki N(2015)Qualitative analysis of gene regulatory networks by temporal logicTheoretical Computer Science10.1016/j.tcs.2015.06.017594:C(151-179)Online publication date: 23-Aug-2015
https://dl.acm.org/doi/10.1016/j.tcs.2015.06.017
Claessen KFisher JIshtiaq SPiterman NWang Q(2013)Model-Checking Signal Transduction Networks through Decreasing Reachability SetsProceedings of the 25th International Conference on Computer Aided Verification - Volume 804410.5555/2958031.2958078(85-100)Online publication date: 13-Jul-2013
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Yordanov BAppleton EGanguly RGol ECarr SBhatia SHaddock TBelta CDensmore DRosenstiel WMacii E(2012)Experimentally driven verification of synthetic biological circuitsProceedings of the Conference on Design, Automation and Test in Europe10.5555/2492708.2492767(236-241)Online publication date: 12-Mar-2012
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Fisher JHarel DHenzinger T(2011)Biology as reactivityCommunications of the ACM10.1145/2001269.200128954:10(72-82)Online publication date: 1-Oct-2011
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Dubrova ETeslenko M(2011)A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean NetworksIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2010.208:5(1393-1399)Online publication date: 1-Sep-2011
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Fages FRizk A(2009)From model-checking to temporal logic constraint solvingProceedings of the 15th international conference on Principles and practice of constraint programming10.5555/1788994.1789023(319-334)Online publication date: 20-Sep-2009
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Efficient parameter search for qualitative models of regulatory networks using symbolic model checking

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