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EC-MOAN: Escherichia Coli - Modeling and Analysis

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EC-MOAN - Home | ec-moan.org Reviews

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EC-MOAN: Escherichia Coli - Modeling and Analysis

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EC-MOAN - Home

http://www.ec-moan.org/deliverables.html

This page provides an overview of the deliverables, which are here. Available online as http:/ www.ec-moan.org. Mid term management decsription in PDF. D02 Progress report (midterm). D02-a: Publishable Executive Summary; in PDF. D02-b: Periodic Activity Report; in PDF. D02-c: Plan for Using and Disseminating the knowledge; in PDF. D02-d: Periodic Management Report; in PDF. D03-a: Periodic Activity Report (end of project); in PDF. D03-b: Final Activity Report; in PDF. D03-e: Final Management Report; in PDF.

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EC-MOAN - Home

http://www.ec-moan.org/models.html

Ammonium assimilation model (AmtB transporter and protein level regulation). Modelling is an important methodology in systems biology research. In this paper, we presented a kinetic model for the complex ammonium assimilation regulation system of. See dx.doi.org/10.1016/j.jbiotec.2009.09.003. Central carbon metabolic models. Central nitrogen metabolic models. Qualitative model of network of global regulators in E. coli. The adaptation of the bacterium. Using an ensemble approach. The results show tha...

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EC-MOAN - Home

http://www.ec-moan.org/tools.html

BioDiVinE - Parallel Model-Checker for Multi-Affine ODE Models. BioDiVinE tool adapts parallel LTL model checking algorithms for rectangular abstraction of multi-affine ODE models. Biological models described in terms of mass action kinetics are supported. The tool is accompanied with a simple GUI that allows specification of reactions. The tool package includes a visualisation utility Simaff that allows untimed simulation and 2D depiction of rectangular phase spaces. GeNeSim/DiVinE is an experimental pr...

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EC-MOAN - Home

http://www.ec-moan.org/objectives.html

This project research objectives are:. To develop an integrated model of the E. coli stress response system, focusing on the metabolic, genetic and signaling modules that regulate nitrogen and carbon source limitations. To develop mathematical methods for system reduction and approximation, in order to deal with large-scale models in which different time scales and many unknown parameter values occur. Is a specific targeted research project supported by 6th Framework Programme FP6-2005-NEST-PATH-COM.

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http://www.ec-moan.org/publications.html

J Barnat, L. Brim, I. Cerna, S. Drazan, and D. Safranek. Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. In Proceedings of From Biology to Concurrency and Back. ENTCS, Vol. 194/3, Elsevier Science, 2008. PT Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong. Temporal logic patterns for querying dynamic models of cellular interaction networks. INRIA Research Report RR-6470, 2008. In press. Special issue ECCB-2008. Blom, S.C.C. And Haverkort, B.R.H.M. In Proceedings of ...

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Ibis : Modeling, simulation, measurement, and control of bacterial regulatory networks

http://ibis.inrialpes.fr/rubrique51.html?menu=menu1

Models : Development and reduction of models of bacterial regulatory networks. Methods : Analysis and simulation of bacterial regulatory networks. Data : High-precision measurements of gene expression in bacteria. GNA : Genetic Network Analyzer. ISee : In Silico biology e-learning environment. Procrustes : Pattern-based property editor. WellInverter : web application for analyzing reporter gene data. WellReader : Analysis of fluorescence and luminescence reporter gene data. Software and database releases.

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The aim of our research is to enhance our understanding of the molecular mechanisms underlying the behavior of complex living systems. In particular, we investigate how large and complex regulatory networks control the response of a living cell to its ever-changing environment. The stress response to environmental events is induced by the interaction of several interwoven modules with complex dynamic behavior, acting on different time scales. And the International E. coli Alliance. They could improve man...

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