Agent-based model of response of E.coli to different levels of oxygen supply (with FNR and ArcBA) Version 1
The model presents the response of E.coli to different levels of oxygen supply, in which the oxidases, Cyo and Cyd, and their regulators, FNR and ArcBA systems, are included. The initial file 0.xml and supporting documents are for the model with FNR only. Four 0.xml files provided are at AAU level 31, 85, 115 and 217 respectively. The ArcBA system can be activated by revising the number of agents, ArcB, ArcA dimer, ArcA monomer, ArcA tetramer and ArcA octamer, in the initial file. The model needs to be compiled and run in the FLAME environment. The related software of FLAME can be obtained from http://www.flame.ac.uk/download/.
SEEK ID: https://fairdomhub.org/models/105?version=1
8 items are associated with this Model:- Model files.rar (Unknown file type - 4.51 MB)
- Agent description.pdf (PDF document - 1.32 MB)
- General model description.pdf (PDF document - 420 KB)
- Model interaction rules and parameters.pdf (PDF document - 295 KB)
- Model stategraph.pdf (PDF document - 52.8 KB)
- Model process order graph.pdf (PDF document - 60.4 KB)
- Model visualisation in 2D.pdf (PDF document - 1.11 MB)
- Model output diagram.pdf (PDF document - 66.4 KB)
Organism: Escherichia coli
Model type: Agent based modelling
Model format: Not specified
Execution or visualisation environment: FLAME
Model image: No image specified
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Created: 23rd Jan 2013 at 12:08
Last updated: 28th Jan 2013 at 10:38
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Version 1 (earliest) Created 23rd Jan 2013 at 12:08 by Hao Bai
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Projects: SUMO
Institutions: University of Sheffield
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=55
