Time-dependent simulations
Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.
SEEK ID: https://fairdomhub.org/assays/122
Modelling analysis
Projects: COSMIC
Investigation: The effect of pH upon the metabolic shift in Clostridium acetobutylicum in continuous culture.
Study: Modelling the effect of pH on the metabolic shift
Assay position:
Biological problem addressed: Metabolic Network
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
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Created: 8th Nov 2010 at 17:07
Last updated: 8th Nov 2017 at 14:21
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Projects: COSMIC
Institutions: University of Nottingham
I am a Birmingham and MRC Fellow in mathematical biology. Specialising in the modelling of gene regulation networks using both numerical and analytical approaches, my work spans a range of biological applications, from drug development to bioenergy to understanding bacterial behaviour. My MRC fellowship gave me the opportunity to gain experimental training in order to generate the complementary data required to adopt a truly interdisciplinary approach to mathematical modelling in biology.
I worked ...
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 Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=54
Submitter: Christina Döring
Studies: Effect of pH on the metabolome, Effect of pH on the proteome, Effect of pH upon the transcriptome, Identification of clusters of co-regulated and anti-regulated genes, Modelling the effect of pH on the metabolic shift
Assays: Comparison of the proteome between pH 5.7 (acidogenesis) and pH 4.5 (sol..., Comparison of the transcriptome between pH 5.7 (acidogenesis) and pH 4.5..., Comparison of the transcriptome between pH 5.8 (acidogenesis) and pH 4.5..., Identification of dynamically similar transcript profiles, Steady state study of the effect of gene regulation on yields of end-pro..., Study of the end products of the acidogenesis and solventogenesis pathways, Time-dependent simulations
Mathematical modelling of the dynamic shift experiments and the effect of pH upon gene regulation.
Submitter: Sebastian Curth
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Clostridium acetobutylicum
Genotypes: wild-type
Phenotypes: wild-type
Comment: Not specified
An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum, incorporating the effect of pH upon gene regulation and subsequent end-product levels.
The zip file containes 4 models (in SBML), each representing slightly different experimental conditions.
Creators: Sara Jabbari, Sylvia Haus
Submitter: The JERM Harvester
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
