Example for model derivation from KEGG
SEEK ID: https://fairdomhub.org/assays/202
Modelling analysis
Projects: COSMIC
Investigation: Modular Model Building
Study: Automated Model Building
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
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Created: 11th Dec 2012 at 11:51
Last updated: 8th Nov 2017 at 14:21
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Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin
I am a biotechnologist with main focus on theoretical studies. Currently, I am working on the implementation of a parameter estimation algorithm on GPUs to reduce the computational burden of huge ODE systems. I am a PAL and I am looking forward to communication with other SYSMO members.
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
Automated model building using Taverna workflows from KEGG-Database
Conversion from KEGG Reactome Information to SBTOOLBOX2 format.
Submitter: Sebastian Curth
Investigation: Modular Model Building
Assays: Example for model derivation from KEGG, Integration of data into the model
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
- automated integration of transcriptomic and reactome data to differential equations
- structure of the paths is maintained
- continuous fermentation model in standard format for data integration, two component model (cell and fermenter)
call >> Kegg2SBToolbox2('model_map.txt', 'reactions_compounds_final.csv','extracellular.txt','testmodel.txt') for an example
where model_map is the desired mapping of species, reaction_compounds_final.csv is the entire network, extracellular.txt is a manual ...
