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
Biological problem addressed: Model Analysis Type
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
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Created: 11th Dec 2012 at 12:51
Last updated: 8th Nov 2017 at 15:21
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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.
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
Snapshots: No snapshots
Conversion from KEGG Reactome Information to SBTOOLBOX2 format.
Person responsible: Sebastian Curth
Snapshots: No snapshots
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
...
