KEGG Data Mining
Using Taverna for mining and MATLAB for conversion into specific formats (cytoscape, SBTOOLBOX2)
SEEK ID: https://fairdomhub.org/assays/196
Modelling analysis
Projects: COSMIC
Investigation: Modular Model Building
Study: Reactome Analysis
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
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Creators and Submitter
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Created: 29th Nov 2012 at 11:25
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
Creation of the KEGG based Reactome
Submitter: Sebastian Curth
Investigation: Modular Model Building
Assays: Graph Analysis, KEGG Data Mining
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
Basic Graph statistics
RCM: Reaction-Compound Mapping, an edge between nodes means reaction contains metabolite MMM: Metabolite-Metabolite Mapping, an edge between nodes means these metabolites are reaction partners
_comp: entire network after removal of duplicated edges _del: taken from the entire network the largest connected subgraph after deletion of a set of nodes
betw: betweeness of nodes clos: closeness of nodes neigh: neighbours node_degree: number of edges per node path: shortest paths ...
RCM: Reaction-Compound Mapping, an edge between nodes means reaction contains metabolite MMM: Metabolite-Metabolite Mapping, an edge between nodes means these metabolites are reaction partners
_comp: entire network after removal of duplicated edges _del: taken from the entire network the largest connected subgraph after deletion of a set of nodes _upload: entire network before removal of duplicated edges
X_depthY: subgraphs where X is a chosen central component and Y is the Yth of neighbour to ...
Out
Columnwise datamatrix of reactions, gene identifiers, substrates and products. The direction of reactions is not given.
