Assays

Data is taken from "Genome-Wide Gene Expression Analysis of the Switch between Acidogenesis and Solventogenesis in Continuous Cultures of Clostridium acetobutylicum." Grimmler et al. 2011 DOI: 10.1159/000320973

Submitter: Sebastian Curth

Biological problem addressed: Gene Expression

Investigation: The effect of pH upon the metabolic shift in Cl...

Study: Identification of clusters of co-regulated and ...

Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)

Models: No Models

SOPs: No SOPs

Data files: 1 hidden item

Snapshots: No snapshots

Created: 3rd Nov 2011 at 14:45, Last updated: 8th Nov 2017 at 14:21

Theoretical calculation of quenching time and quenching temperature

COSMIC

No description specified

Submitter: Sebastian Curth

Biological problem addressed: Model Analysis Type

Investigation: General Method Development

Study: Development of a rapid quenching system

Organisms: No organisms

Models: Script for the calculation of theoretical coil ...

SOPs: No SOPs

Data files: Example calculation of coil length and quenchin..., quenching time as function of coil length and q...

Snapshots: No snapshots

Created: 26th Apr 2012 at 11:19, Last updated: 8th Nov 2017 at 14:21

KEGG Data Mining

COSMIC

Using Taverna for mining and MATLAB for conversion into specific formats (cytoscape, SBTOOLBOX2)

Submitter: Sebastian Curth

Biological problem addressed: Model Analysis Type

Investigation: Modular Model Building

Study: Reactome Analysis

Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)

Models: No Models

SOPs: No SOPs

Data files: Network statistics of Reactome, Results of Reaction Mining, Taverna Workflow for Compound Annotation from KEGG, Taverna Workflow for Gene-Reaction-Substrate-Pr..., Visualisation of Reaction Networks in C. acetob...

Snapshots: No snapshots

Created: 29th Nov 2012 at 11:25, Last updated: 8th Nov 2017 at 14:21

Graph Analysis

COSMIC

Cytoscape based analysis and yED based representation of clostridial Reactomes

Submitter: Sebastian Curth

Biological problem addressed: Model Analysis Type

Investigation: Modular Model Building

Study: Reactome Analysis

Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)

Models: No Models

SOPs: No SOPs

Data files: Network statistics of Reactome, Visualisation of Reaction Networks in C. acetob...

Snapshots: No snapshots

Created: 29th Nov 2012 at 11:29, Last updated: 8th Nov 2017 at 14:21

Example for model derivation from KEGG

COSMIC

No description specified

Submitter: Sebastian Curth

Biological problem addressed: Model Analysis Type

Investigation: Modular Model Building

Study: Automated Model Building

Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)

Models: No Models

SOPs: No SOPs

Data files: Conversion Script for Model Building from KEGG-..., Extracellular Compounds for Toy Model, Reactome Data of C. acetobutylicum for Toy Model, Toy Model Map

Snapshots: No snapshots

Created: 11th Dec 2012 at 11:51, Last updated: 8th Nov 2017 at 14:21

Integration of data into the model

COSMIC

No description specified

Submitter: Sebastian Curth

Biological problem addressed: Model Analysis Type

Investigation: Modular Model Building

Study: Automated Model Building

Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)

Models: No Models

SOPs: No SOPs

Data files: Example Data Input for Conversion from Standard..., Integration script

Snapshots: No snapshots

Created: 11th Dec 2012 at 14:55, Last updated: 8th Nov 2017 at 14:21

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