ATCC824
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wild-type
wild-type
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Created: 28th Apr 2010 at 16:21
Last updated: 19th Oct 2012 at 15:57
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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.
Investigation of the dynamic switch at pH values between 5.8 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7 and 4.5).
Submitter: Sara Jabbari
Assay type: Genomics
Technology type: Microarray
Investigation: The effect of pH upon the metabolic shift in Cl...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Comparison of the transcriptome at steady state in acidogenesis and at steady state in solventogenesis.
Submitter: Sara Jabbari
Assay type: Genomics
Technology type: Microarray
Investigation: The effect of pH upon the metabolic shift in Cl...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: No SOPs
Data files: Transcriptome data of Clostridium acetobutylicu..., Transcriptome data of Clostridium acetobutylicu...
Snapshots: No snapshots
Investigation of all steady state pH-values between pH 5.7 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7).
Submitter: Sara Jabbari
Assay type: Proteomics
Technology type: Technology Type
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH on the proteome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: Standard operating procedure to analyze the int...
Data files: Proteome Reference maps of Clostridium acetobuy..., Proteome of Clostridium acetobutylicum growing ...
Snapshots: No snapshots
Measurements of acetone, butanol, acetate, butyrate and ethanol taken during dynamic shift (pH 5.8, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5) and at steady state (pH 5.7, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5).
Submitter: Sara Jabbari
Assay type: Metabolomics
Technology type: Technology Type
Investigation: The effect of pH upon the metabolic shift in Cl...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: No SOPs
Data files: End products of Clostridium acetobutylicum grow..., End products of Clostridium acetobutylicum grow...
Snapshots: No snapshots
Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.
Submitter: Sara Jabbari
Biological problem addressed: Metabolic Network
Investigation: The effect of pH upon the metabolic shift in Cl...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
Models: Dynamic shift model of the effect of pH upon so...
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Steady state study of the effect of altering gene regulation on yields of end-products, focusing on butanol.
Submitter: Sara Jabbari
Biological problem addressed: Gene Expression
Investigation: The effect of pH upon the metabolic shift in Cl...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
Models: Dynamic shift model of the effect of pH upon so...
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Using PCA, three components, beam size 8. Clustering via MCL from Biolayout Express 3D
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...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
Models: No Models
SOPs: No SOPs
Data files: 1 hidden item
Snapshots: No snapshots
Submitter: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Investigation on the effect of pulsed metabolit...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: No SOPs
Data files: Chemostat Fermentation B, Chemostat Fermentation C
Snapshots: No snapshots
Submitter: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Investigation on the effect of pulsed metabolit...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: No SOPs
Data files: Chemostat Fermentation B, Chemostat Fermentation C, Fermentation D, Fermentation E, Fermentation F, Fermentation G
Snapshots: No snapshots
Submitter: Sebastian Curth
Assay type: Transcriptional Profiling
Technology type: Microarray
Investigation: Investigation on the effect of pulsed metabolit...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Submitter: John Raedts
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Identification of regulatory metabolites in the...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: Extraction protocol
Data files: No Data files
Snapshots: No snapshots
Submitter: Daniel Hönicke
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Altering the expression pattern in Clostridium ...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type)
SOPs: No SOPs
Data files: Data DNA microarray analyses of C. acetobutylic...
Snapshots: No snapshots
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
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
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
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