Sebastian Curth

Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves

Automated model building using Taverna workflows from KEGG-Database

methods developed during COSMIC

Conversion from KEGG Reactome Information to SBTOOLBOX2 format.

Annotation retrieval

Creation of the KEGG based Reactome

Provided with genomic data over different pH values we have the opportunity to study the similarity of gene expression profiles and cluster groups of very simlar gene expression profiles. Via PCA we can furthermore study dynamic similarity and compe genes that are possible co-regulators or anti-regulators in the clostridial metabolism.

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

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

Cytoscape based analysis and yED based representation of clostridial Reactomes

call ConvertStdModel2SBTtest('Conti_Ferm_Std', 'CD_Transcriptomic.csv', 'glucose.csv', 'OD.csv',0)

transcriptome, glucose, biomass data inside

acetic acid pulse 100mM acetic acid step 50mM, 70mM

• 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 ...

acetic acid addition

step experiment: 50mM, 70mM, 100mM, 120mM

pulse 200mM

pulse acetic acid: 70mM (2x), 80mM, shift to 4.5, pulse acetic acid: 70mM

acetic acid addition 70mM

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.

acetic acid puls during acidogenesis shift to solventogensis back-shift to acidogenesis butyric acid puls during acidogenesis

butyric acid pulse during acidogenesis acetic acid pulse during acidogenesis butyric acid pulse during solventogenesis

input: array of investigated quenching temperatures and volumetric flows output: quenching time and coil length as function of quenching temperature, and quenching time as function of temperature for varying coil lengths

Progress Meeting