Sebastian Henkel

PhD student as research associate at the Institute for System Dynamics (ISYS), Universität Stuttgart, Germany. Engineering background→modelling, identification and analyses.

The goal of this project is to obtain a complete and quantitative description of the catabolism and bioenergetics of E. coli grown under a variety of (an)aerobic respiratory conditions, including the relationships between flux (physiology) and the regulatory networks. The data will be quantitative and reproducible, and will therefore be suitable for mathematical modelling and for experimental redesign in the light of new insights arising from the models.

Detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of Escherichia coli. Tools: mainly MATLAB, Mathematica, SBML.

The SUMO consortium generates experimental data (concentrations of metabolites, proteins, mRNA under different conditions), simulation data (concentrations, fluxes under different conditions, plots, visualisations) and models (only partly SBML compatible). These data are stored in a wiki (trac) site in a semi-formal structure, with csv files (comma separated values) as the exchange format. The wiki allows other SUMO partners to access the data that is stored there. Data are annotated by formalized documentation pages in the wiki for every experiment. Experimental data are primarily used by the modelling work packages of the consortium. Different experimental groups in the consortium need to access that data in order to compare their results. The benefits that this data might have for other SysMO consortia that are not directly interested in redox control is limited in the short term. We use the wiki for the discussion and documentation of standard operating procedures (SOPs). We have developed Taverna workflows to support the data analysis and provide an integrated mechanism for the laboratory and modelling investigations. The workflow has been upload into myExperiment.

Sebastian Henkel, Institute for System Dynamics, Universität Stuttgart, Germany.

sebastian.henkel(atatat)isys.uni-stuttgart.de