Current Topics for Diploma Thesis
Thesis in collaboration between the German Cancer Research Centre in Heidelberg and the Jena Centre for Bioinformatics (JCB)
We are looking for highly motived Diploma (MSc) students that are
interested in cross-disciplinary research on in-silico modelling
of cell cycle regulation.
The thesis will be carried out in close collaboration with
the German Cancer Research Centre (DKFZ) in Heidelberg.
Funding for traveling will be available.
We offer for example the following three topics:
1.) Stability Analysis of Reaction-Diffusion Model of Mitotic Checkpoints
- This topic requires some basic mathematical knowledge on
partial differential equations.
- The topic might even be suitable for applied mathematics students.
- You will stay most of the time in Heidelberg for that topic.
2.) Rule-Based Model of Mitotic Control Mechanisms
- A tool is already available that can be used as a starting point.
- Usuful skills: systems biology, simulation and modelling, biophysics
- Location can be Heidelberg or Jena.
3.) Mitotic Control Knowledge Base
- The aim is to find a way to collect knowledge about the key-players of mitotic control in a computational knowledge base.
- Useful skills: bioinformatics, artificial intelligence, knowledge representation
- Location can be Heidelberg or Jena.
Students from all disciplins are welcome to apply.
You can contact in Heidelberg or Jena:
Thesis in collaboration with the Helmholtz Centre for Environmental Research (UFZ), Leipzig and
the Jena Centre for Bioinformatics
Topic: Discovery of Biodegradation Pathways by Artificial In Silico Network Evolution
Description:
The degradation of organic contaminants in subsurface environments is mainly mediated by microbial activity. With microbial consortia in the soil consisting of many microbial species, degradation pathways often involve more than one species. In contrast, current reactive transport models simulating the fate of environmental pollutants either aggregate microbial activity as a whole or link degradation rates to the activity of individual species only, neglecting the enzymatic details of the involved degradation pathways. In this work, hypothetical biochemical degradation pathways will be evolved in silico to explain a given spatial concentration profile for contaminants, intermediate and end products in a typical degradation scenario. For this purpose, the software package SBMLevolver, developed at the University of Jena, will be used to evolve biochemical reaction networks, taking enzymatic reactions from the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) as building blocks for the evolutionary process. The evolved networks are then implemented into the Biogeochemical Reaction Network Simulator (BRNS), an established reactive transport code used at the UFZ. Evolved degradation pathways will be compared to established enzymatic degradation pathways, and simulation results obtained using the evolved network will be compared to results of the aggregated model.
Tasks:
1. Coupling of SBMLevolver and BRNS. The reaction networks in SBMLevolver are formulated in the Systems Biology Markup Language (SBML). A converter is required to transform the network descriptions into ODE formulations in Maple format as required by the BRNS. As reactive transport simulations are usually time consuming, SBMLevolver shall be extended to make use of a cluster system for parallel BRNS runs.
2. Evolving biodegradation networks. A typical aquifer degradation scenario is selected, and degradation networks following predefined criteria (e.g., number of microbial species, types of reaction kinetics) are evolved. The best solutions are compared to established pathways, and simulation results are compared to established aggregated model results.
Requirements:
The work is suitable for computer scientists, bioinformaticians, systems scientists (and related) with profound knowledge of C++, Evolutionary Algorithms, chemical reaction kinetics, and the willingness to travel between Leipzig and Jena. The optimal candidate has furthermore experiences with SBML, Maple, Fortran, 1 shell scripts, and cluster computing. The place of work is Leipzig.
Contact:
- Florian Centler (Email: florian.centler@ufz.de, Tel.: +49 341 2351336), Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Peter Dittrich (FSU Jena)
Peter Dittrich
Friedrich-Schiller-University Jena
& Jena Centre for Bioinformatics
Institute of Computer Science
Ernst-Abbe-Platz 1-4
D-07743 Jena, Germany
Tel.: (+49) 3641 9 46460
Fax.: (+49) 3641 946302
