Efficient Markov Chain Monte Carlo Techniques for Studying Large-scale Metabolic Models

Quantifying the activity of enzymes operating within the large-scale biochemical network is a fundamental challenge in Systems Bio(tech)nology. Here the unknown quantities must be inferred from models that are incomplete and measurements that involve errors. For such challenges, Bayesian analysis using Markov Chain Monte Carlo (MCMC) has become a standard tool.

Project description:
For addressing high dimensional parameter inference problems with Bayesian statistics, powerful MCMC methods have emerged, for example the MCMC differential evolution and the Riemann Manifold Langevin Monte Carlo method. Because of the specific structure of the inference problems occurring in metabolic models, direct application of these MCMC algorithms is not possible.
In this project, you will bring MCMC methods into the setting of metabolic flux inference and with inspiration from existing algorithms, develop tailored MCMC algorithm(s). The ensuing algorithm(s) will be implemented in an existing C++ framework, validated and benchmarked with a realistic case study.
The focus of the project can develop either more in the mathematical theory of MCMC or practical implementation of code for the Jülich supercomputers.

Weitere Informationen

Unternehmen

Helmholtz Gemeinschaft

Bereich/Abteilung

IBG-1: Biotechnology Forschungszentrum Jülich

Abschlussart

Masterarbeit

Ansprechpartner/in

Dr. Katharina Nöh | k.noeh@fz-juelich.de
Axel Theorell, MSc. | a.theorell@fz-juelich.de

Modeling and Simulation Group
IBG-1: Biotechnology
Forschungszentrum Jülich
52425 Jülich
Germany

http://www.fz-juelich.de/ibg/ibg-1/modsim
http://github.com/modsim

Branche

Bio- und Gentechnologie

Anforderungen

You are highly motivated, with an interest in probability theory and mathematics. Very good practical C++ programming skills allow you to make your ideas happen and you have strong interest in curiosity-driven multidisciplinary research.

Zusatzinformationen

About us:
The “Modeling and Simulation Group” is part of the IBG‐1, located at the Research Center Jülich (Forschungszentrum Jülich GmbH). We offer a multidisciplinary and interesting research environment within a young and dynamic group. The project is an excellent example for research at the interface of computational systems biology and mathematics.