The Cologne University Bioinformatics Center (CUBIC) participates with research projects, know-how transfer, and teaching. The center resides to the University of Cologne which provides financial support for the construction of new premises. Five research groups from the Institute of Biochemistry, Institute of Computer Science/Mathematics and Institute for Genetics are mainly involved in setting up the center, managing research projects and the teaching assignment.
Research projects at CUBIC are primarily focused on the integration of genome, proteome, function and metabolome data as well as on the development and optimization of computer tools for protein drug development and design.
Metabolome-driven bioinformatics: Using GC/MS, knockout experiments and 2D-Gelelectrophoresis as basic methods we analyse the metabolic profile of the model organism Corynebacterium glutamicum. Combined with parameters available from different databases the information about metabolites and catalyzed reactions is used for complete in silico simulation processes of metabolic and regulatory pathways.
Because of the fact that only inadequate experimental and genome annotation data are available, most of the biological simulations are qualitative. In order to get a more detailed image of metabolism we analyse substrate-product chains from databases like BRENDA. Furthermore we develop and integrate simulation techniques with different level of details ranging from the most exact quantum chemical level for calculation of thermodynamic reaction parameters in molecular systems via force field based calculations for structure optimization up to simulation of metabolical networks with Petri nets and the flux balance method.
Computer tools for protein structure and design: In the past we have published effective methods for protein-protein docking, protein superposition and protein-design. Presently we develop fast and precised docking algorithms as well as an energy function which parameterizes and verifies possible confirmations of protein-protein docking simulations.
Metabolic information system BRENDA: Compared to a one-dimensional description of gene or protein sequences, expression level or molecular 3D structures, the multidimensional description of protein functions creates high demands on data structure, nomenclature and the standardiszation of experimental procedures. Therefore we develop experimental standards and the application of a standardized ontology.
Since April 2002 CUBIC offers a postgraduate course in bioinformatics. Scientists, who have an educational background in life sciences, mathematics, physics or computer science, will learn skills and techniques in bioinformatics. Within the one-year course the participants are trained to apply and develop modern bioinformatics tools. The course contains three training parts. Depending on their qualification, students will be first taught either in basics of life science or in computer science and mathematics. After this introductory course which should facilitate the gateway into bioinformatics, the course continues with the theoretical base and tools in applied bioinformatics. In order to gain insight into current computational life science research, students will work on their own research/development project either in industry or an academic research group. The contents of the course is equivalent to a MSc. Program.
Each student will have an individual computer for full-time access for practice. To guarantee a first-rate education CUBIC limits access to 30 students per year. For highly qualified students the center offers scholarships in an amount of 1000 EUR/month. The course is designed for international participants and is held in English language.
*CUBIC is funded by Federal Ministry of Education and Research
