B9 Integrated databases, bioinformatic tools, analysis and modelling for system biology with B. megaterium and A. niger
The new subproject B9 provides the platform for the integration of various bioinformatics approaches taken by groups of the SFB. This includes the development of methods, software and databases as well as the establishment of a communication platform. The subproject deals with the following specific aims in detail:
Development of an automatic method and software for deduction and completion of metabolic networks:
Modelling and simulation of metabolic networks by the use of graph-theoretical methods and metabolic flow analysis, as performed in projects B4 (Jahn/Nörtemenn/Jänsch) and B10 (Schomburg/Jahn/Franco-Lara), or by differential equation systems are always based on the prediction of given enzymes and transport systems. Genome annotations which are inevitably incomplete and/or false according to the current state of research require a lot of time spent for manual curation. An automatic method is to increase the efficiency.
Modelling and simulation of regulatory networks for A. niger:
Methods for DNA pattern analysis are further developed in projects B4 (Jahn/Nörtemenn/Jänsch) und B10 (Schomburg/Jahn/Franco-Lara) in order to help to extend the existing data on gene regulatory networks and signal transduction paths. In accordance with B4, this data will be integrated into kinetic models for pH-dependent protein production and cell growth of A. niger.
Further development of methods for topological analysis of metabolic networks of B. megaterium and A. niger:
Based on publications about network analysis (Pathway Hunter Tool), methods for identifying critical points in metabolic networks will be developed further.
Development of a communication and data platform for the SFB:
An open source groupware tool (e.g. EGROUPWARE or PHPROJEKT) will be employed as platform to store and make the results of the different projects available to the other groups.