BCB - Berliner Centre for Genome-Based Bioinformatics

Funding: Bundesministerium für Bildung und Forschung, 2002 - 2006

The promise of Bioinformatics is to bridge the gap between genome research and medicine. It is the goal of the Berlin Center for Genome Based Bioinformatics (BCB) to realize this vision. The cooperating groups of BCB will attack the major problems in the informational synthesis of genome data

• genomic annotation and knowledge management,
• prediction of structure and function of gene products,
• cellular and disease modelling.

Scientific efforts will be closely integrated with and complemented by educational efforts specifically promoting short-term education of bioinformatics specialists through a 1.5 year curriculum at Technische Fachhochschule Berlin (TFH), and a MSc course in bioinformatics at Freie Universität Berlin (FUB) in close collaboration with Humboldt Universität zu Berlin (HUB).

Project partner: Charite, Max-Planck-Institute for Molecular Genetics, Freie Universität Berlin, Technische Fachhochschule Berlin, Max-Delbrück-Zentrum, Zuse Institut Berlin

Columba - An integrated database of protein structures, sequences, and annotations

Funding: Bundesministerium für Bildung und Forschung, 2002 - 2006

Researchers interested in the analysis of protein structures often require not only the actual structure, but also textual annotation that is spread over different datasources.

In the project Columba we integrate many resources on proteins. Columba is centered around protein structures obtained from the Protein Data Bank (PDB). We add as much annotations as possible to the structures by describing their properties. These annotation include folding classification from SCOP and CATH, secondary structures calculated with DSSP, enzyme annotation from the ENZYME database, participation in metabolic pathways from KEGG, taxonomic classification from the NCBI Taxonomy, and function characterisation from Gene Ontology.

Co-operation: Kristian Rother, Robert Preissner (Charitè); Prof. Freytag (HUB Informatik); Thomas Steinke (ZIB); Ina Koch (TFH Berlin)

Ali Baba - Mining Scientific Literature

Funding: Bundesministerium für Bildung und Forschung, 2002 - 2006

The extraction of interactions taking place between various biological objects from text has become a major point of research for text mining during the last years. Our group focuses on the collection of interaction networks, both to provide quick overviews over specified subparts of domains, and to build complete interaction graphs that can be queried afterwards. We put our current emphasis on mining protein-protein interactions from scientific publications.
[related text mining projects]

Querying and Analyzing Biological Networks

Graphs are playing an increasingly important role in many areas of biology. Examples are metabolic networks, networks of gene regulation, graphs formed of protein-protein interactions and complexes, and cascades in signal transduction. The size of the graphs under study have, due to improved experimental techniques, considerably grown in size, with many networks today reaching tens of thousands of nodes. In our project, we develop algorithms and systems for efficiently handling graphs of such sizes. In particular, we study graph-based query languages, indexing, cluster-based analysis and visualization.

Aladin - Almost Hands-Off Data Integration for the Life Sciences

Funding: Bundesministerium für Bildung und Forschung (Leser), Deutsche Forschungsgemeinschaft (Naumann)

Aladin aims - as Columba - on integration of databases in the life sciences. But opposed to Columba, Aladin's challenge is to integrate the data sources automatically. The fundamental idea is to work data-centric instead of schema-centric, which is besides its known disadvantages especially unsuitable for life science databases. Another major point for Aladin is to use domain-specific knowledge for integration strategies, e.g. common properties and structures of life science databases.

Co-operation: Felix Naumann (Information Integration Group, Humboldt-Universität zu Berlin)

Interdisciplinary Network for Bioinformatic and Linguistics

Funding: Berliner Senat, 2003 - 2006

The project studies the two areas where linguistics and bioinformatics try to solve common problems. First, evolutionary biology tries to uncover the ancestral relationships between species. Similarly, historical linguistics is interested in the relationships of languages and dialects. Both use phylogenetic methods for this analysis. Second, biological databases annotate their objects with controlled vocabularies, ontologies, and thesauri, to denote gene function and structure. In a similar fashion, corpora in linguistic research are annotated with multiple and possible structured layers of knowledge describing morphology, syntax, and semantics of words and sentences. Both rely on efficient methods for dealing with large amounts of complex and structured annotation. In the project, we exploit and further develop synergies between these independent, yet highly related branches of research.

Co-operation: Prof. Lüdeling, Prof. Donhauser (Institut für Deutsche Sprache, Humboldt-Universität zu Berlin)

Deutsch.Diachron.Digital (DDD)

Funding: Grant proposal under evaluation

The project Deutsch.Diachron.Digital is a German-wide and interdisciplinary initiative for the development of a digital reference corpus of German, starting from the very first manuscripts of predecessors of the German language to current time. Within this consortium, our group is responsible for the development of the central corpus database.

Graduate School for Model-Based Development of Self-Organizing Networks for catastrophy Management

Funding: Deutsche Forschungsgemeinschaft, 2006-2010

Recent progress in basic research has lead to visions how to use new self-organizing networks for advanced information systems. These networks function without central administration – all nodes are able to adapt themselves to new environments autonomously and independently. The addition of new nodes or failure of individual nodes does not significantly impact the network’s ability to function properly. Information systems and underlying technologies for self-organizing networks, in the context of a specific application domain, are the central topic of research for this graduate school. The research focuses on the important technologies needed at each individual node of a self-organizing network. Research challenges within this graduate school include: finding a path through a network with the help of new routing protocols and forwarding techniques, replication of decentralized data, automated deployment and update of software components at runtime as well as work-load balancing among terminal devices with limited resources. Furthermore, non-functional aspects such as reliability, latency and robustness will be studied.