Chair of Theoretical Computer Science
BioPath

BioPath

Introduction

BioPath was motivated by the famous Boehringer wall chart "Biochemical Pathways". This chart gives a condensed view to the biochemical knowledge and represents biochemical pathways and regulation. It is well recognized by students and researchers, and is widely distributed. The chart is a hardcopy. It cannot grow with the enormous expansion of the scientific knowledge in biochemistry and molecular biology. And it cannot give dynamic views to a specific problem and extract just the data for a single query.

BioPath is a platform for a convenient electronic access to the biochemical knowledge. It provides information from different views and in distinct levels of detail. BioPath provides powerful search mechanisms for substances and reaction networks, it gives access to different types of information on enzymes, reactions and metabolism and automatically computes visual representations of complex reactions nets. BioPath is easy to use and can be updated and extended.

Current activities are the improvement and adaptation of the major components of BioPath.

References

  • Michael Forster, Andreas Pick, Marcus Raitner, Falk Schreiber, Franz J. Brandenburg
    The System Architecture of BioPath
    In Silico Biology (2), 2002
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  • Falk Schreiber
    High Quality Visualization of Biochemical Pathways in BioPath
    In Silico Biology (2), 2002
    html
  • Franz J. Brandenburg, Michael Forster, Andreas Pick, Marcus Raitner, Falk Schreiber
    BioPath
    In Proceedings of the 9th International Symposium on Graph Drawing (GD'01), LNCS 2265, Springer Verlag, 455-456, 2002
  • Falk Schreiber
    Visualisierung biochemischer Reaktionsnetze
    Dissertation, Universität Passau, 2001
  • Johann Gasteiger, Dietrich Trümbach
    Biochemical Pathways as a Reaction Database
    Keynote lecture, In Proceedings of the German Conference on Bioinformatics, page 121, Logos Verlag, Berlin, 2000
    ps
  • Dietrich Trümbach, Johann Gasteiger
    Interaktive biochemische Stoffwechselwege
    In Proceedings of the Workshop Informationssysteme in der Biotechnologie, Workshop der GI-FG 4.0.2, pages 7-8, 2000
    ps
  • Dietrich Trümbach, Johann Gasteiger
    Reaction Substructure Search applied to Biochemical Pathways
    Poster Abstract of the German Conference on Bioinformatics, Poster Nr. 46, 2000
    ps
  • Falk Schreiber
    Dynamic Visualization of Biochemical Pathways
    In Proceedings of the Workshop on Innovations in Biochemical Visualisation, European Media Laboratory (EML), Heidelberg, 2000
  • Carl-Christian Kanne, Guido Moerkotte
    Efficient Storage of XML data
    In Proceedings of the 16th International Conference on Data Engineering, page 198, 2000
  • Carl-Christian Kanne, Falk Schreiber, Dietrich Trümbach
    Electronic Biochemical Pathways
    In Proceedings of the 7th International Symposium on Graph Drawing (GD'99), 1731 of LNCS, pages 418-419, Springer Verlag, 1999
    ps
  • Carl-Christian Kanne, Falk Schreiber, Dietrich Trümbach
    Interactive Biochemical Pathways (Poster)
    In Proceedings of the German Conference on Bioinformatics (GCB'99), pages 204-205, 1999
    ps
  • Franz J. Brandenburg, Bernhard Gruber, Michael Himsolt, Falk Schreiber
    Automatische Visualisierung biochemischer Information
    In Proceedings of the Workshop Molekulare Bioinformatik, GI Jahrestagung, 24-38, Shaker Verlag, 1998
    ps
  • Franz J. Brandenburg, Bernhard Gruber, Michael Himsolt, Falk Schreiber
    Visualization of Biochemical Information
    In Proceedings of the Workshop Modelling and Simulation of Gene and Cell Regulation and Metabolic Pathways, Schloss Dagstuhl, Report No. 215, pages 60-61, 1998

Partners

BioPath has been developed in the research project "Multimediale Weiterentwicklung der Biochemical Pathways", which has been supported by the Federal Ministry of Education and Research (BMBF). The cooperating project partners are:

Logo Spektrum Akademischer Verlag

Spektrum Akademischer Verlag
Slevogtstr. 3-5 
D-69126 Heidelberg

Logo Uni Erlangen Nürnberg

Universität Erlangen-Nürnberg
Computer-Chemie-Zentrum und Institut für Organische Chemie
Prof. Dr. Johann Gasteiger
Nägelsbachstraße 25
D-91052 Erlangen

Logo Uni Mannheim

Universität Mannheim
Lehrstuhl für Praktische Informatik III
Professor Dr. Guido Moerkotte
B6, 29, Gebäudeteil C Raum: Raum C0.10
D-68131 Mannheim

Logo Uni Passau

Universität Passau
Lehrstuhl für Informatik mit Schwerpunkt Theoretische Informatik
Professor Dr. Franz J. Brandenburg
Innstraße 33
D-94030 Passau