Thanks to all speakers and all participants.

For further details: see the meeting page.

Welcome to the SABIO-Reaction Kinetics Database (Software version 20091201) Please note that we currently support the following browsers (and are testing others): Internet Explorer (version 6.0 onwards) FireFox (version 2.0 onwards) Netscape 7 onwards What is SABIO-RK? Citing SABIO-RK Data Provenance Main Features Web Services Documentation Terms and Conditions Contact Publications What is SABIO-RK?     TOP The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modellers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. Information about reactions and their kinetics can be exported in SBML (Systems Biology Mark-Up Language ) format. This project is sponsored by the Klaus Tschira Foundation and partially by the German BMBF (Bundesministerium f�r Bildung und Forschung).

Citing SABIO-RK     TOP Please use the following reference to cite SABIO-RK: SABIO-RK: Integration and Curation of Reaction Kinetics Data Wittig U., Golebiewski, M., Kania, R., Krebs, O., Mir, S., Weidemann, A., Anstein, S., Saric, J. and Rojas, I.. In proceedings of the 3rd International workshop on Data Integration in the Life Sciences 2006 (DILS'06). Hinxton, UK. Lecture Notes in Bioinformatics, 4075: 94-103(2006). Abstract

Data Provenance     TOP There are two main sources for the data contained in SABIO. Most of the reactions, their association with pathways and their enzymatic classification, is extracted from the KEGG (KEGG: Kyoto Encyclopedia of Genes and Genomes) database. The other main source of data are publications. The reaction kinetics data are obtained by manual extraction from literature sources and curated. Release Information      TOP Current release: 1.0 (Short tutorial with screen shots ) Main Features: Allows the querying for reactions: within pathway(s) having certain reactant(s) classified with EC Number reported to occur in organism(s) -- from curated data reported to occur in tissue(s)/cell type(s) -- from curated data reported to occur in cellular location -- from curated data reported to occur at a certain temperature/pH -- from curated data reported about in certain publication -- giving PubMed ID Link to Swissprot and PubMed Generation of SBML format file, containing information about the reactions, their kinetic laws (if existing) and parameter definition and values. PLEASE NOTE: the SBML file generated needs to be edited before it can be used by most modelling tools supporting SBML, given that the system will create as many unit definition as defined for the parameters. Thus the user needs to preform the unit convertion in order to have all parameter values defined using the same basic units. We plan to include information about in vivo compound concentrations in the near future, which can then included into the SBML file. Currently all compound concentration will be set to 1. Note: The curret version has been tested using FireFox and Miscrosoft Explorer, we cannot guarantee it will work properly under other browsers. Web Services     TOP You can also access The SABIO-RK Database programmatically using web services. For details and instructions, please visit the web service home Terms and Conditions      TOP The terms and conditions for use of SABIO-RK can be found here. Contact     TOP Scientific Databases and Visualization Group at the EML Research in Heidelberg, Germany. Email: sabiork at eml-r.org We welcome any suggestions and contributions to the database. Publications     TOP You can find more information on SABIO-RK in the following publications: SABIO-RK: a database for biochemical reactions and their kinetics Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Ulrike Wittig BMC Systems Biology 2007, 1(Suppl 1):S6 (8 May 2007) http://www.biomedcentral.com/1752-0509/1/S1/S6 Integration of SABIO-RK in workbenches for kinetic model design Martin Golebiewski, Saqib Mir, Renate Kania, Olga Krebs, Andreas Weidemann, Ulrike Wittig, Isabel Rojas BMC Systems Biology 2007, 1(Suppl 1):P4 (8 May 2007) http://www.biomedcentral.com/1752-0509/1/S1/P4 Storing and annotating of kinetic data Rojas I, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Wittig U. In Silico Biol. 2007;7(2 Suppl):S37-44. PMID: 17822389 http://www.bioinfo.de/isb/2007/07/S1/05/ © EML Research gGmbH