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SABIO-RK--database for biochemical reaction kinetics.

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually … extracted from the literature and data directly submitted from lab experiments. The database content includes kinetic parameters in relation to biochemical reactions and their biological sources with no restriction on any particular set of organisms. Additionally, kinetic rate laws and corresponding equations as well as experimental conditions are represented. All the data are manually curated and annotated by biological experts, supported by automated consistency checks. SABIO-RK can be accessed via web-based user interfaces or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language), e.g. for import in modelling tools.

Authors: U. Wittig, R. Kania, M. Golebiewski, M. Rey, L. Shi, L. Jong, E. Algaa, A. Weidemann, H. Sauer-Danzwith, S. Mir, O. Krebs, M. Bittkowski, E. Wetsch, I. Rojas, W. Muller

Date Published: 22nd Nov 2011

Publication Type: Journal

A-R-E: The Author-Review-Execute Environment

Abstract (Expand)

The Author-Review-Execute (A-R-E) is an innovative concept to offer under a single principle and platform an environment to support the life cycle of an (executable) paper; namely the authoring of the … paper, its submission, the reviewing process, the author's revisions, its publication, and finally the study (reading/interaction) of the paper as well as extensions (follow ups) of the paper. It combines Semantic Wiki technology, a resolver that solves links both between parts of documents to executable code or to data, an anonymizing component to support the authoring and reviewing tasks, and web services providing link perennity.

Authors: Wolfgang Müller, Isabel Rojas, Andreas Eberhart, Peter Haase, Michael Schmidt

Date Published: 2011

Publication Type: Journal

Enzyme kinetics informatics: from instrument to browser.

Abstract (Expand)

A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw … experimental data from which the parameters were calculated. This is largely due to the lack of software or standards to support the capture, analysis, storage and dissemination of such experimental data. Introduced here is an integrative system to manage experimental enzyme kinetics data from instrument to browser. The approach is based on two interrelated databases: the existing SABIO-RK database, containing kinetic data and corresponding metadata, and the newly introduced experimental raw data repository, MeMo-RK. Both systems are publicly available by web browser and web service interfaces and are configurable to ensure privacy of unpublished data. Users of this system are provided with the ability to view both kinetic parameters and the experimental raw data from which they are calculated, providing increased confidence in the data. A data analysis and submission tool, the kineticswizard, has been developed to allow the experimentalist to perform data collection, analysis and submission to both data resources. The system is designed to be extensible, allowing integration with other manufacturer instruments covering a range of analytical techniques.

Authors: N. Swainston, M. Golebiewski, H. L. Messiha, N. Malys, R. Kania, S. Kengne, O. Krebs, S. Mir, H. Sauer-Danzwith, K. Smallbone, A. Weidemann, U. Wittig, D. B. Kell, P. Mendes, W. Muller, N. W. Paton, I. Rojas

Date Published: 27th Aug 2010

Publication Type: Journal

SBML2LATEX: Conversion of SBML files into human-readable reports

Abstract

Not specified

Authors: A. Drager, H. Planatscher, D. Motsou Wouamba, A. Schroder, M. Hucka, L. Endler, M. Golebiewski, W. Muller, A. Zell

Date Published: 14th May 2009

Publication Type: Journal

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