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104 Publications visible to you, out of a total of 104
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

Big data: The future of biocuration

Abstract

Not specified

Authors: Doug Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St Pierre, Simon Twigger, Owen White, Seung Yon Rhee

Date Published: 4th Sep 2008

Publication Type: Journal

Classification of chemical compounds to support complex queries in a pathway database.

Abstract (Expand)

Data quality in biological databases has become a topic of great discussion. To provide high quality data and to deal with the vast amount of biochemical data, annotators and curators need to be supported … by software that carries out part of their work in an (semi-) automatic manner. The detection of errors and inconsistencies is a part that requires the knowledge of domain experts, thus in most cases it is done manually, making it very expensive and time-consuming. This paper presents two tools to partially support the curation of data on biochemical pathways. The tool enables the automatic classification of chemical compounds based on their respective SMILES strings. Such classification allows the querying and visualization of biochemical reactions at different levels of abstraction, according to the level of detail at which the reaction participants are described. Chemical compounds can be classified in a flexible manner based on different criteria. The support of the process of data curation is provided by facilitating the detection of compounds that are identified as different but that are actually the same. This is also used to identify similar reactions and, in turn, pathways.

Authors: U. Wittig, A. Weidemann, R. Kania, C. Peiss, I. Rojas

Date Published: 17th Jul 2008

Publication Type: Journal

Developing a protein-interactions ontology.

Abstract

Not specified

Authors: E. Ratsch, J. Schultz, J. Saric, P. C. Lavin, U. Wittig, U. Reyle, I. Rojas

Date Published: 17th Jul 2008

Publication Type: Journal

SYCAMORE--a systems biology computational analysis and modeling research environment

Abstract (Expand)

SYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model … checking and the estimation of unknown kinetic parameters based on protein structures. In addition, it offers some guidance in order to allow non-expert users to perform basic computational modelling tasks.

Authors: A. Weidemann, S. Richter, M. Stein, S. Sahle, R. Gauges, R. Gabdoulline, I. Surovtsova, N. Semmelrock, B. Besson, I. Rojas, R. Wade, U. Kummer

Date Published: 13th Jun 2008

Publication Type: Journal

Storing and annotating of kinetic data.

Abstract (Expand)

This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such … annotations support the definition of cross links to other related databases and augment the semantics of the data stored in the database.

Authors: I. Rojas, M. Golebiewski, R. Kania, O. Krebs, S. Mir, A. Weidemann, U. Wittig

Date Published: 14th Sep 2007

Publication Type: Journal

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