Systematic integration of experimental data and models in systems biology

BMC Bioinformatics

Methodology Article

Jill Wishart¹  Naglis Malys¹  Evangelos Simeonidis²  Hans V Westerhoff³  David S Broomhead⁴  Peter Li⁵  Douglas B Kell⁵  Catherine Winder⁵  Hanan L Messiha⁵  Kathleen Carroll⁶  Simon J Gaskell⁶  Warwick Dunn⁶  Dieter Weichart⁶  Farid Khan⁶  Irena Spasic⁷  Joseph O Dada⁸  Carole A Goble⁸  Daniel Jameson⁹  Neil Swainston⁹  Norman W Paton⁹  Pedro Mendes^1,10 

[1] Manchester Centre for Integrative Systems Biology, The University of Manchester, M1 7DN, Manchester, UK;Faculty of Life Sciences, The University of Manchester, M13 9PL, Manchester, UK;Manchester Centre for Integrative Systems Biology, The University of Manchester, M1 7DN, Manchester, UK;School of Chemical Engineering and Analytical Science, The University of Manchester, M60 1QD, Manchester, UK;Manchester Centre for Integrative Systems Biology, The University of Manchester, M1 7DN, Manchester, UK;School of Chemical Engineering and Analytical Science, The University of Manchester, M60 1QD, Manchester, UK;Department of Molecular Cell Physiology, Vrije Universiteit, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands;Manchester Centre for Integrative Systems Biology, The University of Manchester, M1 7DN, Manchester, UK;School of Mathematics, The University of Manchester, M13 9PL, Manchester, UK;School of Chemistry, The University of Manchester, M13 9PL, Manchester, UK;School of Chemistry, The University of Manchester, M13 9PL, Manchester, UK;Manchester Centre for Integrative Systems Biology, The University of Manchester, M1 7DN, Manchester, UK;School of Computer Science & Informatics, Cardiff University, CF24 3AA, Cardiff, UK;School of Computer Science, The University of Manchester, M13 9PL, Manchester, UK;School of Computer Science, The University of Manchester, M13 9PL, Manchester, UK;Manchester Centre for Integrative Systems Biology, The University of Manchester, M1 7DN, Manchester, UK;School of Computer Science, The University of Manchester, M13 9PL, Manchester, UK;Manchester Centre for Integrative Systems Biology, The University of Manchester, M1 7DN, Manchester, UK;Virginia Bioinformatics Institute, Virginia Tech, Washington Street 0477, 24061, Blacksburg, VA, USA;

关键词: System Biology;    Metabolic Network;    System Biology Markup Language;    Saccharomyces Genome Database;    System Biology Model;   

DOI  :  10.1186/1471-2105-11-582

 received in 2010-06-18, accepted in 2010-11-29,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources.ResultsTaverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis.ConclusionsDistributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

【 授权许可】

CC BY   
© Li et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.