Paper Info
Title
Systematic integration of experimental data and models in systems biology.
Abstract
The 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.Taverna 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.Distributed 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.
Year
DOI
Venue
2010
10.1186/1471-2105-11-582
BMC Bioinformatics
Keywords
Field
DocType
workflows,systems biology,bioinformatics,web service,parameter estimation,microarrays,biological systems,optimization,algorithms,kinetics,metabolic network,glycolysis,biochemical pathways,system biology,reconstruction,enzyme kinetics,data integrity,mathematical model
Data integration,Experimental data,Computer science,Metabolic network,Systems biology,Interoperation,Bioinformatics,Workflow,SBML,Markup language
Journal
Volume
Issue
ISSN
11
1
1471-2105
Citations 
PageRank 
References 
17
0.75
23
Authors
21
Name
Order
Citations
PageRank
Peter Li1140488.11
Joseph O. Dada2332.81
Daniel Jameson338626.54
Irena Spasić435432.55
Neil Swainston527414.07
Kathleen Carroll6170.75
Warwick Dunn7745.38
Farid Khan8170.75
Naglis Malys9181.21
Hanan L Messiha10221.21
Evangelos Simeonidis11934.73
Dieter Weichart12170.75
Catherine Winder13281.36
Jill Wishart14170.75
David S. Broomhead15292.67
Carole Goble167252788.90
Simon J Gaskell17252.45
Douglas B Kell18100494.11
Hans V. Westerhoff1933329.11
Pedro Mendes2034953.14
Norman W. Paton213059359.26