eprintid: 20076
rev_number: 16
eprint_status: archive
userid: 1589
dir: disk0/00/02/00/76
datestamp: 2016-02-17 09:47:22
lastmod: 2024-03-09 10:17:47
status_changed: 2016-02-17 09:47:22
type: article
metadata_visibility: show
creators_name: Surovtsova, Irina
creators_name: Simus, Natalia
creators_name: Hübner, Katrin
creators_name: Sahle, Sven
creators_name: Kummer, Ursula
title: Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics
subjects: 570
divisions: 140001
divisions: 708000
divisions: 716000
divisions: 718000
divisions: 721000
divisions: 852300
abstract: Background: Given the complex mechanisms underlying biochemical processes systems biology researchers tend to build ever increasing computational models. However, dealing with complex systems entails a variety of problems, e.g. difficult intuitive understanding, variety of time scales or non-identifiable parameters. Therefore, methods are needed that, at least semi-automatically, help to elucidate how the complexity of a model can be reduced such that important behavior is maintained and the predictive capacity of the model is increased. The results should be easily accessible and interpretable. In the best case such methods may also provide insight into fundamental biochemical mechanisms.   Results: We have developed a strategy based on the Computational Singular Perturbation (CSP) method which can be used to perform a "biochemically-driven" model reduction of even large and complex kinetic ODE systems. We provide an implementation of the original CSP algorithm in COPASI (a COmplex PAthway SImulator) and applied the strategy to two example models of different degree of complexity - a simple one-enzyme system and a full-scale model of yeast glycolysis.   Conclusion: The results show the usefulness of the method for model simplification purposes as well as for analyzing fundamental biochemical mechanisms. COPASI is freely available at http://www.copasi.org.
date: 2012
publisher: BioMed Central
id_scheme: DOI
ppn_swb: 1656588846
own_urn: urn:nbn:de:bsz:16-heidok-200760
language: eng
bibsort: SUROVTSOVASIMPLIFICA2012
full_text_status: public
publication: BMC Systems Biology
volume: 6
number: 14
place_of_pub: London
pagerange: 1-16
issn: 1752-0509
citation:   Surovtsova, Irina ; Simus, Natalia ; Hübner, Katrin ; Sahle, Sven ; Kummer, Ursula  (2012) Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics.  BMC Systems Biology, 6 (14).  pp. 1-16.  ISSN 1752-0509     
document_url: https://archiv.ub.uni-heidelberg.de/volltextserver/20076/1/12918_2011_Article_857.pdf