Dataset Information

Smallbone2010_Genome_Scale_Yeast_Kinetics

ABSTRACT: This is the model described in the article: Towards a genome-scale kinetic model of cellular metabolism Smallbone K, Simeonidis E, Swainston N, Mendes P. BMC Syst Biol. 2010 Jan 28;4(1):6. PMID: 20109182 , doi: 10.1186/1752-0509-4-6 Abstract: CKGROUND: Advances in bioinformatic techniques and analyses have led to the availability of genome-scale metabolic reconstructions. The size and complexity of such networks often means that their potential behaviour can only be analysed with constraint-based methods. Whilst requiring minimal experimental data, such methods are unable to give insight into cellular substrate concentrations. Instead, the long-term goal of systems biology is to use kinetic modelling to characterize fully the mechanics of each enzymatic reaction, and to combine such knowledge to predict system behaviour. RESULTS: We describe a method for building a parameterized genome-scale kinetic model of a metabolic network. Simplified linlog kinetics are used and the parameters are extracted from a kinetic model repository. We demonstrate our methodology by applying it to yeast metabolism. The resultant model has 956 metabolic reactions involving 820 metabolites, and, whilst approximative, has considerably broader remit than any existing models of its type. Control analysis is used to identify key steps within the system. CONCLUSIONS: Our modelling framework may be considered a stepping-stone toward the long-term goal of a fully-parameterized model of yeast metabolism. The model (see additional file 1) is available in SBML format from the BioModels database (BioModels ID: MODEL1001200000) and at http://www.mcisb.org/resources/genomescale/ . This SBML representation of the yeast metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org). This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

OTHER RELATED OMICS DATASETS IN: PXD016589PRJNA84673PRJNA89881PRJNA89887PRJNA89909PRJNA89879

SUBMITTER: Kieran Smallbone

PROVIDER: MODEL1001200000 | BioModels | 2005-01-01

REPOSITORIES: BioModels

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Dataset's files

Source:

			Action	DRS
	MODEL1001200000?filename=MODEL1001200000-biopax2.owl	Owl
	MODEL1001200000?filename=MODEL1001200000-biopax3.owl	Owl
	MODEL1001200000?filename=MODEL1001200000.m	Other
	MODEL1001200000?filename=MODEL1001200000.pdf	Pdf
	MODEL1001200000?filename=MODEL1001200000.png	Other

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Publications

Towards a genome-scale kinetic model of cellular metabolism.

Smallbone Kieran K Simeonidis Evangelos E Swainston Neil N Mendes Pedro P

BMC systems biology 20100128

<h4>Background</h4>Advances in bioinformatic techniques and analyses have led to the availability of genome-scale metabolic reconstructions. The size and complexity of such networks often means that their potential behaviour can only be analysed with constraint-based methods. Whilst requiring minimal experimental data, such methods are unable to give insight into cellular substrate concentrations. Instead, the long-term goal of systems biology is to use kinetic modelling to characterize fully th ...[more]

PMID: 20109182

Publication: 1/249

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