Motivation: Models of regulatory networks become more
difficult to construct and understand as they grow in size and
complexity. Modelers naturally build large models from smaller
components that each represent subsets of reactions within the
larger network. To assist modelers in this process, we present
model aggregation, which defines models in terms of components
that are designed for the purpose of being combined., Results:
We have implemented a model editor that incorporates model
aggregation, and we suggest supporting extensions to the
Systems Biology Markup Language (SBML) Level 3. We
illustrate aggregation with a model of the eukaryotic cell
cycle ‘engine’ created from
smaller pieces., Availability: Java implementations are
available in the JigCell Aggregation Connector. See
http://jigcell.biol.vt.edu., Contact: shaffer@vt.edu
%0 Journal Article
%1 randhawa_model_2009
%A Randhawa, Ranjit
%A Shaffer, Clifford A.
%A Tyson, John J.
%D 2009
%J Bioinformatics
%K modularity
%N 24
%P 3289--3295
%R 10.1093/bioinformatics/btp581
%T Model aggregation: a building-block approach to creating large macromolecular regulatory networks
%U http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788926/
%V 25
%X Motivation: Models of regulatory networks become more
difficult to construct and understand as they grow in size and
complexity. Modelers naturally build large models from smaller
components that each represent subsets of reactions within the
larger network. To assist modelers in this process, we present
model aggregation, which defines models in terms of components
that are designed for the purpose of being combined., Results:
We have implemented a model editor that incorporates model
aggregation, and we suggest supporting extensions to the
Systems Biology Markup Language (SBML) Level 3. We
illustrate aggregation with a model of the eukaryotic cell
cycle ‘engine’ created from
smaller pieces., Availability: Java implementations are
available in the JigCell Aggregation Connector. See
http://jigcell.biol.vt.edu., Contact: shaffer@vt.edu
@article{randhawa_model_2009,
abstract = {Motivation: Models of regulatory networks become more
difficult to construct and understand as they grow in size and
complexity. Modelers naturally build large models from smaller
components that each represent subsets of reactions within the
larger network. To assist modelers in this process, we present
model aggregation, which defines models in terms of components
that are designed for the purpose of being combined., Results:
We have implemented a model editor that incorporates model
aggregation, and we suggest supporting extensions to the
Systems Biology Markup Language ({SBML)} Level 3. We
illustrate aggregation with a model of the eukaryotic cell
cycle {\textquoteleft}engine{\textquoteright} created from
smaller pieces., Availability: Java implementations are
available in the {JigCell} Aggregation Connector. See
http://jigcell.biol.vt.edu., Contact: shaffer@vt.edu},
added-at = {2014-01-19T15:15:23.000+0100},
author = {Randhawa, Ranjit and Shaffer, Clifford A. and Tyson, John J.},
bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788926/},
bdsk-url-2 = {http://dx.doi.org/10.1093/bioinformatics/btp581},
biburl = {https://www.bibsonomy.org/bibtex/2554ff06d9433dfe133637be6657f779b/neurokernel},
doi = {10.1093/bioinformatics/btp581},
interhash = {6a867b491efbc4358e1e19b9cedefc35},
intrahash = {554ff06d9433dfe133637be6657f779b},
issn = {1367-4803},
journal = {Bioinformatics},
keywords = {modularity},
month = dec,
note = {{PMID:} 19880372 {PMCID:} {PMC2788926}},
number = 24,
pages = {3289--3295},
shorttitle = {Model aggregation},
timestamp = {2014-01-19T15:15:23.000+0100},
title = {Model aggregation: a building-block approach to creating large macromolecular regulatory networks},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788926/},
urldate = {2012-11-27},
volume = 25,
year = 2009
}