Exact hybrid particle/population simulation of rule-based models of biochemical systems.
Identifieur interne : 003165 ( PubMed/Corpus ); précédent : 003164; suivant : 003166Exact hybrid particle/population simulation of rule-based models of biochemical systems.
Auteurs : Justin S. Hogg ; Leonard A. Harris ; Lori J. Stover ; Niketh S. Nair ; James R. FaederSource :
- PLoS computational biology [ 1553-7358 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
Abstract
Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility.
DOI: 10.1371/journal.pcbi.1003544
PubMed: 24699269
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Stover</name><affiliation><nlm:affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Nair, Niketh S" sort="Nair, Niketh S" uniqKey="Nair N" first="Niketh S" last="Nair">Niketh S. Nair</name><affiliation><nlm:affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Faeder, James R" sort="Faeder, James R" uniqKey="Faeder J" first="James R" last="Faeder">James R. Faeder</name><affiliation><nlm:affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24699269</idno><idno type="pmid">24699269</idno><idno type="doi">10.1371/journal.pcbi.1003544</idno><idno type="wicri:Area/PubMed/Corpus">003165</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003165</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Exact hybrid particle/population simulation of rule-based models of biochemical systems.</title><author><name sortKey="Hogg, Justin S" sort="Hogg, Justin S" uniqKey="Hogg J" first="Justin S" last="Hogg">Justin S. Hogg</name><affiliation><nlm:affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Harris, Leonard A" sort="Harris, Leonard A" uniqKey="Harris L" first="Leonard A" last="Harris">Leonard A. Harris</name><affiliation><nlm:affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Stover, Lori J" sort="Stover, Lori J" uniqKey="Stover L" first="Lori J" last="Stover">Lori J. Stover</name><affiliation><nlm:affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Nair, Niketh S" sort="Nair, Niketh S" uniqKey="Nair N" first="Niketh S" last="Nair">Niketh S. Nair</name><affiliation><nlm:affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Faeder, James R" sort="Faeder, James R" uniqKey="Faeder J" first="James R" last="Faeder">James R. Faeder</name><affiliation><nlm:affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PLoS computational biology</title><idno type="eISSN">1553-7358</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Models, Biological</term><term>Models, Chemical</term><term>Monte Carlo Method</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Models, Biological</term><term>Models, Chemical</term><term>Monte Carlo Method</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24699269</PMID><DateCreated><Year>2014</Year><Month>04</Month><Day>04</Day></DateCreated><DateCompleted><Year>2014</Year><Month>12</Month><Day>08</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1553-7358</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>4</Issue><PubDate><Year>2014</Year><Month>Apr</Month></PubDate></JournalIssue><Title>PLoS computational biology</Title><ISOAbbreviation>PLoS Comput. Biol.</ISOAbbreviation></Journal><ArticleTitle>Exact hybrid particle/population simulation of rule-based models of biochemical systems.</ArticleTitle><Pagination><MedlinePgn>e1003544</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pcbi.1003544</ELocationID><Abstract><AbstractText>Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hogg</LastName><ForeName>Justin S</ForeName><Initials>JS</Initials><AffiliationInfo><Affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Harris</LastName><ForeName>Leonard A</ForeName><Initials>LA</Initials><AffiliationInfo><Affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stover</LastName><ForeName>Lori J</ForeName><Initials>LJ</Initials><AffiliationInfo><Affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nair</LastName><ForeName>Niketh S</ForeName><Initials>NS</Initials><AffiliationInfo><Affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Faeder</LastName><ForeName>James R</ForeName><Initials>JR</Initials><AffiliationInfo><Affiliation>Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>UL1 TR000005</GrantID><Acronym>TR</Acronym><Agency>NCATS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>T32EB009403</GrantID><Acronym>EB</Acronym><Agency>NIBIB NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P41GM103712</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>T32 EB009403</GrantID><Acronym>EB</Acronym><Agency>NIBIB NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P41 GM103712</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>04</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>United 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