{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=curation_notes.txt"],"Owl":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=Ferrel2011-biopax3.owl","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=Ferrel2011-biopax2.owl"],"Xml":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=Ferrel2011.xml","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=manifest.xml"],"Other":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=curation_image.png","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=Ferrel2011-matlab.m","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=Ferrel2011-octave.m","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=Ferrel2011.ode","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=Ferrel2011.cps","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=metadata.rdf","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000935?filename=Ferrel2011.sedml"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"submitter":["Matthieu MAIRE"],"curationStatus":["Manually curated"],"modellingApproach":["ordinary differential equation model"],"levelVersion":["L2V4"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/BIOMD0000000935"],"publication_pubmed":["21414480"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["Ferrel2011 Cdk1 and APC regulation in cell cycle in Xenopus laevis"],"publication_year":["2011"],"submissionId":["MODEL1809040003"],"publication_authors":["James E Ferrell, Tsai TY, Qiong Yang"],"first_author":["James E Ferrell"],"publication":["21414480,\n Computational modeling and the theory of nonlinear dynamical systems allow one to not simply describe the events of the cell cycle, but also to understand why these events occur, just as the theory of gravitation allows one to understand why cannonballs fly in parabolic arcs. The simplest examples of the eukaryotic cell cycle operate like autonomous oscillators. Here, we present the basic theory of oscillatory biochemical circuits in the context of the Xenopus embryonic cell cycle. We examine Boolean models, delay differential equation models, and especially ordinary differential equation (ODE) models. For ODE models, we explore what it takes to get oscillations out of two simple types of circuits (negative feedback loops and coupled positive and negative feedback loops). Finally, we review the procedures of linear stability analysis, which allow one to determine whether a given ODE model and a particular set of kinetic parameters will produce oscillations.. 6, 144.\n Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA. james.ferrell@stanford.edu"],"submitter_mail":["matt.maire@free.fr"],"submitter_affiliation":["EMBL-EBI"],"publicationId":["BIOMD0000000935"],"pubmed_abstract":["Computational modeling and the theory of nonlinear dynamical systems allow one to not simply describe the events of the cell cycle, but also to understand why these events occur, just as the theory of gravitation allows one to understand why cannonballs fly in parabolic arcs. The simplest examples of the eukaryotic cell cycle operate like autonomous oscillators. Here, we present the basic theory of oscillatory biochemical circuits in the context of the Xenopus embryonic cell cycle. We examine Boolean models, delay differential equation models, and especially ordinary differential equation (ODE) models. For ODE models, we explore what it takes to get oscillations out of two simple types of circuits (negative feedback loops and coupled positive and negative feedback loops). Finally, we review the procedures of linear stability analysis, which allow one to determine whether a given ODE model and a particular set of kinetic parameters will produce oscillations."],"pubmed_title":["Modeling the cell cycle: why do certain circuits oscillate?"],"pubmed_authors":["Ferrell James E JE, Tsai Tony Yu-Chen TY, Yang Qiong Q"],"pubmed_abstract_synonyms":["Xenopus, phapii, IPP2A2, determination, igaad, StF-IT-1, Gravities, Cell, Division Cycles, PHAPII, group, 5730420M11Rik, Review Literature, I-2PP2A, Gravistimulation, renal dysfunction, PIG7, Cycle, chemical analysis, Dm I-2, I2PP2A, G Force, Renal Dysfunction, Arthrogryposis, Xenopus , and cholestasis, Cell Division Cycles, Cycles, Multicase, SET, Force, G, HLA-DR-associated protein II, i2pp2a., Division Cycle, ARCS1, ensemble, DI-2, Review, Academic, TAF-I, I-2Dm, ipp2a2, Cell Division Cycle, cell-division cycle, and cholestasis 1, Xenopus , 2pp2a, Cell Division, CG4299, ARC syndrome, CG10574, Gravity, DmelCG4299, I-2PP1, IGAAD, set, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, 2PP2A, DmelCG10574, taf-ibeta, Cell Cycles, Arthrogryposis multiplex congenita, dSET, dSet, And Cholestasis, TAF-Ibeta, assay, Review of Reported Cases, glutamine:preQ0-tRNA amidinotransferase, Feedbacks, SIMPLE, AA407739, G Forces, ArcS, ARCS, TP53I7"],"name_synonyms":["SRM5, Regulations, D-APC1, D-APC2, D-Axin, 2.7.11.22, e-apc, Daxin, 2.7.11.23, apc, axn, Social Controls, Cell division control protein 2 homolog, cdc, DP3, PPP1R46, DP2, d-axin, 1802), Cdc2a, Cycle, DAPC, CG6193, l(2)31Eh, swo2, Min, BTPS2, GSK3beta, clawed frog, CG1451, D-APC, Formal Social Controls, dApc, dAPC, Dmcdc2, Cell Division Cycles, Cycles, X. laevis., CDC28A, Cell Division Cycle, cell-division cycle, P34CDC2, mAPC, Cell Division, CG7926, AI047805, Social, dAPC2/E-APC, Xenopus laevis (Daudin, CDK1/CDC2, cdc2Dm, cdk1, CG5363, dCdk1, Cell Cycles, Cdc2, CDC2, cyclosome, CDK1, Dcdc2, Cdk1, DmelCG6193, Dm cdc2, dAxin, DmelCG1451, dApc2, din, l(3)S044230, Formal Social Control, E-APC, DP2.5, African clawed frog, HSL5, common platanna, clawed frog , d-APC, Cell, Division Cycles, APC2, dAXIN, Apc1, APC1, xapc, E-APC dAPC2, Social Control, group 4, apc 1, DmCdc2, apc1, axin, Bufo laevis, apc2, Xenopus leavis, DmCdk1, d-APC2, DmelCG5363, p34-lt-CDC2-gt-, dAPC2, dAPC1, AU020952, 5363, Division Cycle, CC1, 0442/30, Control, tws1, AW124434, Controls, Cell division protein kinase 1, Dm APC2, Dm APC1, DAxin, p34, p34 protein kinase, GS, DmelCG7926, Cdk-1, APC, regulation, platanna, anaphase promoting complex, X. laevi, Regulation, Platanna, CDCDm, Platannas"],"description_synonyms":["Regulations, SRM5, D-APC1, D-APC2, D-Axin, 2.7.11.22, e-apc, Daxin, 2.7.11.23, apc, axn, Social Controls, Cell division control protein 2 homolog, cdc, DP3, PPP1R46, DP2, d-axin, 1802), Cdc2a, Cycle, DAPC, CG6193, l(2)31Eh, swo2, Min, BTPS2, GSK3beta, clawed frog, CG1451, D-APC, Formal Social Controls, dApc, dAPC, Dmcdc2, Cell Division Cycles, Cycles, X. laevis., CDC28A, Cell Division Cycle, cell-division cycle, P34CDC2, mAPC, Cell Division, CG7926, Social, AI047805, dAPC2/E-APC, Xenopus laevis (Daudin, CDK1/CDC2, cdc2Dm, cdk1, CG5363, dCdk1, Cell Cycles, Cdc2, CDC2, cyclosome, CDK1, Dcdc2, Cdk1, DmelCG6193, Dm cdc2, dAxin, DmelCG1451, dApc2, din, l(3)S044230, Formal Social Control, E-APC, DP2.5, African clawed frog, HSL5, common platanna, clawed frog , d-APC, Cell, Division Cycles, APC2, dAXIN, Apc1, APC1, xapc, E-APC dAPC2, Social Control, group 4, apc 1, DmCdc2, apc1, axin, Bufo laevis, apc2, Xenopus leavis, DmCdk1, d-APC2, DmelCG5363, p34-lt-CDC2-gt-, dAPC2, dAPC1, AU020952, 5363, Division Cycle, CC1, 0442/30, Control, tws1, Controls, AW124434, Cell division protein kinase 1, Dm APC2, Dm APC1, DAxin, p34, p34 protein kinase, GS, DmelCG7926, Cdk-1, regulation, APC, platanna, anaphase promoting complex, X. laevi, Regulation, Platanna, CDCDm, Platannas"],"pubmed_title_synonyms":["Cell Division Cycles, Cell Division Cycle, Cycles, cell-division cycle, Cell Division, Cell Cycles., Division Cycle, Cell, Cycle, Division Cycles"],"additional_accession":[]},"is_claimable":false,"name":"Ferrel2011 - Cdk1 and APC regulation in cell cycle in Xenopus laevis","description":"Mathematical model of the regulation of Cdk1 and APC in cell cycle in Xenopus Laevis","dates":{"last_modification":"2024-08-22","publication":"2024-09-02","submission":"2018-09-04"},"accession":"BIOMD0000000935","cross_references":{"pubmed":["21414480"],"ncit":["C13361","C64382"],"biomodels__db":["MODEL1809040003","BIOMD0000000935"],"pato":["PATO:0002354"],"go":["GO:0051726"],"taxonomy":["8355"],"uniprot":["P35567","P70039"]}}