{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Pdf":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003.pdf"],"Owl":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003-biopax3.owl","https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003-biopax2.owl"],"Svg":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003.svg"],"Xml":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003_url.xml","https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003_urn.xml"],"Other":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003.vcml","https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003.m","https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003.xpp","https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003.sci","https://www.ebi.ac.uk/biomodels/model/download/MODEL1510190003?filename=MODEL1510190003.png"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Andrew J Millar"],"curationStatus":["Non-curated"],"modellingApproach":["ordinary differential equation model"],"levelVersion":["L2V4"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL1510190003"],"publication_pubmed":["26468131"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["Flis2015   Plant clock gene circuit (P2011.4.1 PLM 1042 ver 1)"],"publication_year":["2015"],"submissionId":["MODEL1510190003"],"publication_authors":["Anna Flis, Aurora Piñas Fernández, Tomasz Zielinski, Virginie Mengin, Ronan Sulpice, Kevin Stratford, Alastair Hume, Alexandra Pokhilko, Megan M Southern, Daniel D Seaton, Harriet G McWatters, Mark Stitt, Karen J Halliday, Andrew J Millar"],"first_author":["Anna Flis"],"publication":["26468131,\n                            Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell(-1)) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell(-1)) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.. 10, 5.\n                            Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany."],"submitter_mail":["andrew.millar@ed.ac.uk"],"submitter_affiliation":["Institute of Molecular Plant Sciences, University of Edinburgh"],"pubmed_abstract":["Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell(-1)) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell(-1)) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible."],"pubmed_title":["Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure."],"pubmed_authors":["Flis Anna A, Fernández Aurora Piñas AP, Zielinski Tomasz T, Mengin Virginie V, Sulpice Ronan R, Stratford Kevin K, Hume Alastair A, Pokhilko Alexandra A, Southern Megan M MM, Seaton Daniel D DD, McWatters Harriet G HG, Stitt Mark M, Halliday Karen J KJ, Millar Andrew J AJ"],"description_synonyms":["Hac-1/Dark, dark/dapaf-1/hac-1, Radiation, Dapaf-1/HAC-1, D-Apaf-1, UNQ391/PRO726, DmelCG6829, dApaf-1, anon-53Fa, l(2)SH0173, Visible Light, Light, apaf1, Apaf-1, CD258, Ly113, Dark/Hac-1/dApaf1, APAF1, Hac1, LIGHT, Dark/Hac-1/dApaf-1, Hac-1, Apaf1, Dark, ARK, Dark/Apaf-I, CG6829, Visible Radiations, Radiations, Visible Radiation, HVEML, hac-1, HVEM-L, Photoradiation, dapaf-1, arc, Dark/Dapaf-1/HAC1, dapaf, hac1, Visible, dark, dark/hac-1/dapaf-1., ark, dApaf-1/DARK/HAC-1, T1, LTg, dapaf-1S, TNFSF14, apaf-1, dapaf-1L, Photoradiations, DARK, TR2, dApaf1, dArk, Dapaf-1, dAPAF-1"],"name_synonyms":["plantae, bHLHe8, clk, Xclk, Materials, Genetic, Material, Pflanze, Plant, KAT13D, Genetic Materials, Cistron, Gene, INSDC_feature:gene, mKIAA0334, PLM., 5330400M04Rik, XClock, Cistrons, Genetic Material, viridiplantae"],"pubmed_abstract_synonyms":["MGC130048, Ribonucleic, Materials, A., A4, Arabis thaliana, Social Controls, dmTAF[[II]]230, Calculators, Readability, Arabidopsis thalianas, exact), Protor-1, A. thalianas, Software Engineering, Non Polyadenylated, Formal Social Controls, Computer Program, RNA Gene Products, Arhgap8, gamma sarcoglycan, Malted Grain, me75, Grain, Gene Expressions, TFIID TAF250, cel, Open, Mouse-ear Cress, Tissue, KAT13D, Computer Programs and Programming, Resources., plants, mKIAA0334, PP610, D17Mit170, Mouse-ear, T1, MYB-RELATED DNA BINDING PROTEIN, Social, Sprouted, Gm9907, CCA1, TNT1, gamma-sarcoglycan, protor1, Arabidopses, protor2, dTAF[[II]]230, ribose nucleic acid, pp610, land plants, ribonucleic acids, SG-gamma, TAF200, Digital Computers, A. thaliana, TAFII-250, Tl3, TAF250/230, XClock, Tl2, beta-D-fructofuranosyl, Source Softwares, Software Tools, Programs, BC042423, Program, Computer Applications, Plant Sprouts, TAFII250, Ribonukleinsaeure, EARLY FLOWERING 4, Computer Applications Software, Computer Applications Softwares, Genetic Materials, pentosenucleic acids, Arabidopsis thaliana (thale cress), sarcoglycan, Ribonucleic acids, simple tissue, Seed, Softwares, LATE ELONGATED HYPOCOTYL, Genetic Material, AV314029, Computers, Acid, Seeds, table sugar, Software Applications, MtCCA, 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside, Source Software, alpha-D-Glucopyranoside, Plant, Control, A030004J04Rik, circadian clock associated 1, INSDC_feature:gene, Controls, gamma (35kDa dystrophin-associated glycoprotein), CG17603, Hardware, TAF[[II]], 葉 (Japanese, Seedling, Grains, Applications, Arabidopsis, higher plants, Health, DMDA, Digital Computer, Taf250, Material, 35kD dystrophin-associated glycoprotein, SR3-5, C78947, Cistron, Feedbacks, Regulation, Programmable Calculator, TAF230, Computer Software Applications, Regulations, Plant Sprout, Sucrose, d230, SGCG_HUMAN, Protor1, Health Resource, Programmable, number, Gene, beta-D-Fruf-(2<->1)-alpha-D-Glcp, dTAFII250, Computer, 5330400M04Rik, LATE ELONGATED HYPOCOTYL 1, EfW1, presence, TYPE, PROTOR-1, DAGA4, clk, T28M21_24, dmTAF1, RGD1560743, Taf230, Peat, Sprouted Seed, 35DAG, Gene Products, thalianas, Sacharose, Malted, Low, T28M21.24, MAM, gamma-SG, SCG3, Resources, Application, TAF250, bHLHe8, Open Source Softwares, Taf200, dTAF[[II]]250, Genetic, Saccharose, Cresses, cell, Software Application, Aggregation, Humus, Open Source Software, Taf1p, LHY1, Outlines, Expressions, AU043908, Computer Software Application, Non-Polyadenylated RNA, dTAF250, thale-cress, Tools, Soils, Cress, Expression, Mouse ear, SUCROSE, TAF, Applications Software, Open Source, RNA, TAF[[II]]250, PROTOR1, cou, Computer Software, Malted Grains, 35 kDa dystrophin-associated glycoprotein, Arbisopsis thaliana, Formal Social Control, Arabidopsis thaliana, ELFR, l(3)84Ab, FLJ20185k, Computer Hardware, RNS, BG:DS00004.13, Cistrons, Sprout, Cell, SGCG, LGMD2C, Tool, dTAF230, count in organism, Software Tool, Lr, sacarosa, Resource, Social Control, yeast nucleic acid, sucrose, p230, MEF, Mef, TAF[[II]]250/230, TFIID, SIFD, T25K16_6, ENSMUSG00000053512, Software, F19D11.11, thale cress, mouse-ear cress, Taf[[II]]250, ribonucleic acid, T25K16.6, Sprouts, TAF[[II]]230, DMDA1, Digital, Programmable Calculators, Non Polyadenylated RNA, Engineering, Non-Polyadenylated, thaliana, TAF[II]250, Ribonucleic Acid, Calculator, Understanding, Mouse-ear Cresses, beta-D-fructofuranosyl alpha-D-glucopyranoside, hoja (Spanish, Computer Programs, Xclk, DmelCG17603, Applications Softwares, Cane sugar, Data, SCARMD2, Sprouted Seeds, Bra, C030017C09Rik, regulation, earth, White sugar, TAF1"],"pubmed_title_synonyms":["plantae, bHLHe8, ribonucleic acid, Acid, RNA, Ribonucleic, Materials, Genetic, ribose nucleic acid, Pflanze, Non Polyadenylated RNA, ribonucleic acids, Plant, KAT13D, Non-Polyadenylated, Gene, INSDC_feature:gene, RNS, Ribonucleic Acid, mKIAA0334, 5330400M04Rik, XClock, Cistrons, viridiplantae, RNA Gene Products., Non-Polyadenylated RNA, clk, Xclk, Material, yeast nucleic acid, Ribonukleinsaeure, Gene Products, Genetic Materials, pentosenucleic acids, Cistron, Ribonucleic acids, Non Polyadenylated, Genetic Material, single-organism behavior"],"additional_accession":[]},"is_claimable":false,"name":"Flis2015 - Plant clock gene circuit (P2011.4.1 PLM_1042 ver 1)","description":"\n      \n         cL_m_degr, param m1, modified to ensure light rate > dark rate.\n      \n    ","dates":{"last_modification":"2015-11-20","publication":"2015-11-20","submission":"2015-10-19"},"accession":"MODEL1510190003","cross_references":{"pubmed":["26468131"],"biomodels__db":["MODEL1510190003"]}}