BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=curation_notes.txthttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=manifest.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631.odehttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631_url.sedmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=curation_image.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=metadata.rdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631.scihttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631-octave.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631-matlab.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000631?filename=BIOMD0000000631.mprimaryOK200Vijayalakshmi ChelliahManually curatedordinary differential equation modelL2V3https://www.ebi.ac.uk/biomodels/BIOMD000000063126904049falseBioModelsSBMLModelsDeCaluwe2016 Circadian Clock2016MODEL1601130000Joëlle De Caluwé, Qiying Xiao, Christian Hermans, Nathalie Verbruggen, Jean-Christophe Leloup, Didier GonzeJoëlle De Caluwé26904049, The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock gene mRNA/protein and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes). Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24 h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the core clock as well as clock-dependent processes.. null, 7. Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de Bruxelles Brussels, Belgium.viji@ebi.ac.ukEMBL-EBIBIOMD0000000631The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock gene mRNA/protein and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes). Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24 h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the core clock as well as clock-dependent processes.A Compact Model for the Complex Plant Circadian Clock.De Caluwé Joëlle J, Xiao Qiying Q, Hermans Christian C, Verbruggen Nathalie N, Leloup Jean-Christophe JC, Gonze Didier DfalseDeCaluwe2016 - Circadian Clock DeCaluwé2016 - Circadian Clock This model is described in the article: A Compact Model for the Complex Plant Circadian Clock. De Caluwé J, Xiao Q, Hermans C, Verbruggen N, Leloup JC, Gonze D. Front Plant Sci 2016; 7: 74 Abstract: The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock gene mRNA/protein and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes). Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24 h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the core clock as well as clock-dependent processes. This model is hosted on BioModels Database and identified by: BIOMD0000000631. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. 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. 2024-08-212024-09-022016-01-13BIOMD000000063126904049MODEL1601130000BIOMD0000000631GO:0042752GO:0043153GO:0005623GO:1904797GO:0006351GO:0009642GO:0006402GO:0009646GO:2000765GO:0006412GO:0042176GO:0030163GO:2000144GO:0010944GO:0045893GO:00801893702BTO:0000613839341819296819292831793836259832518818596823817818903825075P92973Q6R0H1Q93WK5Q8L500Q6LA42Q9LKL2O04211Q9SNB4Q8W2F3Q84LH8Q8L5W8O80536