Studies

The models in this record were published in Flis et al. Royal Society Open Biology 2015. Their original IDs in the PlaSMo resource and IDs in Biomodels are given below. Please select files for download from the 'Related Items' list or the object tree/graph, below. 'SUBMITTED' is the original model version; 'SIMPLIFIED' removes SBML elements that were incompatible with SloppyCell software.

<strong>Original model</strong>: Arabidopsis clock model P2011.1.1 from
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Photothermal model for Arabidopsis development, as published, converted to Simile format by Yin-Hoon Chew. Note that the XML file is just a dummy SBML file, the .SML is the working model file. Simile can read csv files (as attached) for meteorological data (hourly temperature, sunrise, sunset). Users only need to change the directory of the input variables. I have also attached the set of parameter values for each genotype.<br><br><strong>Related Publications</strong></strong><br>Wilczek
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Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.<br><br><strong>Related Publications</strong></strong><br>Sorokina et al (2011). BMicroarray data can predict diurnal changes of starch content in the picoalga Ostreococcus.. BMC Systems Biology. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21352558<br><br><strong>Originally submitted to PLaSMo on 2011-08-12 15:34:00</strong></strong>
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The model shows how the <em>CONSTANS</em> gene and protein in <em>Arabidopsis thaliana</em> forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (<a
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Andrew's work-in-progress P2012 version. <strong>NB KNOWN PROBLEMS</strong> do not use lightly. Derived from PLM_49, after removing ABA regulation and tidying up the SBML in COPASI. Please see version comments for IMPORTANT notes.<br><br><strong>Originally submitted to PLaSMo on 2013-02-26 17:23:01</strong></strong>

Draft of MEP pathway for isoprenoid synthesis, created 2012-2013 by Oender Kartal in the Gruissem lab. He notes "It contains some annotations and references for the parameter values and rate equations and produces a stable steady state, so you can do some control analysis. It simulates day-metabolism, since the MEP Pathway is supposedly active during the day." Unpublished, for use by TiMet consortium only.<br><br><strong>Originally submitted to PLaSMo on 2013-09-13
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This is a version derived from a model from the article: <strong>Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. </strong> Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ <em>Mol. Syst. Biol.</em>2006;Volume:2;Page:59 <a href="http://www.ncbi.nlm.nih.gov/pubmed/17102804">17102804</a>, &nbsp; The model describes a three loop circuit of the Arabidopsis
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This version is derived from a model from the article: <strong>Extension of a genetic network model by iterative experimentation and mathematical analysis. </strong>Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ <em>Mol. Syst. Biol. </em>2005; 1: 2005.0013 <a href="http://www.ncbi.nlm.nih.gov/pubmed/16729048">16729048</a>, &nbsp;SBML model of the interlocked feedback loop network The model describes the circuit
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Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms.&nbsp; &nbsp; Molecular Systems Biology <b>9</b> Article number: 650&nbsp;&nbsp;doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance <i>via</i> CRY signalling controls the <i>Arabidopsis</i>
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A cell-level model of the Arabidopsis root elongation zone. This spatial model is divided up into biological cells which are further divided into simulation boxes. The original model was designed to investigate how canal cells can accumulate auxin over time rather than to investigate the transport of auxin through the canal cells per se. The main outputs of the simulations in the original paper were the steady state ratios of auxin in the canal cell protoplasts to that in the parenchyma cell
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A cell-level model of the Arabidopsis root elongation zone. This spatial model is divided up into biological cells which are further divided into simulation boxes. The original model was designed to investigate how canal cells can accumulate auxin over time rather than to investigate the transport of auxin through the canal cells per se. The main outputs of the simulations in the original paper were the steady state ratios of auxin in the canal cell protoplasts to that in the parenchyma cell
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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.<br><br><strong>Originally submitted to PLaSMo on 2012-05-31 22:18:27</strong></strong>

P2011 model from PLM_43 version 6, optimised by Andrew Millar with SBSI PGA optimisation. A limited parameter set were free to optimise over &lt; 10-fold range (less for RNA degradation rates), against ROBuST RNA data for clock genes in WT and mutants at 17C in LD, and period data in the same mutants in LL. The full SBSI costing is included, using costs from mid-June 2012 (note that costs returned with original optimisation in May were incorrectly reported).<br><br><strong>Originally
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This model is termed P2012 and derives from the article: <strong>Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs</strong>. Alexandra Pokhilko, Paloma Mas &amp; Andrew J Millar BMC Syst. Biol. 2013; 7: 23, submitted 10 Oct 2012 and published 19 March 2013. <a href="http://dx.doi.org10.1186/1752-0509-7-23">Link</a> The model describes the circuit depicted in Fig. 1 of the paper (GIF will be attached soon). It
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This model is termed P2011 and derives from the article: <strong>The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops</strong><strong>. </strong>Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday &amp; Andrew J Millar <em>Mol. Syst. Biol. </em>2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. <a href="http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html">Link</a>
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This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. <strong>Derived from Original model</strong>: P2011.1.2 is public model ID PLM_71 version 1, <a href="http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1">http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1
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This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. <strong>Derived from Original model</strong>: P2011.1.2 is public model ID PLM_71 version 1, <a href="http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1">http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1
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This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. <strong>Derived from Original model</strong>: P2011.1.2 is public model ID PLM_71 version 1, <a href="http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1">http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1
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This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. <strong>Derived from Original model</strong>: P2011.1.2 is public model ID PLM_71 version 1, <a href="http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1">http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1
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Creator - Dr. Daniel D. Seaton. Graphical overview of Arabidopsis clock model P2011 in SBGN, from SBGN-ED in VANTED v2. N.B. to pass PlaSMo validation before update, the &lt;sbgn&gt; tag was back-edited from the correct string &lt;sbgn xmlns="http://sbgn.org/libsbgn/0.2"&gt; to &lt;sbgn xmlns="http://sbgn.org/libsbgn/pd/0.1"&gt; in this file. The file is still correctly opened in VANTED after this modification. The unmodified version is also attached.
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The model is an extensio of PLM_67v3 with an additional an additional variable Temp in ODE 25. This change allows to simulated warm pulses that affect EC stability using COPASI.&nbsp;<br><br><strong>Originally submitted to PLaSMo on 2014-03-10 13:16:25</strong></strong>

Model that eliminates several light inputs. RVE8, NOX are incorporated. Individual representation of CCA1 and LHY. Several changes in conections and light inputs. Fogelmark reports eight parameter sets. This SBML file contains the first parameter set <br><br><strong>Related Publications</strong></strong><br>Fogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from:
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To check if all works fine after struts update. Checking editorial options<br><br><strong>Additional Attributes</strong></strong><br>tested: <p>
Yes, against schema</p>
<br><br><strong>Originally submitted to PLaSMo on 2013-11-22 15:15:40</strong></strong>

dfds <br><br><strong>Originally submitted to PLaSMo on 2015-09-02 18:27:55</strong></strong>

<br><br><strong>Related Publications</strong></strong><br>Me and Helena (2014). some book. <br>Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2<br>Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP
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Construction of a Genome scale constrained-based metabolic modeling of M. hyopneumonia

Proteomics Average and SD data for time series data, 6h, 12h, 24h, 48h,72, 96h per protein

This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).<br><br><strong>Originally submitted to PLaSMo on 2010-05-04
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"TRIFFID (Top-down Representation of Interactive Foliage and Flora Including Dynamics)" is a dynamic global vegetation model, which updates the plant distribution and soil carbon based on climate-sensitive CO2 fluxes at the land-atmosphere interface. The surface CO2 fluxes associated with photosynthesis and plant respiration are calculated in the MOSES 2 tiled land-surface scheme (Essery et al (In preparation)), on each atmospheric model timestep (normally 30 minutes), for each of 5
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Cytoscape silqueue specific protein detection<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:44:13</strong></strong>