Assays

Model files for FMv1.5, based on FMv1 of Chew et al. PNAS 2014, as extended by Hannah Kinmonth-Schultz and Daniel Seaton, in Matlab.
**Files used for published simulations will be attached here upon final publication, possibly with a later version that increases commenting. Our apologies for any delay.**

This is the SimileXML for the Salazar2009_FloweringPhotoperiod model in PlaSMo. It corresponds to Model 3 in the publication of Salazar et al 2009. The Simile version of this model is also attached here. Instructions to run the Photoperiodism Model in Simile 1.       Save all the files into the same folder. 2.       Copy and paste the attached ‘lightfunction.pl’ file in the following folder:            Program File > Simile6.0 (or other software version)> Functions 3.       Download the
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This is the SimileXML for the Salazar model linked to the T6P/TPS pathway (Wahl et al. Science 2013). The Simile version of this model and the parameter file are also attached here. Time series data of T6P and FT mRNA for Col wild type and tps1 mutant from Fig. 1 in Wahl et al were used to re-optimise Bco, KCO, kT6P and vT6P (which replaces VCO). Note: This set of parameter values has only been optimised and tested for a 16:8 light:dark cycle, and the initial values in the Simile model are for
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This is part of the GreenLab Functional-Structural Plant Model for Arabidopsis published in Christophe et al 2008. This model was re-factored, to facilitate the integration in the Chew et al Framework Model, and it cannot be run as a standalone model.  Related PublicationsAngélique Christophe A E, Véronique Letort B, Irène Hummel A, Paul-Henry Cournède B, Philippe de Reffye C, Jérémie Lecœur (2008). A model-based analysis of the dynamics of carbon balance at the whole-plant level in Arabidopsis
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This is the Framework Model (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111) that links the following: 1. Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - Carbon Dynamic Model 2. Part of the Christophe et al 2008 Functional-Structural Plant Model 3. Chew et al 2012 Photothermal Model 4. Salazar et al 2009 Photoperiodism Model   To run the model in Simile, please download the Evaluation Edition of the software from http://www.simulistics.com/products/simile.php
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This is a photothermal model for Arabidopsis that predicts flowering time, published in Chew et al (2012). It is an improved version of the model in Wilczek et al (Science 2009). A Simile version of the model is attached. Instructions to run the Photothermal Model in Simile 1.       Download the Simile file attached or import the XML into Simile:            a.       File > Import > XML Model Description 2.       To run the model:            a.       Model > Run or click on the ‘Play’
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Data derived from protein samples

Data derived from RNAseq

Scripts for running network simulations

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Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
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Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
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Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
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Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Related PublicationsMe and Helena (2014). some book. 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_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
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