PlaSMo model repository

Collection of models submitted to PLaSMo by Uriel Urquiza Garcia and automatically transferred to FAIRDOM Hub.

Project to test effects of temperature cycles on expression of Arabidopsis florigen gene FT, and whether these are mediated by temperature-dependent leaf development or temperature-specific FT expression, or both. Re-used and extended Arabidopsis Framework Model v1 to address this question. Led by Hannah Kinmonth-Schultz in Kim and Imaizumi labs, collaborating with Millar lab.

Collection of models submitted to PLaSMo by Yin Hoon and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Tomasz Zielinski and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Alexandra Graf and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Carl Troein and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Richard Adams and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Jonathan Massheder and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Rob Smith and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Martin Beaton and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Maria-Luisa Guerriero and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Alexandra Pokhilko and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Daniel Seaton and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Chris Davey and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Robert Muetzelfeldt and automatically transferred to FAIRDOM Hub.

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. 

Originally submitted to PLaSMo on 2014-03-10 13:16:25

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 Related PublicationsFogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003705Originally
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Assays for model composition here, in order to share model files; potentially training and validation data in other Studies.

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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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.

Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012,
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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.Related PublicationsWilczek et al. (2009). Effects of Genetic Perturbation
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Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.

Related Publications
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

Originally submitted to PLaSMo on 2011-08-12 15:34:00

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana 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 (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al.,
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Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS 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.

Originally submitted to PLaSMo on 2013-02-26 17:23:01

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.

Originally submitted to PLaSMo on 2013-09-13 09:10:53

This is a version derived from a model from the article: Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ Mol. Syst. Biol.2006;Volume:2;Page:59 17102804,   The model describes a three loop circuit of the Arabidopsis circadian clock. It provides initial conditions, parameter values and reactions for the production rates of the following species: LHY
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This version is derived from a model from the article: Extension of a genetic network model by iterative experimentation and mathematical analysis. Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ Mol. Syst. Biol. 2005; 1: 2005.0013 16729048,  SBML model of the interlocked feedback loop network The model describes the circuit depicted in Fig. 4 and reproduces the simulations in Figure 5A and 5B. It provides initial conditions, parameter values and rules for the
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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.    Molecular Systems Biology 9 Article number: 650  doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould, Ugarte, Domijan et al. doi:10.1038/msb.2013.7Originally
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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.

Originally submitted to PLaSMo on 2012-05-31 22:18:27

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 Related PublicationsFogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003705Originally
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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. 

Originally submitted to PLaSMo on 2014-03-10 13:16:25

The models in this record were 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.

Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6

Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412
Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64
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The models in this record were 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.

Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6

Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412
Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64
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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. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.6.1 is public model ID PLM_1044, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national
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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. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.3.1 is public model ID PLM_1041, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national
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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 model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached
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This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached
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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
...

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
...

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
...

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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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.
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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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Data file for PLaSMo accesssion ID PLM_74, version 1

Data file for PLaSMo accesssion ID PLM_74, version 1

Data file for PLaSMo accesssion ID PLM_74, version 1

Data file for PLaSMo accesssion ID PLM_75, version 1

Data file for PLaSMo accesssion ID PLM_76, version 1

Data file for PLaSMo accesssion ID PLM_76, version 1

Data file for PLaSMo accesssion ID PLM_73, version 1

Data file for PLaSMo accesssion ID PLM_9, version 1

Data file for PLaSMo accesssion ID PLM_9, version 1

Data file for PLaSMo accesssion ID PLM_8, version 1

Data file for PLaSMo accesssion ID PLM_30, version 1

Data file for PLaSMo accesssion ID PLM_30, version 1

Data file for PLaSMo accesssion ID PLM_30, version 1

Data file for PLaSMo accesssion ID PLM_30, version 1

Data file for PLaSMo accesssion ID PLM_70, version 2

Data file for PLaSMo accesssion ID PLM_70, version 1

Data file for PLaSMo accesssion ID PLM_70, version 1

Data file for PLaSMo accesssion ID PLM_70, version 1

Data file for PLaSMo accesssion ID PLM_70, version 1

Data file for PLaSMo accesssion ID PLM_70, version 1

Simplified model file for PLaSMo accession ID PLM_71, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_71, version 2

Simplified model file for PLaSMo accession ID PLM_71, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_71, version 1

Originally submitted model file for PLaSMo accession ID PLM_1041, version 1

Simplified model file for PLaSMo accession ID PLM_1041, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_73, version 1

Originally submitted model file for PLaSMo accession ID PLM_75, version 1

Originally submitted model file for PLaSMo accession ID PLM_74, version 1

Originally submitted model file for PLaSMo accession ID PLM_76, version 1

Simplified model file for PLaSMo accession ID PLM_9, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_9, version 2

Simplified model file for PLaSMo accession ID PLM_9, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_9, version 1

Simplified model file for PLaSMo accession ID PLM_10, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_10, version 1

Simplified model file for PLaSMo accession ID PLM_8, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_8, version 1

Simplified model file for PLaSMo accession ID PLM_50, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_50, version 2

What is PlaSMo?
PlaSMo stands for Plant Systems-biology Modelling; Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.

The original PlaSMo project description is included within the attached document.

Our aims

To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being lost

To represent these models in a declarative XML-based
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