PlaSMo model repository
OverviewWhat 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.
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 format, which is closer to the systems biology standard SBML
- To evaluate the behaviour of the models represented in this format against the output of the original models
- To produce a portal to disseminate the models, and examples of their output, in XML format; so that they can be used in the programming language and computating environment of a scientist's choice
- To provide an interface to enable researchers to share reviews, annotations and enhancements of models
Who is it for?
- Plant scientists wishing to apply systems biology approaches to the study of plant growth and development
- Crop scientists and the plant breeding and agricultural industries
- Current and retired mathematical modellers wishing to safeguard their models and make them more widely available
- Those researching plant responses to climate change
- Those needing to model the growth of new crops or new uses of existing crops, such as bioenergy production
PlaSMo has moved
PlaSMo project used to have its dedicated repository under http://plasmo.ed.ac.uk. All PlaSMo resources have been migrated into the FairdomHub in order to benefit from rich SEEK features and assure data longevity. You can access the list of all the PlaSMo models here.
You can read more about PlaSMo in the project document
Our funders
PlaSMo was establised with funding from the BBSRC's Bioinformatics and Biological Resources initiative and is maintained with funding from the European Commission's FP7 Collaborative Project TiMet.
Programme: SynthSys
SEEK ID: https://fairdomhub.org/projects/129
Public web page: Not specified
Organisms: Arabidopsis thaliana, Ostreococcus tauri
FAIRDOM PALs: No PALs for this Project
Project created: 28th Nov 2018
Related items
Projects: PlaSMo model repository
Institutions: University of Edinburgh
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Institutions: University of Edinburgh
https://orcid.org/0000-0003-1756-3654
Projects: Systo models, PlaSMo model repository, Agro-ecological modelling
Institutions: University of Edinburgh
Projects: PlaSMo model repository
Institutions: University of Edinburgh
Projects: Millar group, PlaSMo model repository, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, Light and plant development, Light control of leaf development, Toggle switch, Reduce Complexity (RCO) reconstruction, Model Driven Prime Editing, PULSE 2.0, Plant optogenetics
Institutions: University of Edinburgh, Heinrich Heine University of Düsseldorf
https://orcid.org/0000-0002-7975-5013
Projects: FAIRDOM user meeting, PlaSMo model repository
Institutions: University of Edinburgh
SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Web page: http://www.synthsys.ed.ac.uk
Collection of models submitted to PLaSMo by Uriel Urquiza Garcia and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: F2014.1 - PLM_1030, PLM_67v3withTempPulse - PLM_81
Assays: F2014.1 - PLM_1030, version 1, PLM_67v3withTempPulse - PLM_81, version 1
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.
Submitter: Andrew Millar
Collection of models submitted to PLaSMo by Yin Hoon and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Chew_et_al_2012_Photothermal_Model - PLM_73, Chew_et_al_2014_Framework_Model - PLM_76, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75, Salazar Photoperiodism Model with T6P - PLM_82, Salazar_et_al_2009_Photoperiodism_Model - PLM_74
Assays: Chew_et_al_2012_Photothermal_Model - PLM_73, version 1, Chew_et_al_2014_Framework_Model - PLM_76, version 1, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75..., Salazar Photoperiodism Model with T6P - PLM_82, version 1, Salazar_et_al_2009_Photoperiodism_Model - PLM_74, version 1
Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis clock model P2011, graphical diagram - PLM_1045, Arabidopsis clock model P2011.3.1 - PLM_1041, Arabidopsis clock model P2011.4.1 - PLM_1042, Arabidopsis clock model P2011.5.1 - PLM_1043, Arabidopsis clock model P2011.6.1 - PLM_1044, Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, Arabidopsis_clock_P2011 - PLM_64, Arabidopsis_clock_P2012 - PLM_70, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, AuxSim - PLM_27, AuxSim full - PLM_30, DomijanTS_AtClock2011 - PLM_50, Locke2005_CircadianClock_tanh - PLM_8, Locke2006_CircadianClock_tanh - PLM_10, OK MEP pathway 2013 - PLM_72, P2012_AJMv2_NoABA - PLM_69, Salazar2009_FloweringPhotoperiod - PLM_9, Sorokina2011_Ostreo_starch - PLM_44, Wilczek photothermal Science - PLM_48
Assays: Arabidopsis clock model P2011, graphical diagram - PLM_1045, version 1, Arabidopsis clock model P2011.1.2 - PLM_71, version 1, Arabidopsis clock model P2011.2.1 - PLM_71, version 2, Arabidopsis clock model P2011.3.1 - PLM_1041, version 1, Arabidopsis clock model P2011.4.1 - PLM_1042, version 1, Arabidopsis clock model P2011.5.1 - PLM_1043, version 1, Arabidopsis clock model P2011.6.1 - PLM_1044, version 1, Arabidopsis_clock_P2011 - PLM_64, version 1, Arabidopsis_clock_P2011 - PLM_64, version 2, Arabidopsis_clock_P2011 - PLM_64, version 3, Arabidopsis_clock_P2011 - PLM_64, version 4, Arabidopsis_clock_P2012 - PLM_70, version 1, Arabidopsis_clock_P2012 - PLM_70, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 1, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 3, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 4, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 5, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 6, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, version 1, AuxSim - PLM_27, version 1, AuxSim full - PLM_30, version 1, DomijanTS_AtClock2011 - PLM_50, version 1, DomijanTS_AtClock2011 - PLM_50, version 2, Locke2005_CircadianClock_tanh - PLM_8, version 1, Locke2006_CircadianClock_tanh - PLM_10, version 1, OK MEP pathway 2013 - PLM_72, version 1, P2012_AJMv2_NoABA - PLM_69, version 1, P2012_AJMv2_NoABA - PLM_69, version 2, Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2, Sorokina2011_Ostreo_starch - PLM_44, version 1, Wilczek photothermal Science - PLM_48, version 1, Wilczek photothermal Science - PLM_48, version 2
Collection of models submitted to PLaSMo by Tomasz Zielinski and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Checking upload for andrew - PLM_1040, Plasmo test model1 - PLM_80
Assays: CHecking if all works - PLM_1000, version 111, Checking upload for andrew - PLM_1040, version 1, Plasmo test model1 - PLM_80, version 1, Test created 1552502361596, Test created 1552502791700, Test created 1552503965203, Test created 1552503978484, Test created 1552504117107, Test created 1552504664537, Test created 1552504857803, Test created 1552505193451
Collection of models submitted to PLaSMo by Alexandra Graf and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: TiMet 2011 PP interaction network - PLM_56, TiMet 2011 Pollen network - PLM_54, TiMet 2011 Root network - PLM_55, TiMet 2011 flower specific protein detection network - PLM_57, TiMet 2011 seed network - PLM_53, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_58, TiMet 2011 silqueue specific protein detection network - PLM_59
Assays: TiMet 2011 PP interaction network - PLM_56, version 1, TiMet 2011 Pollen network - PLM_54, version 1, TiMet 2011 Pollen network - PLM_54, version 2, TiMet 2011 Root network - PLM_55, version 1, TiMet 2011 flower specific protein detection network - PLM_57, version 1, TiMet 2011 seed network - PLM_53, version 1, TiMet 2011 seed network - PLM_53, version 2, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_5..., TiMet 2011 silqueue specific protein detection network - PLM_59, version 1
Collection of models submitted to PLaSMo by Carl Troein and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, T2011 Ostreococcus clock, CCA1 degr L - PLM_85, T2011 Ostreococcus clock, CCA1 prod D - PLM_88, T2011 Ostreococcus clock, CCA1 prod L - PLM_87, T2011 Ostreococcus clock, TOC1 act D - PLM_92, T2011 Ostreococcus clock, TOC1 act L - PLM_91, T2011 Ostreococcus clock, TOC1 degr D - PLM_90, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, T2011 Ostreococcus clock, acc immediate - PLM_83, T2011 Ostreococcus clock, acc on - PLM_84, Troein Ostreococcus clock 1-loop - PLM_7
Assays: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, version 1, T2011 Ostreococcus clock, CCA1 degr L - PLM_85, version 1, T2011 Ostreococcus clock, CCA1 prod D - PLM_88, version 1, T2011 Ostreococcus clock, CCA1 prod L - PLM_87, version 1, T2011 Ostreococcus clock, TOC1 act D - PLM_92, version 1, T2011 Ostreococcus clock, TOC1 act L - PLM_91, version 1, T2011 Ostreococcus clock, TOC1 degr D - PLM_90, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 2, T2011 Ostreococcus clock, acc immediate - PLM_83, version 1, T2011 Ostreococcus clock, acc on - PLM_84, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 2
Collection of models submitted to PLaSMo by Richard Adams and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, Neurospora Circadian Clock 3-variable model - PLM_51, Neurospora Circadian Clock 3-variable model - sinusoidal light oscillati...
Assays: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, version 1, Neurospora Circadian Clock 3-variable model - PLM_51, version 1, Neurospora Circadian Clock 3-variable model - sinusoidal light oscillati...
Collection of models submitted to PLaSMo by Jonathan Massheder and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: LINTUL_V2 - PLM_42, SUCROS1 - PLM_24
Assays: LINTUL_V2 - PLM_42, version 1, SUCROS1 - PLM_24, version 1
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.
Submitter: BioData SynthSys
Studies: Central plant metabolism - PLM_61, Glycolysis SBGN - PLM_60, Insulin-like growth factor signaling - PLM_62, Martin test - PLM_65, Neuronal muscle signalling - PLM_63
Assays: Central plant metabolism - PLM_61, version 1, Glycolysis SBGN - PLM_60, version 1, Insulin-like growth factor signaling - PLM_62, version 1, Martin test - PLM_65, version 1, Martin test - PLM_65, version 2, Neuronal muscle signalling - PLM_63, version 1
Collection of models submitted to PLaSMo by Maria-Luisa Guerriero and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: arabidopsis_clock_biopepa - PLM_47
Collection of models submitted to PLaSMo by Alexandra Pokhilko and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis_clock_2011 - PLM_43, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, Arabidopsis_clock_extend - PLM_6
Assays: Arabidopsis_clock_2011 - PLM_43, version 1, Arabidopsis_clock_2011 - PLM_43, version 2, Arabidopsis_clock_2011 - PLM_43, version 3, Arabidopsis_clock_2011 - PLM_43, version 4, Arabidopsis_clock_2011 - PLM_43, version 5, Arabidopsis_clock_2011 - PLM_43, version 6, Arabidopsis_clock_2011 - PLM_43, version 7, Arabidopsis_clock_2011 - PLM_43, version 8, Arabidopsis_clock_2011 - PLM_43, version 9, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 1, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 2, Arabidopsis_clock_extend - PLM_6, version 1, Arabidopsis_clock_extend - PLM_6, version 2, Arabidopsis_clock_extend - PLM_6, version 3
Collection of models submitted to PLaSMo by Daniel Seaton and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Assays: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20..., Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20..., Modelling circadian regulation of flowering time and hypocotyl elongatio...
Collection of models submitted to PLaSMo by Chris Davey and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: AFRC Wheat 2 evapw submodel - PLM_33, AFRC Wheat 2 jdaydif submodel - PLM_34, AFRC Wheat 2 julday submodel - PLM_35, AFRC Wheat 2 ldim submodel - PLM_36, AFRC Wheat 2 photpd submodel - PLM_37, AFRC Wheat 2 tdays submodel - PLM_38, AFRC Wheat 2 vappres submodel - PLM_39, AFRC Wheat 2 vernal submodel - PLM_40, AFRC Wheat 2 weathr submodel - PLM_41, AFRC Wheat2 dev submodel - PLM_32, AFRCtest2 - PLM_25, Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, Miscanmod - PLM_3
Assays: AFRC Wheat 2 evapw submodel - PLM_33, version 1, AFRC Wheat 2 jdaydif submodel - PLM_34, version 1, AFRC Wheat 2 julday submodel - PLM_35, version 1, AFRC Wheat 2 ldim submodel - PLM_36, version 1, AFRC Wheat 2 photpd submodel - PLM_37, version 1, AFRC Wheat 2 tdays submodel - PLM_38, version 1, AFRC Wheat 2 vappres submodel - PLM_39, version 1, AFRC Wheat 2 vernal submodel - PLM_40, version 1, AFRC Wheat 2 weathr submodel - PLM_41, version 1, AFRC Wheat2 dev submodel - PLM_32, version 1, AFRCtest2 - PLM_25, version 1, Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, version 1, C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, version 1, Miscanmod - PLM_3, version 1
Collection of models submitted to PLaSMo by Robert Muetzelfeldt and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: 3PG - PLM_12, CENTURY_Rowe_daily - PLM_22, DALEC - PLM_23, LINTUL - PLM_4, McMurtrie vegetation model - PLM_11, TRIFFID - PLM_5
Assays: 3PG - PLM_12, version 1, CENTURY_Rowe_daily - PLM_22, version 1, DALEC - PLM_23, version 1, LINTUL - PLM_4, version 1, McMurtrie vegetation model - PLM_11, version 1, McMurtrie vegetation model - PLM_11, version 2, TRIFFID - PLM_5, version 1
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.Â
Originally submitted to PLaSMo on 2014-03-10 13:16:25
Submitter: BioData SynthSys
Investigation: Urquiza Garcia, Uriel
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 ...
Submitter: BioData SynthSys
Investigation: Urquiza Garcia, Uriel
Assays: F2014.1 - PLM_1030, version 1
Assays for model composition here, in order to share model files; potentially training and validation data in other Studies.
Submitter: Andrew Millar
Investigation: Temperature effects on Arabidopsis floral induc...
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 ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Salazar_et_al_2009_Photoperiodism_Model - PLM_74, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Salazar Photoperiodism Model with T6P - PLM_82, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75...
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 ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
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’ ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Chew_et_al_2012_Photothermal_Model - PLM_73, version 1
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, ...
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 ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Wilczek photothermal Science - PLM_48, version 1, Wilczek photothermal Science - PLM_48, version 2
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
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
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., ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2
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
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: P2012_AJMv2_NoABA - PLM_69, version 1, P2012_AJMv2_NoABA - PLM_69, version 2
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
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
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 ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
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 ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
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 ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: DomijanTS_AtClock2011 - PLM_50, version 1, DomijanTS_AtClock2011 - PLM_50, version 2
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 ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: AuxSim full - PLM_30, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: AuxSim - PLM_27, version 1
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
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 1, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 3, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 4, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 5, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 6
Model files for FMv1.5. The model is based on FMv1 of Chew et al. PNAS 2014, which is also in FAIRDOMHub and linked to the Model record as an 'Attribution'. FMv1 was extended in this work by Hannah Kinmonth-Schultz and Daniel Seaton, in Matlab.
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Temperature effects on Arabidopsis floral induc...
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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Urquiza Garcia, Uriel
Study: F2014.1 - PLM_1030
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.Â
Originally submitted to PLaSMo on 2014-03-10 13:16:25
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Urquiza Garcia, Uriel
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 PLM64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM64 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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 PLM64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM64 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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 PLM71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM71&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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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 PLM71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM71&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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
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’ ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
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. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
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. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
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. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
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. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
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. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
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. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
Data file for PLaSMo accesssion ID PLM_74, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Download
Data file for PLaSMo accesssion ID PLM_74, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_74, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_75, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_76, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_76, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_73, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_9, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_9, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_8, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_30, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_30, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_30, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_30, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Originally submitted model file for PLaSMo accession ID PLM_1030, version 1
Creators: BioData SynthSys, Uriel Urquiza Garcia, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Simplified model file for PLaSMo accession ID PLM_71, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_71, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Simplified model file for PLaSMo accession ID PLM_71, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_71, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_1041, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Simplified model file for PLaSMo accession ID PLM_1041, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_73, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Not specified
Model format: Simile XML v3
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_75, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Not specified
Model format: Simile XML v3
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_74, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: Simile XML v3
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_76, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Not specified
Model format: Simile XML v3
Environment: Not specified
Simplified model file for PLaSMo accession ID PLM_9, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_9, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Simplified model file for PLaSMo accession ID PLM_9, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_9, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Simplified model file for PLaSMo accession ID PLM_10, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_10, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Simplified model file for PLaSMo accession ID PLM_8, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_8, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Simplified model file for PLaSMo accession ID PLM_50, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Not specified
Model format: SBML
Environment: Not specified
Abstract
Authors: Karl Fogelmark, Carl Troein
Date Published: 17th Jul 2014
Publication Type: Not specified
Abstract (Expand)
Authors: A. Pokhilko, A. P. Fernandez, K. D. Edwards, M. M. Southern, K. J. Halliday, A. J. Millar
Date Published: 6th Mar 2012
Publication Type: Not specified
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 ...
Creator: BioData SynthSys
Submitter: BioData SynthSys
