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Arabidopsis clock model P2011.4.1 - PLM_1042

Arabidopsis clock model P2011.4.1 - PLM_1042

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 P2011.4.1 is public model ID PLM_1042, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national supercomputer HECTOR, as described in Flis et al. RSOB 2015.

In the model name, Plasmo ID PLM_67 was a private, working version. t34 is the private optimisation run number.

Related Publications
Flis et al (2015). Open Infrastructure. RSOB. Retrieved from: dx.doi.org/10.1098/rsob.150042

Originally submitted to PLaSMo on 2015-09-02 19:14:50

SEEK ID: https://fairdomhub.org/studies/485

Investigation: Millar, Andrew (ex-PlaSMo models)

Projects: Millar group, PlaSMo model repository

Person responsible: BioData SynthSys

Experimentalists: Not specified

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Andrew Millar

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Created: 10th Jan 2019 at 17:38

Last updated: 22nd Jan 2019 at 18:16

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People (2)
Projects (2)
Investigations (1)
Assays (1)
Models (2)

BioData SynthSys

Projects: PlaSMo model repository

Institutions: University of Edinburgh

Andrew Millar

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

Roles: Project Coordinator, Vice Coordinator

Expertise: Data Management, Molecular Biology, Genetics, Deterministic modelling of gene regulation networks, Systems Biology, circadian rhythms, arabidopsis thaliana, Mathematical modelling

Tools: Deterministic models, Stochastic models, SBML, Transcriptomics, Proteomics

PlaSMo model repository

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.

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
...

Programme: SynthSys

Public web page: Not specified

Organisms: Arabidopsis thaliana, Ostreococcus tauri

Millar group

Andrew Millar's research group, University of Edinburgh

Programme: SynthSys

Public web page: http://www.amillar.org

Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri

Millar, Andrew (ex-PlaSMo models)

Millar group, PlaSMo model repository

All contributors

Andrew Millar

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

Snapshots: No snapshots

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 P2011.3.1 - 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 models P2011.1.2 and P2011.2.1 - PLM_71, version 1, Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, version 2, 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

Created: 10th Jan 2019 at 17:37, Last updated: 6th May 2019 at 10:10

Arabidopsis clock model P2011.4.1 - PLM_1042, version 1

Millar group, PlaSMo model repository

All contributors

BioData SynthSys

Andrew Millar

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 P2011.4.1 is public model ID PLM_1042, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis clock model P2011.4.1 - PLM_1042

Organisms: No organisms

Models: Arabidopsis clock model P2011.4.1 - PLM_1042, v..., Arabidopsis clock model P2011.4.1 - PLM_1042, v...

SOPs: No SOPs

Data files: No Data files

Created: 10th Jan 2019 at 17:39, Last updated: 22nd Jan 2019 at 18:16