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Arabidopsis clock model P2011.1.2 - PLM_71, version 1, SUBMITTED

Arabidopsis clock model P2011.1.2 - PLM_71, version 1, SUBMITTED
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Originally submitted model file for PLaSMo accession ID PLM_71, version 1

SEEK ID: https://fairdomhub.org/models/388?version=1

1 item is associated with this Model:

PLM71_1_SUBMITTED.xml (XML document - 82.3 KB)

Organism: Arabidopsis thaliana

Model type: Ordinary differential equations (ODE)

Model format: SBML

Execution or visualisation environment: Not specified

Model image: No image specified

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Andrew Millar

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Creative Commons Attribution 4.0

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Views: 582 Downloads: 37

Created: 10th Jan 2019 at 17:47

Last updated: 20th Dec 2019 at 12:06

Last used: 21st Feb 2020 at 21:18

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Related items

People (2)
Projects (1)
Investigations (1)
Studies (1)
Assays (1)
Publications (1)

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

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

BioData SynthSys

Projects: PlaSMo model repository

Institutions: University of Edinburgh

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, 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 P2011.1.2 - 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

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

Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71

Millar group, PlaSMo model repository

All contributors

BioData SynthSys

Andrew Millar

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,
...

Person responsible: BioData SynthSys

Snapshots: No snapshots

Investigation: Millar, Andrew (ex-PlaSMo models)

Assays: Arabidopsis clock model P2011.1.2 - PLM_71, version 1, Arabidopsis clock model P2011.2.1 - PLM_71, version 2

Created: 10th Jan 2019 at 17:38, Last updated: 24th Jan 2019 at 19:14

Arabidopsis clock model P2011.1.2 - PLM_71, version 1

Millar group, PlaSMo model repository

All contributors

BioData SynthSys

Andrew Millar

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
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis clock models P2011.1.2 and P2011.2....

Organisms: Arabidopsis thaliana

Models: Arabidopsis clock model P2011.1.2 - PLM_71, ver..., Arabidopsis clock model P2011.1.2 - PLM_71, ver...

SOPs: No SOPs

Data files: No Data files

Created: 10th Jan 2019 at 17:39, Last updated: 20th Dec 2019 at 12:07

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

Millar group

All contributors

Andrew Millar

Abstract (Expand)

Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA … profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell(-1)) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell(-1)) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.

Authors: A. Flis, A. P. Fernandez, T. Zielinski, V. Mengin, R. Sulpice, K. Stratford, A. Hume, A. Pokhilko, M. M. Southern, D. D. Seaton, H. G. McWatters, M. Stitt, K. J. Halliday, Andrew Millar

Date Published: 16th Oct 2015

Journal: Open Biol

PubMed ID: 26468131

Citation: Open Biol. 2015 Oct;5(10). pii: 150042. doi: 10.1098/rsob.150042.

Created: 1st Feb 2017 at 22:00

Arabidopsis clock model P2011.1.2 - PLM_71, version 1, SUBMITTED Version 1

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Arabidopsis clock model P2011.1.2 - PLM_71, version 1, SUBMITTED
Version 1