Arabidopsis_clock_2011 - PLM_43

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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication.		The published model version is also in PlaSMo as <a href="http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64">PLM_64 here</a>.<br><br><strong>Originally submitted to PLaSMo on 2011-07-16 12:31:04</strong>

SEEK ID: https://fairdomhub.org/studies/490

Investigation: Pokhilko, Alexandra

Projects: PlaSMo model repository

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BioData SynthSys

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Alexandra Pokhilko, Andrew Millar

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BioData SynthSys

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Created: 10th Jan 2019 at 16:38

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Assays (9)
Data files (0+8)
Models (0+18)
Publications (1)

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BioData SynthSys

Projects: PlaSMo model repository

Institutions: University of Edinburgh

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SynthSys

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

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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

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Pokhilko, Alexandra

PlaSMo model repository

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BioData SynthSys

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

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Created: 10th Jan 2019 at 16:37

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Arabidopsis_clock_2011 - PLM_43, version 1

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukOriginally submitted to PLaSMo on 2011-07-16 12:31:04

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: 2 hidden items

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:39

Arabidopsis_clock_2011 - PLM_43, version 2

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Final model as submitted but with time changed to t for compatibilty with SBSI Originally submitted to PLaSMo on 2011-07-16 ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40

Arabidopsis_clock_2011 - PLM_43, version 3

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Pokhilko Arabidopsis clock model as submitted, SBSI compatible and tanh light function of Kevin Stratford Originally submitted ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40

Arabidopsis_clock_2011 - PLM_43, version 4

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Corrected version for SBSI with Kevin Stratford's tanh light function, as in the Locke tanh models. Confirmed will now run and ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40, Last updated: 10th Jan 2019 at 16:40

Arabidopsis_clock_2011 - PLM_43, version 5

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments this version has a graphical representation in Cell Designer. It runs in Cell Designer, Copasi and SBSI, but not run optimization ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40

Arabidopsis_clock_2011 - PLM_43, version 6

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments this version is similar to version 5 (but csymbol time is replaced to t), it has a graphical representation in Cell Designer, ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40

Arabidopsis_clock_2011 - PLM_43, version 7

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments This version was modified from version 6 in Copasi by replacement of "light function" to L in all equations. Originally submitted ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: 2 hidden items

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40

Arabidopsis_clock_2011 - PLM_43, version 8

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Alexandra's P2011 clock model with:

skeleton photoperiod for Graf et al. PNAS 2010.
parameter changes to simulated prr9 ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: 2 hidden items

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40

Arabidopsis_clock_2011 - PLM_43, version 9

PlaSMo model repository

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BioData SynthSys

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Alexandra's P2011 model with skeleton photoperiod for Graf et al.PNAS 2010.

A Copasi file is attached. Note that another version ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Investigation: Pokhilko, Alexandra

Study: Arabidopsis_clock_2011 - PLM_43

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: 2 hidden items

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40

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The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.

Millar group, TiMet, PlaSMo model repository

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Karen Halliday

Andrew Millar

Abstract (Expand)

Circadian clocks synchronise biological processes with the day/night cycle, using molecular mechanisms that include interlocked, transcriptional feedback loops. Recent experiments identified the evening … complex (EC) as a repressor that can be essential for gene expression rhythms in plants. Integrating the EC components in this role significantly alters our mechanistic, mathematical model of the clock gene circuit. Negative autoregulation of the EC genes constitutes the clock's evening loop, replacing the hypothetical component Y. The EC explains our earlier conjecture that the morning gene Pseudo-Response Regulator 9 was repressed by an evening gene, previously identified with Timing Of CAB Expression1 (TOC1). Our computational analysis suggests that TOC1 is a repressor of the morning genes Late Elongated Hypocotyl and Circadian Clock Associated1 rather than an activator as first conceived. This removes the necessity for the unknown component X (or TOC1mod) from previous clock models. As well as matching timeseries and phase-response data, the model provides a new conceptual framework for the plant clock that includes a three-component repressilator circuit in its complex structure.

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

PubMed ID: 22395476

Citation: Mol Syst Biol. 2012 Mar 6;8:574. doi: 10.1038/msb.2012.6.

Created: 20th Dec 2019 at 11:29, Last updated: 8th Dec 2022 at 17:26