At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67
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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.<br><br><strong>Originally submitted to PLaSMo on 2012-05-31 22:18:27</strong>
SEEK ID: https://fairdomhub.org/studies/497
Millar, Andrew (ex-PlaSMo models)
Projects: Millar group, PlaSMo model repository
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Created: 10th Jan 2019 at 16:38
Last updated: 22nd Jan 2019 at 17:18
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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: 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
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
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
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
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
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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.Version Comments Version 2 is the 'public' version with the StepFunction, PLM_64v4. For some reason this was crashing SBSI, but was then cleaned up by passing through Copasi. Thus the file name of this version was Arabidopsis_clock_P2011_exCopasi.xml
This version should be suitable for SBSI optimisation to LD-LL data sets, because it ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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.
Version Comments
PLM_67v2 set up for LDLL transition at 314h, with wider parameter ranges for most parameters. This is the model file used in LDLL_run2.
Originally submitted to PLaSMo on 2012-05-31 22:18:27
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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.Version Comments PLM_67v3 model, with TWO stepfunctions. Simulates fine but as of 21 March 2013 did not optimise.
Step2 is usually off because amplitude=0, but can produce LD-DD transition at 262h. To do so, initiate with amplitudeStep1=0 and amplitudeStep2=1.
NB the step1 will still go to LL at 314h, so need to stop DD costing before ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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.Version Comments Derived from PLM_67v3 - LDLL transition at 314h, with wider parameter ranges, as used in LDLL_run2 - but with one modification in Copasi, to cL_m degradation to ensure light rate > dark rate. Value of m1 previously 0.54, now 0.3. Simulation in Copasi was identical.
Copasi file also attached. Originally submitted to ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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.
Version Comments
Corrected m1 parameter and range, tested in SBSI
Originally submitted to PLaSMo on 2012-05-31 22:18:27
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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
