Collection of models used in the introduction of absolute units into A. thaliana circadian clock models, with software resources and documentation. The models are inspired by P2011, published in Pokhilko et al 2012. The study contains Assays that link to the P2011 starting model and the models U2019.1  .3 and U2020.1  .3. Each model is shared as a humanreadable file in the Antimony language and the associated, machinereadable SBML file, which was automatically generated using the SBML export routine of Tellurium software. The full computational environment for parameter fitting, using custom costing in SloppyCell, is shared as a Docker image. SBML files were verified using COPASI 4.24 (Build 197) software. The full process is described in Urquiza and Millar, In Silico Plants, 2021. The publication will be linked to the live version of this Investigation but cannot be linked to the Snapshot as no DOI had been assigned when the Snapshot DOI had to be generated.
SEEK ID: https://fairdomhub.org/studies/701
Absolute units in Arabidopsis clock models up to U2020.3
Projects: Millar group
Study position:
Projects: Millar group
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Created: 19th Dec 2019 at 22:19
Last updated: 31st Jul 2021 at 22:35
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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/0000000317563654Roles: Project Coordinator, Vice Coordinator
Expertise: circadian rhythms, arabidopsis thaliana, Mathematical modelling, Data Management, Molecular Biology, Genetics, Deterministic modelling of gene regulation networks, Systems Biology
Tools: Transcriptomics, Proteomics, Deterministic models, Stochastic models, SBML
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/0000000279755013Roles: Postdoc
Expertise: circadian rhythms, Systems Biology, arabidopsis thaliana, Synthetic Biology, Time Series Analysis, photobiology, NanoLUC, LUC, Automation
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
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri
The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work is published in UrquizaGarcia and Millar, Testing the inferred transcription rates of a dynamic, gene network model in absolute units, In Silico Plants, 2021.
Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (first version U2017.1; published as U2019.1) model, rescales ...
Submitter: Andrew Millar
Studies: P2011, U2019 and U2020 models and modelling resources, Rescaling the P2011 model to match RNA data
Assays: P2011.1.2, Reproducibility tool set, TiMet RNA timeseries data and starting models, U2019/U2020 models
Snapshots: Snapshot 1, Snapshot 2, Snapshot 3
P2011.1.2 written in Antimony and converted in SBML using python package Tellurium. Parameters values correspond to P2011.1.2
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units in Arabidopsis clock models up t...
Organisms: No organisms
Models: P2011.1.2 Antimony, P2011.1.2 SBML
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
This section contains the links to the tools used for reproducing the computational results presented in U2019. This is required because SloppyCell is under the risk of becoming rotting code. Using Docker we can assure some persistence for the computational environment that allows to run SloppyCell.
The associated git repository can be found in https://github.com/jurquiza/Urquiza2019a.git which can be cloned.
The docker image can either be pulled from the docker hub site
docker pull ...
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units in Arabidopsis clock models up t...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Collection of clock models that rescale transcript variables to account for absolute units. The relationship between models is summarised in the attached 'model evolution' document and in more detail in the linked publications (preprint version linked in the Snapshot; publication Urquiza and Millar, In Silico Plants 2021 did not have a DOI when Snapshot was created).
Each model is presented three times,

 without a light:dark cycle,

 with an ISSF (Adams et al. JBR 2012) that is set up for ...
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Gene Regulatory Network
Investigation: Absolute units in Arabidopsis clock models up t...
Organisms: Arabidopsis thaliana : Col0 wild type (wildtype / wildtype)
Models: U2019 equation listing, U2019.1, U2019.1_ISSF, U2019.1_ISSF_10xLD_LL, U2019.2, U2019.2_ISSF, U2019.2_ISSF_10xLD_LL, U2019.3, U2019.3_ISSF, U2019.3_ISSF_10xLD_LL, U2020 equation listing, U2020.1, U2020.1_ISSF, U2020.1_ISSF_10xLD_LL, U2020.2, U2020.2_ISSF, U2020.2_ISSF_10xLD_LL, U2020.3, U2020.3_ISSF, U2020.3_ISSF_10xLD_LL
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Model derived from U2019.2, fitted to TiMet data mutants data set. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rated were obtained by taking the product of scaling factor and either transcription or translation, the latter required for ...
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model derived from U2019.1 in which the transcription rates were rescaled to match the scale of TiMet data set for absolute units of RNA concentration. The gmX scaling parameters in the model were fitted numerically. This model has equivalent dynamics to P2011.1.2.
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model derived from U2020.2, fitted to the TiMet RNA data for wildtype and clock mutants. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rates were obtained by taking the product of scaling factor and either transcription or translation, the ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model derived from U2020.1 by fitting the scaling factors for matching TiMet data set for wildtype and clock mutants, in absolute units.
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model derived from U2019.1, in which the way the PRR genes are regulated is modified. Repression mechanism introduced Instead of activation between the PRRs for producing the wave of expression. This is inspired in the result of three models P2012, F2014 and F2016. P2012 introduced TOC1 repression in earlier genes relative to its expression. F2014 introduced also the backward repression of PRR9  PRR7  PRR5, TOC1. However little attention was given to why there is a sharper expression ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Model written in Antimony humanreadable language and then translate into SBML using Tellurium
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: P2011.1.2
Model written in Antimony humanreadable language, Model used in Pokhilko et al 2012
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: P2011.1.2
autogenerated equation listing from the SBML of U2020.3, as a .PDF file
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: PDF (Model description)
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
autogenerated equation listing from the SBML of U2019.3, as a .PDF file
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: PDF (Model description)
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
U2019.3 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
U2020.2 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
U2019.1 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
U2019.3 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
U2019.2 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
Abstract (Expand)
Authors: Uriel UrquizaGarcia, Andrew J Millar
Date Published: 20th Mar 2021
Publication Type: Tech report
DOI: 10.1101/2021.03.18.436071
Citation: biorxiv;2021.03.18.436071v1,[Preprint]
Listing of parameter values, identical to Supplementary Table 2 of the preprint and publication.
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models
This file contains the dependencies required for running SloppyCell and Tellurium together using Jupyter notebooks. It can be used to create a Docker image by executing the command
docker build user/image:version .
The image used for the project can be pulled from Docker hub by typing
docker pull uurquiza/urquiza2019a_tellurium_sloppycell:latest
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: Reproducibility tool set
Contains the summary of model evolution for the Arabidopsis clock in absolute units. In these process two alternative architectures were proposed and fitted to Flis A et al 2015 Open Biology.
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Investigations: Absolute units in Arabidopsis clock models up t...
Studies: P2011, U2019 and U2020 models and modelling res...
Assays: U2019/U2020 models