U2019.3_ISSF Version 1
Simulate Model on Copasi
Simulate Model on JWSU2019.3 that simulates light condition with ISSF
SEEK ID: https://fairdomhub.org/models/773?version=1
1 item is associated with this Model:-
U2019_3_ISSF.xml (XML document - 83.2 KB)
Organism: Arabidopsis thaliana
Model type: Ordinary differential equations (ODE)
Model format: SBML
Execution or visualisation environment: Copasi
Model image: No image specified
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Creators and Submitter
Views: 1835 Downloads: 171 Runs: 29
Created: 1st Mar 2021 at 15:27
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Version 1 (earliest) Created 1st Mar 2021 at 15:27 by Uriel Urquiza-Garcia
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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, BioDare1
Institutions: University of Edinburgh, School of Biological Sciences, University of Edinburgh
https://orcid.org/0000-0003-1756-3654
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/0000-0002-7975-5013
Group Leader in Plant Synthetic Genomics at Heinrich Heine University Düsseldorf and the Cluster of Excellence on Plant Sciences (CEPLAS). My research develops the genetic and cellular methods required for synthetic plant chromosomes to function in living cells — including telomere seeding, neocentromere activation, and heritable gene expression — using Physcomitrium patens as a programmable plant chassis. I use the circadian clock as a quantitative test system to test whether complex gene ...
The Centre for Engineering Biology is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2023 as the successor to SynthSys, itself founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE). CSBE was newly founded in 2007. The Centre for Engineering Biology is a hub organisation that links across multiple, major funding awards, including an Engineering Biology Mission Hub, and EPSRC C-loop.
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, BioDare1
Web page: https://biology.ed.ac.uk/centre-engineering-biology
Andrew Millar's research group, University of Edinburgh
Programme: Centre for Engineering Biology (prev. SynthSys)
Public web page: http://www.amillar.org
The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work is published in Urquiza-Garcia 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 ...
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 human-readable file in the Antimony language and the associated, machine-readable SBML file, which was automatically generated using the SBML export ...
Submitter: Uriel Urquiza-Garcia
Investigation: Absolute units in Arabidopsis clock models up t...
Assays: P2011.1.2, Reproducibility tool set, U2019/U2020 models
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,
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- without a light:dark cycle,
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- 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...
