Reproducibility tool set
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 uurquiza/urquiza2019a_tellurium_sloppycell:latest
or built by running the commd
docker build user/container:version
inside the git folder.
Then container can be started by running sh start.sh in a unix-like env. Window users will need to run the docker command on the terminal by making the adequate changes in the path syntax
SEEK ID: https://fairdomhub.org/assays/1224
Modelling analysis
Projects: Millar group
Investigation: Absolute units in Arabidopsis clock models up to U2020.3
Study: P2011, U2019 and U2020 models and modelling resources
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: No organisms
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Creators and Submitter
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Created: 7th Jan 2020 at 21:28
Last updated: 22nd Mar 2021 at 09:49
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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: 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
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
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
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
