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
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. Each model is presented three times, - without a light:dark cycle, - with an ISSF (Adams et al. JBR 2012) that is set up for LD 12h:12h cycles, and - with an ISSF that runs 10 LD cycles followed by an SBML Event that switches to constant light, matching published simulations. ...
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Model files for FMv1.5. The model is based on FMv1 of Chew et al. PNAS 2014, which is also in FAIRDOMHub and linked to the Model record as an 'Attribution'. FMv1 was extended in this work by Hannah Kinmonth-Schultz and Daniel Seaton, in Matlab.
Mean values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.
The ...
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
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Model associated with the following:
Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim, An explanatory model of temperature influence on flowering through whole-plant accumulation of FLOWERING LOCUS T in Arabidopsis thaliana, in silico Plants, Volume 1, Issue 1, 2019, diz006, https://doi.org/10.1093/insilicoplants/diz006
Creator: Hannah Kinmonth-Schultz
Submitter: Hannah Kinmonth-Schultz
Model type: Not specified
Model format: Matlab package
Environment: Matlab
