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
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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.
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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.