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README.md

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To run the software, MATLAB 2020a or later is required. There are no specific operating or computing requirements.

All files here should be downloaded to the same folder.

The main scripts contain the prefix 'HostAwareMutationModel'. There are three variants, depending on whether your system contains one, two or three synthetic genes. (More can be added by the user if additional code is written):

  1. _1gene: code for one synthetic gene, alongside code to simulate heat maps and contour maps to explore protein yield and cell viability.
  2. _2genes: code for two synthetic genes, alongside a template to explore the behaviour of a toggle switch.
  3. _3genes: code for three synthetic genes, alongside a template to explore the behaviour of a repressilator.

To run an analysis, open one of the main scripts within MATLAB and then press 'Run'. The comments within the main scripts are sufficient to guide the user on how to adjust the model for different systems. These scripts also all include sections for key plots at the end.