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README.md

INITIATOR SET

INITIATOR SET is a module of The GUESS intended to allow the calculation of the probabilities of Alternative Initiation Codons affecting the translation of mRNA strands of nucleotides (A, G, C, U (RNA has U instead of the T seen in DNA. Artificial nucleotides may also be simulated here)) into proteins, and thus provide data for other modules handling protein folding and pathways. It is also intended for the origins of particular proteins to be possible to deduce in terms of mRNA sequences via calculating the AICs that would be present and thus the likelihood of mutations affecting particular proteins, and which genes need to be edited or epigenetically adjusted, for example. Its output data will also have applications in tracking the causes of prion and amyloid diseases, and it can be used in working out which type of gene edit is safest to make where one has a choice and how mutations cause cancer.

INITIATOR SET will be based on the use of Intermine, a bioinformatic data aggregation platform from the University of Cambridge, along with whatever other tools are required to fulfill all the steps of data handling outlined in the diagram in this repository.

Please see the detailed paper document in this repository for more up to date info.

INITIATOR SET is intended to be the first of many modules to be developed for The GUESS in such a way as will work standalone as well as connected to other modules.

  • Daniel Steven Davies / Danfox Davies / Athamanatha Kitsune

Please view CONTRIBUTING.md before contributing.

Running

With Pipenv

  1. Prerequisites:
  2. Open terminal at this location & cd initiator_set/
  3. Run pipenv install which will install some required packages automatically
  4. Run pipenv shell which will open a virtual python environment where the installed packages are available.
  5. To run:
    • Windows run python main.py
    • Unix like (Linux, macos ext) run python3 main.py
    • On Apple silicone it may sometimes help to use a Rosetta terminal, this can be done by installing a third part terminal like Warp, right clicking the application in finder, open "Get info", and select Open using rosetta.

Prerequisites file

  1. Clone the repository: git clone https://gitlab.vulpinedesigns.com/TheGUESSUniversalEditingSuiteandSDK/INITIATOR_SET.git
  2. Navigate to the INITIATOR SET directory: cd initiator_set/
  3. Make script executable and run it (Linux only): chmod +x INITIATOR_SET.sh; ./INITIATOR_SET.sh