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→Initial Steps: Updated initial sections for manuscript
* Make a new branch called '''something-manuscript''' to describe the manuscript you are working on. You will work only on that branch (not on master) until the paper is ready to submit. You can see what branch you are on in Github Desktop by looking on the top bar where it says "Current Branch"
* Create a new folder for your manuscript and separately for your code. Use the existing directory structure to understand where to put your data.
* In the manuscript folder create a word document called manuscript and another illustrator document called figures. These will become the files you will submit. The word document can start with headers for '''Abstract, Introduction, Methods, Results, Discussion , Author Contributions, Acknowledgements, References ''' and '''Figure/Table Legends'''.* Include a cover page with a provisional title and author list.
* In your manuscript folder create a file called README.md using a text editor such as Sublime or Textwrangler. This is where you will note where to find the data that goes into each figure panel. The format of this file is markdown, and an example can be found [https://raw.githubusercontent.com/BridgesLab/TissueSpecificTscKnockouts/master/Manuscripts/Muscle%20Tsc1%20Knockout%20Paper/README.md here].
* Also create a markdown file in that folder called TODO.md. Use this to make little notes to yourself as you are writing (''i.e.'' check on stats for this experiment, or look into more papers on such and such).