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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).
=== Write the Discussion ===
This is where you will summarize your findings, put them in context with what is already known and extend them in to broader directions. Think about the methods/results and discussion as a triangle where the results section is being very specific about what exactly you did and found, and as you write the discussion you are moving from the point of the triangle to the base broadening out your findings to show points of agreement or disagreement with other data and then broadening out even more such that the last section is placing what the research in the broader context of health, biology or nutrition.
=== Write the Introduction ===
Write this last, because now you will know what concepts you need to introduce. This should start with some broad level of significance or importance at a population level, describe the biological process you are studying, summarize key data that were already known and what this study is attempting to accomplish. A lot of this information will already be in your discussion, just framed in a different way. The last bit before the methods should be something along the lines of "using xxx model we investigated the effects of xxx on yyy finding zzzz". The goal of everything before that line is to convince the reader that that sentence is an important thing for us to have done and to report.
=== Write the Abstract and Acknowledgements ===
The abstract should have a couple of sentences describing the research area (introduction) , 1-2 sentences describing the system being used (''i.e.'' a mouse model of dexamethasone administration), 3-4 sentences describing key findings (results) and 1-2 sentences putting those results in context. In the acknowledgements make sure to include any funding to the lab or to any of the investigators that is pertinent to this work. Also cite any core facilities used, and their funding (can often be found on the core websites).