You’ve been working hard, around the clock to get all the data out. You might even have submitted an abstract about your current to the great scientific meeting of your field (and maybe got to travel and present it). Now is time to plant the flag, leave your mark i.e. publish!
By now, you should have read hundreds of manuscripts (see: A single advice about publishing your first scientific paper…), you know the accepted standards of your field, along the way you’ve built your citation library (e.g. Invest in a good manuscript (PDF) management system) and you did all the necessary to write all of your ideas in a easy to find place (e.g. Organizing Creativity).
You’re ready, no sweet, piece of cake…not!
One thing I have learn for myself and from years of supervising graduate students, the first manuscript is the toughest one. From writing to replying to the referees, it will be an experience that you will never forget. Even more so if in addition English is not your native language. This is clearly a time when someone like myself i.e. your supervisor, comes in handy.
Over the years, I found out a simple multi-steps approach that simply work.
1- do not write any text yet.
Rather generate figures and tables you think is necessary for your paper. You can have more than needed. The idea here is to generate a story from your data: what is the message you want to convey with the manuscript and what data (in the form of figures and tables) are needed to support that story, help the readers to follow and agree with you.
Arrange your figures and tables in a logical order to support the above stated goal. This is what I called the “data/story flow”.
2- You are ready to present your results to your supervisor. In my research group, this is done at a group meeting. Why? So the new graduate students can learn from the exercise and that the more senior graduate students can jump in with questions, comments and suggestions.
Usually by the end of the exercise, we will have reduce the number of figures and tables to only those truly necessary. Suggest change to existing figures and tables to make them easier to understand or more explicit in relation to the message that needs to be conveyed. Often, there will be suggestions for new figures / tables to reinforce or better support certain portions of the story. Yes a scientific manuscript is like a good presentation, it is about flow, logical progression i.e. story telling 😉
3- Generate a new version of the “data-story flow” and repeat the step #2 above.
In my experience, by the end of this last iteration, you will be ready to start writing a more structured manuscript with a clear vision of what your paper will be about.
Ruminating... 
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