swcarpentry / modern-scientific-authoring

How to write, publish, and review scientific papers in the early 21st Century
http://swcarpentry.github.io/modern-scientific-authoring/
Other
32 stars 10 forks source link

Choice of Latex for manuscripts in 01-mess.md (and the whole lesson) #12

Open mandel01 opened 8 years ago

mandel01 commented 8 years ago

The intro advises that markdown is currently not recommended for manuscripts for specific reasons. However, for many specialized biology journals Latex is similarly not accepted and senior authors definitely don’t know how to use it. Therefore, as someone who has written 20+ papers but wants a better way, having markdown+pandoc for manuscripts seems like a better option. I am trying to work this out for myself at present and have begun playing with pandoc, etc. I don’t have a full workflow in place but hope to soon. With more experience Greg or Timothée may be able to tell me that I’m wrong!! I also don’t understand Latex enough to know how it underlies pandoc’s conversion. So the current path of the lesson may be exactly what I need.

However, the appeal for me of using markdown+pandoc is that I can use the base text file. My hope is that by combining that with appropriate style sheets, bibliography, and pandoc setup that I can then generate manuscripts appropriate for any journal. Also — and relevant to the topic of “scientific authoring” — I can use it for grant applications, CV, recommendation letters, etc.

This is something I am actively exploring. I’ll continue to follow the lesson and am eager to try things out, but I wanted to raise this concern for biology-focused authors. I know that I can get collaborators to edit text files. I do not think they will (ever) edit Latex, unfortunately, so I am not likely to invest in that except to the extent that it helps to convert from markdown.