How to take notes on a bioinformatics project

Notes on data processing should follow these guidelines:
  • Each entry starts with the date in bold.
  • Each entry is a bulleted list.
  • Bullets should be clear but they do not need to be complete sentences, and people can be referred to by initials for brevity.

Include information about what was done and where to find the results, but do not clutter this document with why anything or how exactly; that information belongs elsewhere.

Information to include
  • Links (or paths) to data, reports, web resources, more detailed summaries, etc.
  • Basic description of what files are made and where to find them.
  • The line of code used to run a process
  • The fact that a process completed successfully or notes about what indicated that it did not.

Information to include elsewhere,
(put a link the in the data processing notes, don’t write it out here)

  • Rational about why the parameters used were chosen.
  • Experiment layout, background, reasoning, results, discussion.
  • Explanations about why a process did not work, and why the fix does.