Documentation and Communication Standards

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  • document by...
    • ...extending or improving existing documentation
    • ...only create new documents when there is no suitable existing document in place (ask you team members)
    • ...ensure that new documents can be reached via a link from the wiki main page (either directly or indirectly through a few more clicks)
    • ...never lecture or explain topics that have been covered by a biology and/or computer science degree

Any background that is pertinent to the topic at hand should be explained. Classic examples are the use of GFF -- track names and contents are obvious for someone with an experimental background in C. elegans genetics, but not so for someone with a biology degree.

  • structure your documentation by...
    • a short intro about the documents contents
    • ...have a table of contents, if there are more than half a dozen headings and/or section headings
    • ...sections should be topical and denoting context (e.g., machine changes, different environments s.a. development, staging or production)
  • executable documentation
    • log which command lines you executed (incl. directory, current user, machine)
    • log the output too, if it is not too much (a dozen lines), or otherwise give an excerpt of a successful command execution
    • describe what is being done (ant dump-genes is not helpful; but saying where the data comes from, where it is being stored, and for what this data dump can be used is helpful)


  • let your senior team members know...
    • ...what you are doing now
    • ...what you are going to do in the next few days
  • let all team members know...
    • ...when you created a new document (Why? Purpose? What are the contents and future directions?)
  • communicate fast...
    • speaking to people in person
    • making use of instant messaging
    • ...revert only to email in exceptional circumstances (Output pasting required, tracking formal documentation s.a. a holiday request, announcements)