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Tentative Workflow

The few example cards and issues are supposed to show how this project layout can be useful. Generally, a common workflow could look like this:

  1. Sprint / sub-project setup

    • create (copy) a new project board for a clearly defined experimental challenge
    • optionally, define one or more Milestones in the issue tracker (e.g. "DNA synthesis xx/2018", "protein production")
    • the first card on the board "ToDo" should probably be "Construct planning"

  2. Construct planning

    • create "DNA request" issues for each required construct in the issue tracker
      • use the "DNA request" template and then apply the "DNA" label
      • assign them to the project board (right column in issue tracker)
    • move DNA cards to "In Progress" and update the issues with benchling and rotmic links as you progress with sequence design

  3. Order fragments, primers, synthetic genes

    • register final construct list in Rotmic (in issue, tick off "rotmic registration" checkbox and update links)
    • place the order (tick of "gene synthesis order" checkbox)

  4. DNA assembly

    • when done, register final and verified samples in Rotmic
    • close the DNA request
      • create "Problem" issues for tracking failed assemblies without getting stuck
    • close the synthesis Milestone when all DNA requests are fulfilled

  5. Protein production

    • create "Protein request" issues, assign them to project board
    • prioritize proteins for production by moving them from "Backlog" to "To Do next"
    • move cards to "In progress" and update issue cards as you go along
    • close Protein requests when proteins samples are ready and registered
    • close any "protein Milestone" when all needed samples are ready

  6. Plan Measurements

    • create "Experiment request" for each planned experiment, assign issue to board
    • create "Material request" for each still missing material / reagent, assign to board
    • add other activities directly to board (without creating issues)
    • create new Milestone(s)
    • create new "standard protocol" pages for often repeated methods

  7. Perform Measurements

    • move "Experiment Request" card into "In Progress" column
    • update "Experiment Request" issues as you go along, create "Problem" issues if needed
    • close Experiment Request when done, work towards closing the Milestone

  8. Finalize project

    • optionally collect core data in repository sub-directories
    • review all open issues and cards
    • close last Milestones
    • close Project board
    • create new Project board for publication or next sprint, assign left-over issues to new Milestones and board