IGEM:IMPERIAL/Methodology/IGEM WetLab Planning Tool

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Why an iGEM planning tool ?

  • During summer 2006, iGEM-Wetlab@imperial was a real mess (some parts were lost, some experiments were useless).
  • Time was lost due to poor stock management or labeling problems.
  • Most of the iGEM participants come to the competition without an extensive wetlab experience. Real need for guidelines and good practices.
  • Due to the standardization and modularity of the BioBricks there is room for a systematic approach to deal with the work flow of the wetLab.

Suggested concepts for an iGEM planning tool

  • BioBricks are the fundamental material:
    • An iGEM project could be fully described from a BioBrick perspective (creation, wetlab manipulation, assembly, characterization ...)
    • Biobricks can have different status, in regards to their wetlab manipulations:
      • Dry DNA from Registry plates
      • Transformed into a given cell strain
      • Mini/Maxi-preped
      • Digested
      • Ligated
      • Sequenced
      • Characterized
      • ....
  • Wetlab Protocols are transformations applied to the BioBrick status (updating their status).
    • they can be viewed as being some sort of transfer functions:
      • Inputs: BioBrick(s) (with a defined status), Consumables, Equipments, Operator(s).
      • Ouputs: BioBrick(s) with new status, Data, Report.
      • The transfer function corresponds to the standard list of wetlab manipulations of a given protocol.
        • it could be interesting to use Gantt Charts to represent protocols (it gives a feel for timing and concurrent actions).
    • A Biobrick wetlab flow can then be described by the assembly of these protocol 'transfer functions'
    • Due to constrains on the status of the BioBrick as Inputs/Outputs, it will be easy for student to check consistency of their BioBrick wetlab flow.
  • Having such a defined framework will allow a systematic labeling strategy:
    • ID associated to BioBrick, Protocol, Operator(s), Date.
  • Should be easier to defined a quality control strategy.

To do list:

  • List all possible status for a BioBrick. work in progress
  • Define a wetlab workflow scenario with all the protocols involved (e.g. ligating 2 parts from Registry DNA plates) to be done
  • Define the interface of each protocol (inputs/ouputs) to be done
  • Represent the workflow. to be done
  • Define a labeling strategy according to workflow. to be done
  • Define a lab notebook strategy to track the workflow. to be done