IGEM:IMPERIAL/Methodology/IGEM WetLab Planning Tool

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