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.
- they can be viewed as being some sort of transfer functions:
- 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