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.
 * 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