Experiment plates are 96-well, and contain 24 repeats of each strain/medium combination. Each plate represents one "trial" in the terminology of the LABORS ontology, and will contain 48 wells of a knockout strain and a 48 wells of a wildtype strain. The chosen metabolites are added to half of these wells. This is a two-factor experiment (knockout vs wildtype and metabolite vs no metabolite).
Each plate is made up to a design of 6 4x4 Latin squares, in order to minimise positional effects (eg plate edge effects).
The Latin squares occupy wells A1-D4, A5-D8, A9-D12, E1-H4, E5-H8, E9-H12. Within each Latin square there are no exact replicates within any row or column. For example, if wildtype with metabolite is grown in well A1, then it can't be replicated in A2, A3, A4, B1, C1 or D1 (these must contain other combinations of these fators).
An example of a Latin square template for the 4 possible combinations of factors is given below:
1 2 3 4 2 3 4 1 3 4 1 2 2 3 4 1 3 4 1 2 4 1 2 3 3 4 1 2 4 1 2 3 1 2 3 4 4 1 2 3 1 2 3 4 2 3 4 1 2 3 4 1 3 4 1 2 4 1 2 3 3 4 1 2 4 1 2 3 1 2 3 4 4 1 2 3 1 2 3 4 2 3 4 1 1 2 3 4 2 3 4 1 3 4 1 2
For code, see laboratory_control.tar.gz