Plate Mode: Working with Spatial Arrays of Resources

Riffyn's Plate Mode can be used to efficiently create runs, name runs, assign resources, name generated resources and write location data to generated resources for processes that are executed as spatial arrays. Experiments do not need to be executed with microtiter plates to take advantage of Plate Mode, but it helps to understand the conventions of plate-formatted experiments to use its interfaces.

In plate-formatted experiments the x- and y-coordinates are generally referred to as "Columns" and "Rows", respectively. Specific positions in each plate are indexed as "Wells," and multiple arrays of the same well indexes are distinguished by their distinct "Plate IDs." Well C3 (Row = "C", Column = "3") is highlighted in this schematic of one 96-well plate:


Plate-formatted experiments usually consist of a series of liquid transfers performed using single-channel or multi-channel pipettes operated by either humans or robots. These experiments are frequently initiated by carefully mapping specific input resources to specific wells of an initial set of plates. Once that complex mapping has been performed, subsequent liquid transfer events between plates often follow standard rules that can be completely specified at the plate level: e.g., "The contents of Plate A were transferred to the upper right quadrant of Plate B."

Plate Mode offers interfaces to facilitate documenting both kinds of liquid transfer events: complex mappings (ETA 2018Q2) and standard plate-to-plate transfers. Both interfaces can be used, like Actual Mode, to create runs, assign input resources and name generated output resources. In addition, Plate Mode interfaces will automatically write a specific location to each generated output resource: e.g., x-, y- and z-coordinates can be written to the system-defined fixed properties called "Column", "Row" and "Plate ID," respectively. The combined yx-coordinates can also be written automatically, e.g., to the system-defined fixed property called "Well." Runs and resources generated using these interfaces are named automatically according to the convention z-yx: e.g., if "Plate ID" = "YYMMDD-A", Row = "C" and Well = "3", the run description and generated resources will be named "Plate YYMMDD-A C3". 

The location data written to these spatial properties is often needed to map file data to runs via Parsely. They can also be used to analyze experiments for correlations between outcomes and the positions where resources were generated, as plate-formatted experiments frequently experience "edge effects" or "hot spots" -- especially when no one is looking for them.


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