IMPORTANT! Create a `protocol-dev` function

[cvallee]

Create a protocol-dev function to process protocol development experiments

[cvallee]

Specs

1. Capture strategy:
   1 cxw file per experiment (1 or 3 constructs with multiple samples, only 1 buffer)
   --> Get construct name from Strept. Capture (for Biotinylated)/Ni-NTA Capture (His-Tag) of experiment (FC2, FC3, FC4 can be different construct)
   --> for each sample look for:
   ---> Binding response (FCX-1 at Rinse time - 1s) ==> can average if FC2, FC3, FC4 is the same protein
   ----> If negative response after injections for any FC ==> set response to 0
   ---> Look for non specific interaction (FC1 i.e. without protein)
   --> Plot:
   ---> sensorgrams
   ---> Samples vs Binding response (hue constructs)
   ---> constructs vs %NSB

2. Buffer screening:
   1 cxw file per many experiments (many buffers, 1 constructs, same sample set as capture)
   1 excel file with "Method dev." sheet with EXPID column.
   --> Map EXPID of RK serie to excel file to get the actual buffer (pH, [salt], detergent type)
   --> for each sample look for:
   ---> Binding response (FCX-1 at Rinse time - 1s) ==> can average
   ----> If negative response after injections for any FC ==> set response to 0
   ---> KD ==> can average
   ---> Look for non specific interaction (FC1 i.e. without protein)
   --> Plot:
   ---> sensorgrams
   ---> Samples vs Binding response (hue buffer)
   ---> Samples vs KD (hue buffers)
   ---> buffers vs %NSB

3. Stability:
   1 cxw file per experiment (1 exp = 1 sample with 1 condition + EXPID in name or in RK serie name)
   1 excel file with "Method dev." sheet with EXPID column.
   Goal: determine the best condition for stability
   --> Plot:
   ---> sensorgrams
   ---> Cycle number (or time if possible) vs Avg binding response (hue condition/filename)
   ---> Cycle number (or time if possible) vs Avg KD (hue condition/filename)

CC @Edacapkin
--> Please share cxw files for all three steps in Sharepoint and send link here

[cvallee]

Capture specs updates:

• Catch capture strategy from Wizards
• Catch construct from Wizards
• Output:
  ---> capture_analysis_folder/
  -------> Plots (sample vs response hue capture for each construct + sample vs response hue construct for each capture + capture_construct vs %NSB)
  ------> Sensorgrams_folder/ (with all the sensorgrams plot including sample ID + capture strategy + construct as title/filename just subtrated and double referenced FCX-1)
  ------> CSV summary