Example of a MIC Assay Analysis

Collecting the inputs:

The first step in the analysis of the MIC assay is to collect all variable inputs .. Link MIC_Input.xlsx template in the repo here MIC_Input.xlsx consists of multiple sheets

Substances

Dataset	External ID	Internal ID	Origin Rack	Origin Position 96	MP Barcode 96	MP Position 96
Cooperation Partner A	12345	1

Organisms

Organism	Rack
Organism A ST1234	1
Organism B ST5678	2
Organism C ST9101	3
…	…

Dilutions

Concentration
50
25
12.5
6.25
3,125
1.56
0.78
0.38
0.2
0.1
0.05

Controls

Dataset	Internal ID	Position
Negative Control	Bacteria + Medium	A23
Negative Control	Bacteria + Medium	C23
Negative Control	Bacteria + Medium	E23
Negative Control	Bacteria + Medium	G23
Negative Control	Bacteria + Medium	I23
Negative Control	Bacteria + Medium	K23
Negative Control	Bacteria + Medium	M23
Negative Control	Bacteria + Medium	O23
Blank	Medium	A24
Blank	Medium	B24
Blank	Medium	C24
Blank	Medium	D24
Blank	Medium	E24
Blank	Medium	F24
Blank	Medium	G24
Blank	Medium	H24
…	…	…
Reference	Rifampicin	N23
Reference	Vancomycin	P23

import rda_toolbox as rda

input_mapping = rda.mic_process_inputs(
    # Input specifications excel:
    "../data/input/MIC_Input.xlsx",
    # Barcode reader file which shows Motherplate to AsT plate mapping
    "../data/input/DiS_MP_AsT_2024-10-08.txt",
    # Barcode reader file which shows Ast plate to AcD plate mapping
    "../data/input/AmA_AsT_AcD_20241009.txt",
)
input_mapping.to_csv("../data/processed/prepared_input_mapping_table.csv", index=False)

Dataset

External ID

Original Rack

Origin Position

Internal ID

MP Barcode 96

MP Position 96

Row_384

Col_384

AsT Barcode 384

Concentration

Position

AcD Barcode 384

Replicate

Organism

Coop Partner A

123456789

2233445566

A1

987654321

3456677889

A1

rawfiles = rda.parse_readerfiles("../data/raw/")
rawfiles.to_csv("../data/processed/rawdata.csv", index=False)

Row_384	Col_384	Raw Optical Density	AcD Barcode 384

processed_data = rda.preprocess(
    rawfiles,
    input_mapping,
    substance_id="Internal ID",
    measurement="Optical Density",
    negative_controls="Bacteria + Medium",
    blanks="Medium",
    norm_by_barcode="AcD Barcode 384"
)