diff --git a/OT2-setup/data/labware.csv b/OT2-setup/data/labware.csv
new file mode 100644
index 0000000..116752d
--- /dev/null
+++ b/OT2-setup/data/labware.csv
@@ -0,0 +1,25 @@
+protocol,location,labware,well_name,reactant,volume
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,A1,pUC19,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,B1,pUC19,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,C1,pUC19,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,D1,pUC19,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,E1,pJKR,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,F1,pJKR,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,G1,pJKR,20
+transformation,1,armadillo_96_wellplate_200ul_pcr_full_skirt,H1,pJKR,20
+transformation,4,usascientific_96_wellplate_2.4ml_deep,A1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,B1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,C1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,D1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,E1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,F1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,G1,cells,300
+transformation,4,usascientific_96_wellplate_2.4ml_deep,H1,cells,300
+transformation,5,usascientific_96_wellplate_2.4ml_deep,A1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,B1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,C1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,D1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,E1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,F1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,G1,SOC,1500
+transformation,5,usascientific_96_wellplate_2.4ml_deep,H1,SOC,1500
diff --git a/OT2-setup/data/spotting-data.csv b/OT2-setup/data/spotting-data.csv
new file mode 100644
index 0000000..88e38bd
--- /dev/null
+++ b/OT2-setup/data/spotting-data.csv
@@ -0,0 +1,97 @@
+plate_location,source_well,destination_well,spotting_volume,agar_plate_weight
+1,A1,A1,5,33
+1,B1,B1,5,33
+1,C1,C1,5,33
+1,D1,D1,5,33
+1,E1,E1,5,33
+1,F1,F1,5,33
+1,G1,G1,5,33
+1,H1,H1,5,33
+1,A2,A2,5,33
+1,B2,B2,5,33
+1,C2,C2,5,33
+1,D2,D2,5,33
+1,E2,E2,5,33
+1,F2,F2,5,33
+1,G2,G2,5,33
+1,H2,H2,5,33
+1,A3,A3,5,33
+1,B3,B3,5,33
+1,C3,C3,5,33
+1,D3,D3,5,33
+1,E3,E3,5,33
+1,F3,F3,5,33
+1,G3,G3,5,33
+1,H3,H3,5,33
+1,A4,A4,5,33
+1,B4,B4,5,33
+1,C4,C4,5,33
+1,D4,D4,5,33
+1,E4,E4,5,33
+1,F4,F4,5,33
+1,G4,G4,5,33
+1,H4,H4,5,33
+1,A5,A5,5,33
+1,B5,B5,5,33
+1,C5,C5,5,33
+1,D5,D5,5,33
+1,E5,E5,5,33
+1,F5,F5,5,33
+1,G5,G5,5,33
+1,H5,H5,5,33
+1,A6,A6,5,33
+1,B6,B6,5,33
+1,C6,C6,5,33
+1,D6,D6,5,33
+1,E6,E6,5,33
+1,F6,F6,5,33
+1,G6,G6,5,33
+1,H6,H6,5,33
+1,A7,A7,5,33
+1,B7,B7,5,33
+1,C7,C7,5,33
+1,D7,D7,5,33
+1,E7,E7,5,33
+1,F7,F7,5,33
+1,G7,G7,5,33
+1,H7,H7,5,33
+1,A8,A8,5,33
+1,B8,B8,5,33
+1,C8,C8,5,33
+1,D8,D8,5,33
+1,E8,E8,5,33
+1,F8,F8,5,33
+1,G8,G8,5,33
+1,H8,H8,5,33
+1,A9,A9,5,33
+1,B9,B9,5,33
+1,C9,C9,5,33
+1,D9,D9,5,33
+1,E9,E9,5,33
+1,F9,F9,5,33
+1,G9,G9,5,33
+1,H9,H9,5,33
+1,A10,A10,5,33
+1,B10,B10,5,33
+1,C10,C10,5,33
+1,D10,D10,5,33
+1,E10,E10,5,33
+1,F10,F10,5,33
+1,G10,G10,5,33
+1,H10,H10,5,33
+1,A11,A11,5,33
+1,B11,B11,5,33
+1,C11,C11,5,33
+1,D11,D11,5,33
+1,E11,E11,5,33
+1,F11,F11,5,33
+1,G11,G11,5,33
+1,H11,H11,5,33
+1,A12,A12,5,33
+1,B12,B12,5,33
+1,C12,C12,5,33
+1,D12,D12,5,33
+1,E12,E12,5,33
+1,F12,F12,5,33
+1,G12,G12,5,33
+1,H12,H12,5,33
\ No newline at end of file
diff --git a/OT2-setup/data/spotting-parameters.json b/OT2-setup/data/spotting-parameters.json
new file mode 100644
index 0000000..91e5081
--- /dev/null
+++ b/OT2-setup/data/spotting-parameters.json
@@ -0,0 +1,16 @@
+{
+    "transformation_plate_name":"armadillo_96_wellplate_200ul_pcr_full_skirt",
+    "agar_plate_name":"armadillo_96_wellplate_200ul_pcr_full_skirt",
+    "pipette_tiprack_name":"opentrons_96_tiprack_20ul",
+    "pipette_tiprack_slots":[6,5],
+    "pipette_name":"p20_multi_gen2",
+    "pipette_mount":"left",
+    "aspirate_rate":30,
+    "dispense_rate":60,
+    "aspirate_height":0.1,
+    "dispense_height":0.1,
+    "dead_volume": 1,
+    "plate_weight":14.11,
+    "agar_density":0.00095,
+    "spotting_height":0.5
+}
\ No newline at end of file
diff --git a/OT2-setup/data/transformation-data.csv b/OT2-setup/data/transformation-data.csv
new file mode 100644
index 0000000..c91d481
--- /dev/null
+++ b/OT2-setup/data/transformation-data.csv
@@ -0,0 +1,33 @@
+dna_well,dna_volume,cells_well,cells_volume,soc_well,soc_volume,transformation_well
+A1,3,A2,30,A1,150,A1
+B1,3,B2,30,B1,150,B1
+C1,3,C2,30,C1,150,C1
+D1,3,D2,30,D1,150,D1
+E1,3,E2,30,E1,150,E1
+F1,3,F2,30,F1,150,F1
+G1,3,G2,30,G1,150,G1
+H1,3,H2,30,H1,150,H1
+A1,2,A2,20,A1,100,A2
+B1,2,B2,20,B1,100,B2
+C1,2,C2,20,C1,100,C2
+D1,2,D2,20,D1,100,D2
+E1,2,E2,20,E1,100,E2
+F1,2,F2,20,F1,100,F2
+G1,2,G2,20,G1,100,G2
+H1,2,H2,20,H1,100,H2
+A1,1,A2,10,A1,50,A3
+B1,1,B2,10,B1,50,B3
+C1,1,C2,10,C1,50,C3
+D1,1,D2,10,D1,50,D3
+E1,1,E2,10,E1,50,E3
+F1,1,F2,10,F1,50,F3
+G1,1,G2,10,G1,50,G3
+H1,1,H2,10,H1,50,H3
+A1,0,A2,30,A1,150,A4
+B1,0,B2,30,B1,150,B4
+C1,0,C2,30,C1,150,C4
+D1,0,D2,30,D1,150,D4
+E1,0,E2,30,E1,150,E4
+F1,0,F2,30,F1,150,F4
+G1,0,G2,30,G1,150,G4
+H1,0,H2,30,H1,150,H4
\ No newline at end of file
diff --git a/OT2-setup/data/transformation-parameters.json b/OT2-setup/data/transformation-parameters.json
new file mode 100644
index 0000000..e1d616e
--- /dev/null
+++ b/OT2-setup/data/transformation-parameters.json
@@ -0,0 +1,25 @@
+{
+    "init_temp":4,
+    "init_time":20,
+    "heat_temp":42,
+    "heat_time":30,
+    "cool_temp":4,
+    "cool_time":2,
+    "inc_temp":37,
+    "inc_time":60,
+    "dna_plate_name":"armadillo_96_wellplate_200ul_pcr_full_skirt",
+    "dna_plate_slot":1,
+    "cells_plate_name": "usascientific_96_wellplate_2.4ml_deep",
+    "cells_plate_slot":4,
+    "soc_plate_name": "usascientific_96_wellplate_2.4ml_deep",
+    "soc_plate_slot": 5,
+    "transformation_plate_name":"armadillo_96_wellplate_200ul_pcr_full_skirt",
+    "right_pipette_tiprack_name":"opentrons_96_tiprack_20ul",
+    "right_pipette_tiprack_slots":[2,3],
+    "right_pipette_name":"p20_multi_gen2",
+    "right_pipette_mount":"right",
+    "left_pipette_tiprack_name":"opentrons_96_tiprack_300ul",
+    "left_pipette_tiprack_slots":[6,9],
+    "left_pipette_name":"p300_multi_gen2",
+    "left_pipette_mount":"left"
+}
\ No newline at end of file
diff --git a/OT2-setup/generate-protocol.sh b/OT2-setup/generate-protocol.sh
new file mode 100755
index 0000000..e1b1157
--- /dev/null
+++ b/OT2-setup/generate-protocol.sh
@@ -0,0 +1,134 @@
+#!/bin/bash
+
+# Function to display usage information
+usage() {
+    echo "Usage: $0 experiment=experiment1,experiment2,... [csv_file=csv1,csv2,...] [json_file=json1,json2,...]"
+    exit 1
+}
+
+# Check if the correct number of arguments is provided
+if [ "$#" -lt 1 ]; then
+    usage
+fi
+
+# Set default values
+csv_files=""
+json_files=""
+
+# Parse command-line arguments
+for arg in "$@"; do
+    case $arg in
+        experiment=*)
+            experiment_types="${arg#*=}"
+            ;;
+        csv_file=*)
+            csv_files="${arg#*=}"
+            ;;
+        json_file=*)
+            json_files="${arg#*=}"
+            ;;
+        *)
+            echo "Error: Invalid argument: $arg"
+            usage
+            ;;
+    esac
+done
+
+# Function to check if a file exists
+check_file_exists() {
+    if [ ! -f "$1" ]; then
+        echo "Error: $1 file not found."
+        exit 1
+    fi
+}
+
+# Function to extract variable from JSON
+extract_variable_from_json() {
+    local json_file="$1"
+    local variable_name="$2"
+    local variable_line=$(grep "$variable_name" "$json_file")
+
+    # Extract the value part
+    local variable_value=$(echo "$variable_line" | cut -d '"' -f 4)
+    echo "$variable_value"
+}
+
+# Function to process each experiment type
+process_experiment_type() {
+    local experiment_type="$1"
+    local input_csv="$2"
+    local input_json="$3"
+
+    local template_py=""
+    
+    case "$experiment_type" in
+        transformation)
+            template_py="./setup/protocol-templates/transformation-template.py"
+            ;;
+        spotting)
+            template_py="./setup/protocol-templates/spotting-template.py"
+            ;;
+        *)
+            echo "Error: Unsupported experiment type: $experiment_type"
+            exit 1
+            ;;
+    esac
+
+    # Check if the template Python file exists
+    check_file_exists "$template_py"
+    
+    # If CSV file not specified, use default in "data" folder
+    if [ -z "$input_csv" ]; then
+        input_csv="data/${experiment_type}-data.csv"
+    fi
+    # If JSON file not specified, use default in "data" folder
+    if [ -z "$input_json" ]; then
+        input_json="data/${experiment_type}-parameters.json"
+    fi
+    
+    # Check if the input CSV file exists
+    check_file_exists "$input_csv"
+    # Check if the input JSON file exists
+    check_file_exists "$input_json"
+
+    # Read contents of input CSV into a variable
+    csv_content=$(<"$input_csv")
+
+    # Define the content for protocol.py
+    new_content="csv_file = \"\"\"\n$csv_content\n\"\"\"\n\n"
+    # Read contents of input JSON into a variable and remove newlines
+    json_content="parameters_json = \"\"\"$(<"$input_json" tr -d '\n' | tr -d '[:space:]'| tr -d '[:space:]')\"\"\"\n"
+
+    # Extract the name from the template file
+    template_name=$(basename "$template_py" | sed 's/.*\([a-zA-Z]\)-template\.py/\1/')
+    # Generate the output file name in the "protocols" folder
+    output_folder="results"
+    output_file="${output_folder}/${experiment_type}-protocol.py"
+
+    # Create the protocols folder if it doesn't exist
+    mkdir -p "$output_folder"
+
+    # If the file exists, append the new content at the top
+    old_content=$(<"$template_py")
+    echo -e "$new_content$json_content$old_content" > "$output_file"
+    echo "Protocol for $experiment_type has been generated. Output file: $output_file"
+
+    # Get the transformation_plate_name and dna_plate_name from the parameters JSON
+    transformation_plate_name=$(extract_variable_from_json "$input_json" "transformation_plate_name")
+    dna_plate_name=$(extract_variable_from_json "$input_json" "dna_plate_name")
+
+    # Call the R scripts 
+    Rscript ./setup/create-labware/visualise-labware.R ./data/labware.csv "${output_folder}"
+    Rscript ./setup/create-labware/visualise-labware-2.R ./data/transformation-data.csv "${output_folder}"
+    Rscript ./setup/instruction-templates/transformation-instruction.R "./data/transformation-parameters.json" "${output_folder}/Instructions.pdf"
+}
+
+# Split comma-separated values into arrays
+IFS=',' read -ra experiment_type_array <<< "$experiment_types"
+IFS=',' read -ra csv_file_array <<< "$csv_files"
+IFS=',' read -ra json_file_array <<< "$json_files"
+
+# Process each experiment type
+for ((i=0; i<"${#experiment_type_array[@]}"; i++)); do
+    process_experiment_type "${experiment_type_array[i]}" "${csv_file_array[i]}" "${json_file_array[i]}"
+done
\ No newline at end of file
diff --git a/OT2-setup/setup/create-labware/labware/armadillo_96_wellplate_200ul_pcr_full_skirt.json b/OT2-setup/setup/create-labware/labware/armadillo_96_wellplate_200ul_pcr_full_skirt.json
new file mode 100644
index 0000000..d5c2bb7
--- /dev/null
+++ b/OT2-setup/setup/create-labware/labware/armadillo_96_wellplate_200ul_pcr_full_skirt.json
@@ -0,0 +1,1045 @@
+{
+    "namespace": "opentrons",
+    "version": 2,
+    "schemaVersion": 2,
+    "parameters": {
+      "loadName": "armadillo_96_wellplate_200ul_pcr_full_skirt",
+      "format": "96Standard",
+      "isTiprack": false,
+      "isMagneticModuleCompatible": true
+    },
+    "metadata": {
+      "displayName": "Armadillo 96 Well Plate 200 µL PCR Full Skirt",
+      "displayCategory": "wellPlate",
+      "displayVolumeUnits": "µL",
+      "tags": []
+    },
+    "brand": {
+      "brand": "Thermo Scientific",
+      "brandId": ["AB2396"],
+      "links": [
+        "https://www.fishersci.com/shop/products/armadillo-96-well-pcr-plate-1/AB2396"
+      ]
+    },
+    "dimensions": {
+      "xDimension": 127.76,
+      "yDimension": 85.48,
+      "zDimension": 16.0
+    },
+    "cornerOffsetFromSlot": {
+      "x": 0,
+      "y": 0,
+      "z": 0
+    },
+    "stackingOffsetWithLabware": {
+      "opentrons_96_pcr_adapter": {
+        "x": 0,
+        "y": 0,
+        "z": 10.95
+      },
+      "opentrons_96_well_aluminum_block": {
+        "x": 0,
+        "y": 0,
+        "z": 11.91
+      }
+    },
+    "stackingOffsetWithModule": {
+      "magneticBlockV1": {
+        "x": 0,
+        "y": 0,
+        "z": 3.54
+      },
+      "thermocyclerModuleV2": {
+        "x": 0,
+        "y": 0,
+        "z": 10.7
+      }
+    },
+    "gripForce": 15,
+    "gripHeightFromLabwareBottom": 10,
+    "ordering": [
+      ["A1", "B1", "C1", "D1", "E1", "F1", "G1", "H1"],
+      ["A2", "B2", "C2", "D2", "E2", "F2", "G2", "H2"],
+      ["A3", "B3", "C3", "D3", "E3", "F3", "G3", "H3"],
+      ["A4", "B4", "C4", "D4", "E4", "F4", "G4", "H4"],
+      ["A5", "B5", "C5", "D5", "E5", "F5", "G5", "H5"],
+      ["A6", "B6", "C6", "D6", "E6", "F6", "G6", "H6"],
+      ["A7", "B7", "C7", "D7", "E7", "F7", "G7", "H7"],
+      ["A8", "B8", "C8", "D8", "E8", "F8", "G8", "H8"],
+      ["A9", "B9", "C9", "D9", "E9", "F9", "G9", "H9"],
+      ["A10", "B10", "C10", "D10", "E10", "F10", "G10", "H10"],
+      ["A11", "B11", "C11", "D11", "E11", "F11", "G11", "H11"],
+      ["A12", "B12", "C12", "D12", "E12", "F12", "G12", "H12"]
+    ],
+    "wells": {
+      "A1": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 14.38,
+        "y": 74.24,
+        "z": 1.05
+      },
+      "B1": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 14.38,
+        "y": 65.24,
+        "z": 1.05
+      },
+      "C1": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 14.38,
+        "y": 56.24,
+        "z": 1.05
+      },
+      "D1": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 14.38,
+        "y": 47.24,
+        "z": 1.05
+      },
+      "E1": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 14.38,
+        "y": 38.24,
+        "z": 1.05
+      },
+      "F1": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 14.38,
+        "y": 29.24,
+        "z": 1.05
+      },
+      "G1": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 14.38,
+        "y": 20.24,
+        "z": 1.05
+      },
+      "H1": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 14.38,
+        "y": 11.24,
+        "z": 1.05
+      },
+      "A2": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 23.38,
+        "y": 74.24,
+        "z": 1.05
+      },
+      "B2": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 23.38,
+        "y": 65.24,
+        "z": 1.05
+      },
+      "C2": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 23.38,
+        "y": 56.24,
+        "z": 1.05
+      },
+      "D2": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 23.38,
+        "y": 47.24,
+        "z": 1.05
+      },
+      "E2": {
+        "depth": 14.95,
+        "totalLiquidVolume": 200,
+        "shape": "circular",
+        "diameter": 5.5,
+        "x": 23.38,
+        "y": 38.24,
+        "z": 1.05
+      },
+      "F2": {
+        "depth": 14.95,
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diff --git a/OT2-setup/setup/create-labware/labware/biorad_384_wellplate_50ul.json b/OT2-setup/setup/create-labware/labware/biorad_384_wellplate_50ul.json
new file mode 100644
index 0000000..7da753f
--- /dev/null
+++ b/OT2-setup/setup/create-labware/labware/biorad_384_wellplate_50ul.json
@@ -0,0 +1,4331 @@
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\ No newline at end of file
diff --git a/OT2-setup/setup/create-labware/labware/biorad_96_wellplate_200ul_pcr.json b/OT2-setup/setup/create-labware/labware/biorad_96_wellplate_200ul_pcr.json
new file mode 100644
index 0000000..ad7970c
--- /dev/null
+++ b/OT2-setup/setup/create-labware/labware/biorad_96_wellplate_200ul_pcr.json
@@ -0,0 +1,1046 @@
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+        "y": 0,
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+        "y": 0,
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+      },
+      "magneticBlockV1": {
+        "x": 0,
+        "y": 0,
+        "z": 3.87
+      }
+    }
+  }
\ No newline at end of file
diff --git a/OT2-setup/setup/create-labware/labware/corning_24_wellplate_3.4ml_flat.json b/OT2-setup/setup/create-labware/labware/corning_24_wellplate_3.4ml_flat.json
new file mode 100644
index 0000000..f2dd560
--- /dev/null
+++ b/OT2-setup/setup/create-labware/labware/corning_24_wellplate_3.4ml_flat.json
@@ -0,0 +1,300 @@
+{
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+      ["A1", "B1", "C1", "D1"],
+      ["A2", "B2", "C2", "D2"],
+      ["A3", "B3", "C3", "D3"],
+      ["A4", "B4", "C4", "D4"],
+      ["A5", "B5", "C5", "D5"],
+      ["A6", "B6", "C6", "D6"]
+    ],
+    "brand": {
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+      "brandId": ["3337", "3524", "3526", "3527", "3473", "3738", "3987"],
+      "links": [
+        "https://ecatalog.corning.com/life-sciences/b2c/US/en/Microplates/Assay-Microplates/96-Well-Microplates/Costar%C2%AE-Multiple-Well-Cell-Culture-Plates/p/3738"
+      ]
+    },
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+    "version": 2,
+    "namespace": "opentrons",
+    "metadata": {
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+      "displayCategory": "wellPlate",
+      "tags": []
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+          "B5",
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+        "metadata": {
+          "wellBottomShape": "flat"
+        }
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+    "cornerOffsetFromSlot": {
+      "x": 0,
+      "y": 0,
+      "z": 0
+    },
+    "stackingOffsetWithLabware": {
+      "opentrons_aluminum_flat_bottom_plate": {
+        "x": 0,
+        "y": 0,
+        "z": 4.15
+      }
+    }
+  }
\ No newline at end of file
diff --git a/OT2-setup/setup/create-labware/labware/corning_96_wellplate_360ul_flat.json b/OT2-setup/setup/create-labware/labware/corning_96_wellplate_360ul_flat.json
new file mode 100644
index 0000000..c598886
--- /dev/null
+++ b/OT2-setup/setup/create-labware/labware/corning_96_wellplate_360ul_flat.json
@@ -0,0 +1,1063 @@
+{
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+          "G12",
+          "H12"
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+        "metadata": {
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+        }
+      }
+    ],
+    "parameters": {
+      "format": "96Standard",
+      "isTiprack": false,
+      "isMagneticModuleCompatible": false,
+      "loadName": "corning_96_wellplate_360ul_flat"
+    },
+    "namespace": "opentrons",
+    "version": 2,
+    "schemaVersion": 2,
+    "stackingOffsetWithLabware": {
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+        "x": 0,
+        "y": 0,
+        "z": 10.22
+      },
+      "opentrons_aluminum_flat_bottom_plate": {
+        "x": 0,
+        "y": 0,
+        "z": 5.45
+      }
+    }
+  }
\ No newline at end of file
diff --git a/OT2-setup/setup/create-labware/labware/nest_96_wellplate_2ml_deep.json b/OT2-setup/setup/create-labware/labware/nest_96_wellplate_2ml_deep.json
new file mode 100644
index 0000000..9fb4bfa
--- /dev/null
+++ b/OT2-setup/setup/create-labware/labware/nest_96_wellplate_2ml_deep.json
@@ -0,0 +1,1137 @@
+{
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+      ["A2", "B2", "C2", "D2", "E2", "F2", "G2", "H2"],
+      ["A3", "B3", "C3", "D3", "E3", "F3", "G3", "H3"],
+      ["A4", "B4", "C4", "D4", "E4", "F4", "G4", "H4"],
+      ["A5", "B5", "C5", "D5", "E5", "F5", "G5", "H5"],
+      ["A6", "B6", "C6", "D6", "E6", "F6", "G6", "H6"],
+      ["A7", "B7", "C7", "D7", "E7", "F7", "G7", "H7"],
+      ["A8", "B8", "C8", "D8", "E8", "F8", "G8", "H8"],
+      ["A9", "B9", "C9", "D9", "E9", "F9", "G9", "H9"],
+      ["A10", "B10", "C10", "D10", "E10", "F10", "G10", "H10"],
+      ["A11", "B11", "C11", "D11", "E11", "F11", "G11", "H11"],
+      ["A12", "B12", "C12", "D12", "E12", "F12", "G12", "H12"]
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+    "brand": {
+      "brand": "NEST",
+      "brandId": ["503001", "503501"],
+      "links": ["https://www.nest-biotech.com/deep-well-plates/59253726.html"]
+    },
+    "metadata": {
+      "displayName": "NEST 96 Deep Well Plate 2mL",
+      "displayCategory": "wellPlate",
+      "displayVolumeUnits": "µL",
+      "tags": []
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+        "x": 0,
+        "y": 0,
+        "z": 2.66
+      }
+    }
+  }
\ No newline at end of file
diff --git a/OT2-setup/setup/create-labware/labware/opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical.json b/OT2-setup/setup/create-labware/labware/opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical.json
new file mode 100644
index 0000000..ee58d91
--- /dev/null
+++ b/OT2-setup/setup/create-labware/labware/opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical.json
@@ -0,0 +1,164 @@
+{
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+      ["A2", "B2", "C2"],
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+      ["A4", "B4"]
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+    "version": 1,
+    "namespace": "opentrons",
+    "metadata": {
+      "displayName": "Opentrons 10 Tube Rack with Falcon 4x50 mL, 6x15 mL Conical",
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+      "isMagneticModuleCompatible": false,
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+        "y": 17.75,
+        "z": 6.85
+      },
+      "A3": {
+        "totalLiquidVolume": 50000,
+        "diameter": 27.81,
+        "shape": "circular",
+        "depth": 113,
+        "x": 71.38,
+        "y": 60.25,
+        "z": 7.3
+      },
+      "B3": {
+        "totalLiquidVolume": 50000,
+        "diameter": 27.81,
+        "shape": "circular",
+        "depth": 113,
+        "x": 71.38,
+        "y": 25.25,
+        "z": 7.3
+      },
+      "A4": {
+        "totalLiquidVolume": 50000,
+        "diameter": 27.81,
+        "shape": "circular",
+        "depth": 113,
+        "x": 106.38,
+        "y": 60.25,
+        "z": 7.3
+      },
+      "B4": {
+        "totalLiquidVolume": 50000,
+        "diameter": 27.81,
+        "shape": "circular",
+        "depth": 113,
+        "x": 106.38,
+        "y": 25.25,
+        "z": 7.3
+      }
+    },
+    "brand": {
+      "brand": "Opentrons",
+      "brandId": [],
+      "links": [
+        "https://shop.opentrons.com/collections/opentrons-tips/products/tube-rack-set-1"
+      ]
+    },
+    "groups": [
+      {
+        "wells": ["A1", "B1", "C1", "A2", "B2", "C2"],
+        "metadata": {
+          "displayName": "Falcon 6x15 mL Conical",
+          "displayCategory": "tubeRack",
+          "wellBottomShape": "v"
+        },
+        "brand": {
+          "brand": "Falcon",
+          "brandId": ["352095", "352096", "352097", "352099", "352196"],
+          "links": [
+            "https://ecatalog.corning.com/life-sciences/b2c/US/en/Liquid-Handling/Tubes,-Liquid-Handling/Centrifuge-Tubes/Falcon%C2%AE-Conical-Centrifuge-Tubes/p/falconConicalTubes"
+          ]
+        }
+      },
+      {
+        "wells": ["A3", "B3", "A4", "B4"],
+        "metadata": {
+          "displayName": "Falcon 4x50 mL Conical",
+          "displayCategory": "tubeRack",
+          "wellBottomShape": "v"
+        },
+        "brand": {
+          "brand": "Falcon",
+          "brandId": ["352070", "352098"],
+          "links": [
+            "https://ecatalog.corning.com/life-sciences/b2c/US/en/Liquid-Handling/Tubes,-Liquid-Handling/Centrifuge-Tubes/Falcon%C2%AE-Conical-Centrifuge-Tubes/p/falconConicalTubes"
+          ]
+        }
+      }
+    ],
+    "cornerOffsetFromSlot": {
+      "x": 0,
+      "y": 0,
+      "z": 0
+    }
+  }
\ No newline at end of file
diff --git a/petridish_16_wellplate.json b/OT2-setup/setup/create-labware/labware/petridish.json
similarity index 83%
rename from petridish_16_wellplate.json
rename to OT2-setup/setup/create-labware/labware/petridish.json
index d10d065..4fd884d 100644
--- a/petridish_16_wellplate.json
+++ b/OT2-setup/setup/create-labware/labware/petridish.json
@@ -26,18 +26,20 @@
         ]
     ],
     "brand": {
-        "brand": "Petri dish",
-        "brandId": []
+        "brand": "Fisherbrand™ ",
+        "brandId": [
+            "12654785"
+        ]
     },
     "metadata": {
-        "displayName": "Petri Dish 16 Well Plate",
+        "displayName": "Petri Dish 90mm 16 wells",
         "displayCategory": "wellPlate",
         "displayVolumeUnits": "µL",
         "tags": []
     },
     "dimensions": {
-        "xDimension": 128,
-        "yDimension": 86,
+        "xDimension": 127,
+        "yDimension": 85,
         "zDimension": 18
     },
     "wells": {
@@ -47,8 +49,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 41.5,
-            "y": 64.5,
+            "x": 41,
+            "y": 65,
             "z": 7
         },
         "B1": {
@@ -57,8 +59,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 41.5,
-            "y": 49.5,
+            "x": 41,
+            "y": 50,
             "z": 7
         },
         "C1": {
@@ -67,8 +69,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 41.5,
-            "y": 34.5,
+            "x": 41,
+            "y": 35,
             "z": 7
         },
         "D1": {
@@ -77,8 +79,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 41.5,
-            "y": 19.5,
+            "x": 41,
+            "y": 20,
             "z": 7
         },
         "A2": {
@@ -87,8 +89,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 56.5,
-            "y": 64.5,
+            "x": 56,
+            "y": 65,
             "z": 7
         },
         "B2": {
@@ -97,8 +99,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 56.5,
-            "y": 49.5,
+            "x": 56,
+            "y": 50,
             "z": 7
         },
         "C2": {
@@ -107,8 +109,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 56.5,
-            "y": 34.5,
+            "x": 56,
+            "y": 35,
             "z": 7
         },
         "D2": {
@@ -117,8 +119,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 56.5,
-            "y": 19.5,
+            "x": 56,
+            "y": 20,
             "z": 7
         },
         "A3": {
@@ -127,8 +129,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 71.5,
-            "y": 64.5,
+            "x": 71,
+            "y": 65,
             "z": 7
         },
         "B3": {
@@ -137,8 +139,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 71.5,
-            "y": 49.5,
+            "x": 71,
+            "y": 50,
             "z": 7
         },
         "C3": {
@@ -147,8 +149,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 71.5,
-            "y": 34.5,
+            "x": 71,
+            "y": 35,
             "z": 7
         },
         "D3": {
@@ -157,8 +159,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 71.5,
-            "y": 19.5,
+            "x": 71,
+            "y": 20,
             "z": 7
         },
         "A4": {
@@ -167,8 +169,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 86.5,
-            "y": 64.5,
+            "x": 86,
+            "y": 65,
             "z": 7
         },
         "B4": {
@@ -177,8 +179,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 86.5,
-            "y": 49.5,
+            "x": 86,
+            "y": 50,
             "z": 7
         },
         "C4": {
@@ -187,8 +189,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 86.5,
-            "y": 34.5,
+            "x": 86,
+            "y": 35,
             "z": 7
         },
         "D4": {
@@ -197,8 +199,8 @@
             "shape": "rectangular",
             "xDimension": 15,
             "yDimension": 15,
-            "x": 86.5,
-            "y": 19.5,
+            "x": 86,
+            "y": 20,
             "z": 7
         }
     },
@@ -232,7 +234,7 @@
         "quirks": [],
         "isTiprack": false,
         "isMagneticModuleCompatible": false,
-        "loadName": "petridish_16_wellplate"
+        "loadName": "petridish_90mm_16_wells"
     },
     "namespace": "custom_beta",
     "version": 1,
diff --git a/OT2-setup/setup/create-labware/labware/usascientific_96_wellplate_2.4ml_deep.json b/OT2-setup/setup/create-labware/labware/usascientific_96_wellplate_2.4ml_deep.json
new file mode 100644
index 0000000..2212ec6
--- /dev/null
+++ b/OT2-setup/setup/create-labware/labware/usascientific_96_wellplate_2.4ml_deep.json
@@ -0,0 +1,1116 @@
+{
+    "ordering": [
+      ["A1", "B1", "C1", "D1", "E1", "F1", "G1", "H1"],
+      ["A2", "B2", "C2", "D2", "E2", "F2", "G2", "H2"],
+      ["A3", "B3", "C3", "D3", "E3", "F3", "G3", "H3"],
+      ["A4", "B4", "C4", "D4", "E4", "F4", "G4", "H4"],
+      ["A5", "B5", "C5", "D5", "E5", "F5", "G5", "H5"],
+      ["A6", "B6", "C6", "D6", "E6", "F6", "G6", "H6"],
+      ["A7", "B7", "C7", "D7", "E7", "F7", "G7", "H7"],
+      ["A8", "B8", "C8", "D8", "E8", "F8", "G8", "H8"],
+      ["A9", "B9", "C9", "D9", "E9", "F9", "G9", "H9"],
+      ["A10", "B10", "C10", "D10", "E10", "F10", "G10", "H10"],
+      ["A11", "B11", "C11", "D11", "E11", "F11", "G11", "H11"],
+      ["A12", "B12", "C12", "D12", "E12", "F12", "G12", "H12"]
+    ],
+    "brand": {
+      "brand": "USA Scientific",
+      "brandId": ["1896-2000"],
+      "links": [
+        "https://www.usascientific.com/2ml-deep96-well-plateone-bulk.aspx"
+      ]
+    },
+    "metadata": {
+      "displayName": "USA Scientific 96 Deep Well Plate 2.4 mL",
+      "displayCategory": "wellPlate",
+      "displayVolumeUnits": "mL",
+      "tags": []
+    },
+    "dimensions": {
+      "xDimension": 127.8,
+      "yDimension": 85.5,
+      "zDimension": 44.1
+    },
+    "wells": {
+      "H1": {
+        "depth": 41.3,
+        "shape": "rectangular",
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+        "x": 14.4,
+        "y": 29.2,
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+        "shape": "rectangular",
+        "xDimension": 8.2,
+        "yDimension": 8.2,
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+    },
+    "groups": [
+      {
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+          "A1",
+          "B1",
+          "C1",
+          "D1",
+          "E1",
+          "F1",
+          "G1",
+          "H1",
+          "A2",
+          "B2",
+          "C2",
+          "D2",
+          "E2",
+          "F2",
+          "G2",
+          "H2",
+          "A3",
+          "B3",
+          "C3",
+          "D3",
+          "E3",
+          "F3",
+          "G3",
+          "H3",
+          "A4",
+          "B4",
+          "C4",
+          "D4",
+          "E4",
+          "F4",
+          "G4",
+          "H4",
+          "A5",
+          "B5",
+          "C5",
+          "D5",
+          "E5",
+          "F5",
+          "G5",
+          "H5",
+          "A6",
+          "B6",
+          "C6",
+          "D6",
+          "E6",
+          "F6",
+          "G6",
+          "H6",
+          "A7",
+          "B7",
+          "C7",
+          "D7",
+          "E7",
+          "F7",
+          "G7",
+          "H7",
+          "A8",
+          "B8",
+          "C8",
+          "D8",
+          "E8",
+          "F8",
+          "G8",
+          "H8",
+          "A9",
+          "B9",
+          "C9",
+          "D9",
+          "E9",
+          "F9",
+          "G9",
+          "H9",
+          "A10",
+          "B10",
+          "C10",
+          "D10",
+          "E10",
+          "F10",
+          "G10",
+          "H10",
+          "A11",
+          "B11",
+          "C11",
+          "D11",
+          "E11",
+          "F11",
+          "G11",
+          "H11",
+          "A12",
+          "B12",
+          "C12",
+          "D12",
+          "E12",
+          "F12",
+          "G12",
+          "H12"
+        ],
+        "metadata": {
+          "wellBottomShape": "u"
+        }
+      }
+    ],
+    "parameters": {
+      "format": "96Standard",
+      "isTiprack": false,
+      "isMagneticModuleCompatible": true,
+      "magneticModuleEngageHeight": 14.94,
+      "loadName": "usascientific_96_wellplate_2.4ml_deep"
+    },
+    "namespace": "opentrons",
+    "version": 1,
+    "schemaVersion": 2,
+    "cornerOffsetFromSlot": {
+      "x": 0,
+      "y": 0,
+      "z": 0
+    }
+  }
\ No newline at end of file
diff --git a/OT2-setup/setup/create-labware/visualise-labware-2.R b/OT2-setup/setup/create-labware/visualise-labware-2.R
new file mode 100644
index 0000000..8dfb981
--- /dev/null
+++ b/OT2-setup/setup/create-labware/visualise-labware-2.R
@@ -0,0 +1,213 @@
+# visualise-labware-2.R
+
+# This script generates plots for labware frames with wells based on CSV containing experiment data and corresponding labware JSON files.
+library(ggplot2)
+library(dplyr)
+library(rjson)
+library(ggforce)
+library(tidyverse)
+
+# This function reads and splits CSV data by different labwares determined by deck location
+read_and_split_csv <- function(csv_file_path) {
+  
+  labware_name = "transformation-parameters"
+  labware_file_path <- file.path("./data", paste0(labware_name, ".json")) # File path for the labware JSON file located in labware folder
+  json_data <- fromJSON(file = labware_file_path)
+
+
+  data <- read.csv(csv_file_path)
+
+  # Create the volume column
+  volume <- paste(data$dna_volume, "ul DNA,", data$cells_volume, "ul cells,", data$soc_volume, "ul SOC")
+
+  # Create a new dataframe with desired columns
+  labwares <- data.frame(
+    well_name = data$transformation_well,
+    dna_volume = data$dna_volume,
+    cells_volume = data$cells_volume,
+    soc_volume = data$soc_volume,
+    volume = volume,
+    reactant = volume,
+    location = "thermocycler",
+    labware = json_data$transformation_plate_name
+  )
+
+  split_labwares <- split(labwares, labwares$location)
+  return(split_labwares)
+}
+
+# Function to check if the labware JSON file exists and if only one labware per deck is specified
+check_labware_exists <- function(labware_name) {
+  if (length(labware_name) > 1) {
+    stop("There cannot be more than one plate on one deck.")
+  }
+  available_labware <- list.files(path = "./setup/create-labware/labware", pattern = ".json", full.names = FALSE)
+  available_labware_names <- tools::file_path_sans_ext(available_labware)
+  if (!labware_name %in% available_labware_names) {
+    stop("The provided labware name does not match any available labware. If using custom labware, add the JSON file to the labware folder.")
+  }
+}
+
+# This function gets the JSON file from the labware folder with all the dimensions of the specified labwares
+get_labware_json <- function(labware_dataframe) {
+  labware_name <- unique(labware_dataframe$labware)
+
+  # check_labware_exists(labware_name) # Check if labware exists and if there is only one labware per deck
+  labware_file_path <- file.path("./setup/create-labware/labware", paste0(labware_name, ".json")) # File path for the labware JSON file located in labware folder
+  json_data <- fromJSON(file = labware_file_path)
+  return(json_data)
+}
+
+# This function extracts well information from the JSON file
+extract_well_info <- function(well) {
+  # Determine the specific shape information based on the well shape
+  shape_info <- switch(
+    well$shape,
+    rectangular = list(well_x_dim = well$xDimension, well_y_dim = well$yDimension), # For rectangular wells, extract x and y dimensions
+    circular = list(diameter = well$diameter) # For circular wells, extract diameter
+  )
+  # Create a data frame containing well coordinates, shape, and shape-specific information
+  data.frame(
+    well_x_coord = well$x,
+    well_y_coord = well$y,
+    shape = well$shape, 
+    shape_info
+  )
+}
+
+# This function parses a JSON file containing labware information and extracts data for each well
+parse_labware_json <- function(json_data) {
+  # Apply the "extract_labware_json" function to get info for each well in the JSON file
+  labware_data <- lapply(json_data$wells, extract_well_info) %>% 
+    bind_rows(.id = "well_name") # Combine into one data frame by well_name as the id column
+  return(labware_data)
+}
+
+# This function merges the labware data extracted from the JSON file with the CSV data based on the common well
+map_wells_with_csv <- function(labware_data, csv_file) {
+  # Merge labware data with CSV data based on the common well
+  mapped_wells <- merge(labware_data, csv_file, by = "well_name", all.x = TRUE)
+  return(mapped_wells)
+}
+
+# This function creates a labware frame to which later the wells are added.
+plot_labware_frame <- function(merged_data, json_data, label, fill, title_size, legend_text_size, legend_key_size) {
+  # Create a base plot for the plate frame with wells
+
+  ggplot(merged_data, aes(well_x_coord, well_y_coord, fill = as.factor(!!rlang::sym(fill)), label = !!rlang::sym(label))) +
+    geom_rect(
+      aes(xmin = 0, xmax = json_data$dimensions$xDimension, ymin = 0, ymax = json_data$dimensions$yDimension), # Create a rectangle representing the plate frame
+      fill = NA, color = "black", linewidth = 0.5
+    ) +
+    labs(title = paste(json_data$metadata$displayName, "in slot", unique(merged_data$location[!is.na(merged_data$location)]))) +
+    theme_void() +
+    theme(
+      legend.position = "bottom",
+      legend.direction = "vertical",
+      legend.justification = "center",
+      legend.box = "horizontal",
+      legend.text = element_text(size = legend_text_size),
+      legend.title = element_blank(),
+      plot.title = element_text(size = title_size, hjust = 0.5)) +
+    guides(fill = guide_legend(override.aes = list(size = legend_key_size)))
+}
+
+# This function adds rectangular wells to the existing labware frame
+plot_rectangular_wells <- function(labware_frame, mapped_wells, max_y_wells, min_x_wells, label_size) {
+  labware_frame + 
+    geom_rect(
+      aes(xmin = well_x_coord - well_x_dim/2, xmax = well_x_coord + well_x_dim - well_x_dim/2, ymin = well_y_coord - well_y_dim/2, ymax = well_y_coord + well_y_dim - well_y_dim/2),
+      color = "black", size = 0.5
+    ) +
+    scale_fill_discrete(na.value = 'white', na.translate = FALSE) +
+    geom_text(
+      aes(x = well_x_coord, y = well_y_coord),
+      size = label_size,
+    ) +
+    geom_text(
+      data = max_y_wells,
+      aes(x = well_x_coord, y = well_y_coord + well_y_dim),
+      label = seq(1, nrow(max_y_wells)), size = 5
+    ) +
+    geom_text(
+      data = min_x_wells,
+      aes(x = well_x_coord - well_x_dim, y = well_y_coord),
+      label = LETTERS[1:nrow(min_x_wells)], size = 5
+    ) +
+    coord_fixed() # Fix aspect ratio
+}
+
+# This function adds circular wells to the existing labware frame
+plot_circular_wells <- function(labware_frame, mapped_wells, max_y_wells, min_x_wells, label_size) {
+  labware_frame + 
+    geom_point(
+      aes(x = well_x_coord, y = well_y_coord),
+      shape = 21, color = "black", size = mapped_wells$diameter*2.5
+    ) +
+    scale_fill_discrete(na.value = 'white', na.translate = FALSE) +
+    geom_text(
+      aes(x = well_x_coord, y = well_y_coord),
+      size = label_size
+    ) +
+    geom_text(
+      data = max_y_wells,
+      aes(x = well_x_coord, y = well_y_coord + diameter),
+      label = seq(1, nrow(max_y_wells)), size = 5
+    ) +
+    geom_text(
+      data = min_x_wells,
+      aes(x = well_x_coord - diameter, y = well_y_coord),
+      label = LETTERS[1:nrow(min_x_wells)], size = 5
+    ) +
+    coord_fixed() # Fix aspect ratio
+}
+
+# This function creates the final labware plot, combining both the labware frame and wells
+labware_plot <- function(mapped_wells, json_data, label, fill, title_size, label_size, legend_text_size, legend_key_size) {
+  labware_frame <- plot_labware_frame(mapped_wells, json_data, label, fill, title_size, legend_text_size, legend_key_size) # Create the base plot for the plate frame with wells
+  max_y_wells <- mapped_wells[mapped_wells$well_y_coord == max(mapped_wells$well_y_coord), ] %>% arrange(well_x_coord) # Extract wells with maximum y coordinates and arrange them by x coordinates (that is the first row to annotate with numbers)
+  min_x_wells <- mapped_wells[mapped_wells$well_x_coord == min(mapped_wells$well_x_coord), ] %>% arrange(desc(well_y_coord)) # Extract wells with minimum x coordinates and arrange them by y coordinates (that is the first column t annotate with letters)
+  
+  # Determine the shape of the wells (rectangular or circular)
+  shape <- unique(mapped_wells$shape)
+  if (length(shape) > 1) {
+    stop("Irregular shapes are not supported. All wells must have the same shape.")
+  }
+  
+  if (shape == "rectangular") {
+    plotted_labware <- plot_rectangular_wells(labware_frame, mapped_wells, max_y_wells, min_x_wells, label_size)
+  } else if (shape == "circular") {
+    plotted_labware <- plot_circular_wells(labware_frame, mapped_wells, max_y_wells, min_x_wells, label_size)
+  }
+  # Reorder reactant levels based on their appearance in the plot, so that the legend keys are in the correct order
+  plotted_labware$data$reactant <- factor(plotted_labware$data$reactant, levels = unique(plotted_labware$data$reactant))
+  return(plotted_labware)
+}
+
+# Main function to generate labware plots
+generate_labware_plots <- function(csv_file_path, output_folder, label = "well_name", fill = "reactant", title_size, label_size, legend_text_size, legend_key_size, plot_width = 25, plot_height = 20, plot_units = "cm") {
+  split_labwares <- read_and_split_csv(csv_file_path) # Create data frames for each unique labware-deck
+  # For each labware data frame run the following functions:
+  for (i in seq_along(split_labwares)) {
+    labware_info <- get_labware_json(split_labwares[[i]])
+    parsed_labware_info <- parse_labware_json(labware_info)
+    mapped_wells_data <- map_wells_with_csv(parsed_labware_info, split_labwares[[i]])
+    plotted_labware <- labware_plot(mapped_wells_data, labware_info, label, fill, title_size = 20, label_size = 5, legend_text_size = 20, legend_key_size = 10)
+
+    # Extract unique reactants and create a filename
+    deck_location <- unique(mapped_wells_data$location[!is.na(mapped_wells_data$location)])
+    filename_suffix <- paste(deck_location, collapse = "-")
+
+    # Save the plot with the corresponding filename
+    output_file <- file.path(output_folder, paste0("slot", filename_suffix, "-labware.png"))
+    ggsave(output_file, plotted_labware, width = plot_width, height = plot_height, units = plot_units, bg = "white")
+  }
+}
+
+# Command-line arguments
+args <- commandArgs(trailingOnly = TRUE)
+csv_file_path <- args[1]
+output_folder <- args[2]
+
+# Generate labware plots
+generate_labware_plots(csv_file_path, output_folder)
diff --git a/OT2-setup/setup/create-labware/visualise-labware.R b/OT2-setup/setup/create-labware/visualise-labware.R
new file mode 100644
index 0000000..12fd82a
--- /dev/null
+++ b/OT2-setup/setup/create-labware/visualise-labware.R
@@ -0,0 +1,214 @@
+# visualise-labware.R
+
+
+# This script generates plots for labware frames with wells based on CSV containing experiment data and corresponding labware JSON files.
+library(ggplot2)
+library(dplyr)
+library(rjson)
+library(ggforce)
+library(tidyverse)
+
+# This function reads and splits CSV data by different labwares determined by deck location
+read_and_split_csv <- function(csv_file_path) {
+  labwares <- read.csv(csv_file_path)
+  split_labwares <- split(labwares, labwares$location)
+  return(split_labwares)
+
+
+  labware_name = "transformation-parameters"
+  labware_file_path <- file.path("./data", paste0(labware_name, ".json")) # File path for the labware JSON file located in labware folder
+  json_data <- fromJSON(file = labware_file_path)
+
+
+  data <- read.csv(csv_file_path)
+
+  # Create the volume column
+  volume <- paste(data$dna_volume, "ul DNA,", data$cells_volume, "ul cells,", data$soc_volume, "ul SOC")
+
+  # Create a new dataframe with desired columns
+  labwares <- data.frame(
+    well_name = data$transformation_well,
+    dna_volume = data$dna_volume,
+    cells_volume = data$cells_volume,
+    soc_volume = data$soc_volume,
+    volume = volume,
+    reactant = volume,
+    location = "thermocycler",
+    labware = json_data$transformation_plate_name
+  )
+
+}
+
+# Function to check if the labware JSON file exists and if only one labware per deck is specified
+check_labware_exists <- function(labware_name) {
+  if (length(labware_name) > 1) {
+    stop("There cannot be more than one plate on one deck.")
+  }
+  available_labware <- list.files(path = "./setup/create-labware/labware", pattern = ".json", full.names = FALSE)
+  available_labware_names <- tools::file_path_sans_ext(available_labware)
+  if (!labware_name %in% available_labware_names) {
+    stop("The provided labware name does not match any available labware. If using custom labware, add the JSON file to the labware folder.")
+  }
+}
+
+# This function gets the JSON file from the labware folder with all the dimensions of the specified labwares
+get_labware_json <- function(labware_dataframe) {
+  labware_name <- unique(labware_dataframe$labware)
+  check_labware_exists(labware_name) # Check if labware exists and if there is only one labware per deck
+  labware_file_path <- file.path("./setup/create-labware/labware", paste0(labware_name, ".json")) # File path for the labware JSON file located in labware folder
+  json_data <- fromJSON(file = labware_file_path)
+  return(json_data)
+}
+
+# This function extracts well information from the JSON file
+extract_well_info <- function(well) {
+  # Determine the specific shape information based on the well shape
+  shape_info <- switch(
+    well$shape,
+    rectangular = list(well_x_dim = well$xDimension, well_y_dim = well$yDimension), # For rectangular wells, extract x and y dimensions
+    circular = list(diameter = well$diameter) # For circular wells, extract diameter
+  )
+  # Create a data frame containing well coordinates, shape, and shape-specific information
+  data.frame(
+    well_x_coord = well$x,
+    well_y_coord = well$y,
+    shape = well$shape, 
+    shape_info
+  )
+}
+
+# This function parses a JSON file containing labware information and extracts data for each well
+parse_labware_json <- function(json_data) {
+  # Apply the "extract_labware_json" function to get info for each well in the JSON file
+  labware_data <- lapply(json_data$wells, extract_well_info) %>% 
+    bind_rows(.id = "well_name") # Combine into one data frame by well_name as the id column
+  return(labware_data)
+}
+
+# This function merges the labware data extracted from the JSON file with the CSV data based on the common well
+map_wells_with_csv <- function(labware_data, csv_file) {
+  # Merge labware data with CSV data based on the common well
+  mapped_wells <- merge(labware_data, csv_file, by = "well_name", all.x = TRUE)
+  return(mapped_wells)
+}
+
+# This function creates a labware frame to which later the wells are added.
+plot_labware_frame <- function(merged_data, json_data, label, fill, title_size, legend_text_size, legend_key_size) {
+  # Create a base plot for the plate frame with wells
+  ggplot(merged_data, aes(well_x_coord, well_y_coord, fill = as.factor(!!rlang::sym(fill)), label = !!rlang::sym(label))) +
+    geom_rect(
+      aes(xmin = 0, xmax = json_data$dimensions$xDimension, ymin = 0, ymax = json_data$dimensions$yDimension), # Create a rectangle representing the plate frame
+      fill = NA, color = "black", linewidth = 0.5
+    ) +
+    labs(title = paste(json_data$metadata$displayName, "in slot", unique(merged_data$location[!is.na(merged_data$location)]))) +
+    theme_void() +
+    theme(
+      legend.position = "bottom",
+      legend.justification = "center",
+      legend.box = "horizontal",
+      legend.text = element_text(size = legend_text_size),
+      legend.title = element_blank(),
+      plot.title = element_text(size = title_size, hjust = 0.5)) +
+    guides(fill = guide_legend(override.aes = list(size = legend_key_size)))
+}
+
+# This function adds rectangular wells to the existing labware frame
+plot_rectangular_wells <- function(labware_frame, mapped_wells, max_y_wells, min_x_wells, label_size) {
+  labware_frame + 
+    geom_rect(
+      aes(xmin = well_x_coord - well_x_dim/2, xmax = well_x_coord + well_x_dim - well_x_dim/2, ymin = well_y_coord - well_y_dim/2, ymax = well_y_coord + well_y_dim - well_y_dim/2),
+      color = "black", size = 0.5
+    ) +
+    scale_fill_discrete(na.value = 'white', na.translate = FALSE) +
+    geom_text(
+      aes(x = well_x_coord, y = well_y_coord),
+      size = label_size,
+    ) +
+    geom_text(
+      data = max_y_wells,
+      aes(x = well_x_coord, y = well_y_coord + well_y_dim),
+      label = seq(1, nrow(max_y_wells)), size = 5
+    ) +
+    geom_text(
+      data = min_x_wells,
+      aes(x = well_x_coord - well_x_dim, y = well_y_coord),
+      label = LETTERS[1:nrow(min_x_wells)], size = 5
+    ) +
+    coord_fixed() # Fix aspect ratio
+}
+
+# This function adds circular wells to the existing labware frame
+plot_circular_wells <- function(labware_frame, mapped_wells, max_y_wells, min_x_wells, label_size) {
+  labware_frame + 
+    geom_point(
+      aes(x = well_x_coord, y = well_y_coord),
+      shape = 21, color = "black", size = mapped_wells$diameter*2.5
+    ) +
+    scale_fill_discrete(na.value = 'white', na.translate = FALSE) +
+    geom_text(
+      aes(x = well_x_coord, y = well_y_coord),
+      size = label_size
+    ) +
+    geom_text(
+      data = max_y_wells,
+      aes(x = well_x_coord, y = well_y_coord + diameter),
+      label = seq(1, nrow(max_y_wells)), size = 5
+    ) +
+    geom_text(
+      data = min_x_wells,
+      aes(x = well_x_coord - diameter, y = well_y_coord),
+      label = LETTERS[1:nrow(min_x_wells)], size = 5
+    ) +
+    coord_fixed() # Fix aspect ratio
+}
+
+# This function creates the final labware plot, combining both the labware frame and wells
+labware_plot <- function(mapped_wells, json_data, label, fill, title_size, label_size, legend_text_size, legend_key_size) {
+  labware_frame <- plot_labware_frame(mapped_wells, json_data, label, fill, title_size, legend_text_size, legend_key_size) # Create the base plot for the plate frame with wells
+  max_y_wells <- mapped_wells[mapped_wells$well_y_coord == max(mapped_wells$well_y_coord), ] %>% arrange(well_x_coord) # Extract wells with maximum y coordinates and arrange them by x coordinates (that is the first row to annotate with numbers)
+  min_x_wells <- mapped_wells[mapped_wells$well_x_coord == min(mapped_wells$well_x_coord), ] %>% arrange(desc(well_y_coord)) # Extract wells with minimum x coordinates and arrange them by y coordinates (that is the first column t annotate with letters)
+  
+  # Determine the shape of the wells (rectangular or circular)
+  shape <- unique(mapped_wells$shape)
+  if (length(shape) > 1) {
+    stop("Irregular shapes are not supported. All wells must have the same shape.")
+  }
+  
+  if (shape == "rectangular") {
+    plotted_labware <- plot_rectangular_wells(labware_frame, mapped_wells, max_y_wells, min_x_wells, label_size)
+  } else if (shape == "circular") {
+    plotted_labware <- plot_circular_wells(labware_frame, mapped_wells, max_y_wells, min_x_wells, label_size)
+  }
+  # Reorder reactant levels based on their appearance in the plot, so that the legend keys are in the correct order
+  plotted_labware$data$reactant <- factor(plotted_labware$data$reactant, levels = unique(plotted_labware$data$reactant))
+  return(plotted_labware)
+}
+
+# Main function to generate labware plots
+generate_labware_plots <- function(csv_file_path, output_folder, label = "volume", fill = "reactant", title_size, label_size, legend_text_size = 5, legend_key_size, plot_width = 25, plot_height = 20, plot_units = "cm") {
+  split_labwares <- read_and_split_csv(csv_file_path) # Create data frames for each unique labware-deck
+  
+  # For each labware data frame run the following functions:
+  for (i in seq_along(split_labwares)) {
+    labware_info <- get_labware_json(split_labwares[[i]])
+    parsed_labware_info <- parse_labware_json(labware_info)
+    mapped_wells_data <- map_wells_with_csv(parsed_labware_info, split_labwares[[i]])
+    plotted_labware <- labware_plot(mapped_wells_data, labware_info, label, fill, title_size = 20, label_size = 5, legend_text_size = 20, legend_key_size = 10)
+    
+    # Extract unique reactants and create a filename
+    deck_location <- unique(mapped_wells_data$location[!is.na(mapped_wells_data$location)])
+    filename_suffix <- paste(deck_location, collapse = "-")
+    
+    # Save the plot with the corresponding filename
+    output_file <- file.path(output_folder, paste0("slot", filename_suffix, "-labware.png"))
+    ggsave(output_file, plotted_labware, width = plot_width, height = plot_height, units = plot_units, bg = "white")
+  }
+}
+
+# Command-line arguments
+args <- commandArgs(trailingOnly = TRUE)
+csv_file_path <- args[1]
+output_folder <- args[2]
+
+# Generate labware plots
+generate_labware_plots(csv_file_path, output_folder)
\ No newline at end of file
diff --git a/OT2-setup/setup/instruction-templates/transformation-instruction.R b/OT2-setup/setup/instruction-templates/transformation-instruction.R
new file mode 100644
index 0000000..f818f5a
--- /dev/null
+++ b/OT2-setup/setup/instruction-templates/transformation-instruction.R
@@ -0,0 +1,93 @@
+# Load required libraries
+library(jsonlite)
+library(gridExtra)
+library(grid)
+library(png)
+
+insert_overview <- function(data, x_margin, y_initial, y_spacing, font_size) {
+  grid.text("E. coli Transformation in OT-2", x = x_margin, y = y_initial, just = "left", gp = gpar(fontsize = font_size + 4, fontface = "bold"))
+  overview <- c("Quick Overview",
+                paste("Add DNA into competent cells in thermocycler."),
+                paste("Incubate the cells at", data$init_temp, "°C for", data$init_time, "minutes."),
+                paste("Heat-shock the cells at", data$heat_temp, "°C for", data$heat_time, "seconds."),
+                paste("Incubate the cells at", data$cool_temp, "°C for", data$cool_time, "minutes."),
+                paste("Add the recovery medium and incubate cells at", data$inc_temp, "°C for", data$inc_time, "minutes."))
+  overview_y_lines <- (y_initial - 2*y_spacing) - seq(0, length(overview) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(overview) - 1)))
+  grid.text(overview, x = x_margin, y = overview_y_lines, just = "left", gp = text_style)
+  return(overview_y_lines[length(overview_y_lines)]-y_spacing)
+}
+
+insert_preparation<- function(x_margin, y_initial, y_spacing) {
+  preparation <- c("Reagents preparation",
+                   "Prepare the reagents and labware according to the below diagrams.",
+                   "Volumes (uL) indicate how much of reagents will be used, so add additional volume.")
+  preparation_y_lines <- y_initial - y_spacing * (1:length(preparation))
+  text_style <- gpar(fontsize = 12, fontface = c("bold", rep("plain", length(preparation) - 1)))
+  grid.text(preparation, x = x_margin, y = preparation_y_lines, just = "left", gp = text_style)
+  return(preparation_y_lines[length(preparation_y_lines)]-y_spacing)
+}
+
+insert_labware <- function(folder_path, width, height, x_margin, y_initial, y_spacing) {
+  image_files <- list.files(folder_path, pattern = "^slot", full.names = TRUE)
+  num_images <- length(image_files)
+  positions <- list()
+  # Generate positions
+  for (i in 1:num_images) {
+    # Calculate position based on index
+    x <- x_margin + width/2 + ((i - 1) %% 2) * width
+    y <- y_initial - height/2 + floor((i - 1) / 2) * - height
+    positions[[i]] <- list(x = x, y = y)
+  }
+  
+  # Insert each image into the PDF
+  for (i in seq_along(image_files)) {
+    if (file.exists(image_files[i])) {
+      image <- readPNG(image_files[i])
+      position <- positions[[i]]
+      grid.raster(image, x = position$x, y = position$y, width = width, height = height)
+    }
+  }
+  
+  return(positions[[num_images]]$y - height/2 - y_spacing)
+}
+
+insert_deck_loading <- function(data, x_margin, y_initial, font_size, y_spacing) {
+  deck <- c("Deck Loading Instructions",
+                paste("Check that", data$right_pipette_name, "is in the right mount, and", data$left_pipette_name, "is in the left mount." ),
+                paste("Slot", paste(data$right_pipette_tiprack_slots, collapse = ", "), ": load", data$right_pipette_tiprack_name, "for the", data$right_pipette_name, "pipette."),
+                paste("Slot", paste(data$left_pipette_tiprack_slots, collapse = ", "), ": load", data$left_pipette_tiprack_name, "for the", data$left_pipette_name, "pipette."),
+                paste("Slot", data$dna_plate_slot, ": load", data$dna_plate_name, " containing DNA."),
+                paste("Slot", data$cells_plate_slot, ": load", data$cells_plate_name, " containing cells."),
+                paste("Slot", data$soc_plate_slot, ": load", data$soc_plate_name, " containing SOC."),
+                paste("Slot 7,8,10,11: load a thermocycler and turn it on."),
+                paste("Thermocycler: load", data$transformation_plate_name, "when instructed on the screen."))
+  deck_y_lines <- y_initial - seq(0, length(deck) - 1) * y_spacing
+  text_style <- gpar(fontsize = font_size, fontface = c("bold", rep("plain", length(deck) - 1)))
+  grid.text(deck, x = x_margin, y = deck_y_lines, just = "left", gp = text_style)
+}
+
+instructions <- function(json_file_path = "./data/transformation-parameters.json", output_file = "./results/Instructions.pdf", x_margin = 0.05, y_spacing = 0.02, labware_width = 0.45, labware_height = 0.27, font_size = 12, y_initial = 0.98) {
+
+  pdf(output_file, width = 8.5, height = 11)
+  par(mar = c(5, 4, 4, 2) + 0.1)
+  json_data <- fromJSON(json_file_path)
+
+  overview <- insert_overview(json_data, x_margin, y_initial, y_spacing, font_size) # Title and Overview
+  preparation <- insert_preparation(x_margin, overview, y_spacing)   # Reagents preparation
+
+
+  labware <- insert_labware("./results", labware_width, labware_height, x_margin, preparation, y_spacing)   # # Insert images and get coordinates
+  deck_loading <- insert_deck_loading(json_data, x_margin, labware, font_size, y_spacing)
+
+  dev.off()
+  
+}
+
+# Command-line arguments
+args <- commandArgs(trailingOnly = TRUE)
+json_file_path <- args[1]
+output_file <- args[2]
+
+# Generateinstructions
+instructions(json_file_path, output_file)
\ No newline at end of file
diff --git a/OT2-setup/setup/protocol-templates/spotting-template.py b/OT2-setup/setup/protocol-templates/spotting-template.py
new file mode 100644
index 0000000..c5e128b
--- /dev/null
+++ b/OT2-setup/setup/protocol-templates/spotting-template.py
@@ -0,0 +1,109 @@
+from opentrons import protocol_api
+import math
+import csv
+import json
+import collections
+
+
+metadata = {
+    'apiLevel': '2.15',
+    'protocolName': 'agar-plate-spotting',
+    'description': 'Protocol for agar plate spotting.',
+    'author': 'Martyna Kasprzyk'
+}
+
+
+def get_parameters(json_file: str) -> dict:
+    """
+    This function parses the json file with the parameters for the experiment and returns them as a dictionary.
+    """
+    parameters = json.loads(json_file) # load and parse the paraemter json file
+    return parameters
+
+def read_csv_file(csv_file):
+
+    csv_data = csv_file.splitlines()[1:] # Discard the blank first line.
+    csv_reader = csv.DictReader(csv_data)
+    
+
+    # if multi channel
+    seen_numbers = {}
+    result_rows = []
+        
+    for row in csv_reader:
+            well = row['source_well']
+            letter, number = well[0], well[1:]
+
+            # Check if the number is already associated with a different letter
+            if number in seen_numbers and seen_numbers[number] != letter:
+                continue
+
+            result_rows.append(row)
+            seen_numbers[number] = letter
+
+    plate_locations = []
+    source_wells = []
+    destination_wells = []
+    spotting_volume = []
+    agar_plate_weight = []
+
+    for row in result_rows:
+
+        if row['plate_location'] not in plate_locations:
+             plate_locations.append(int(row['plate_location']))
+        
+        source_wells.append(row['source_well'])
+        destination_wells.append(row['destination_well'])
+        spotting_volume.append(int(row['spotting_volume']))
+        agar_plate_weight.append(float(row['plate_weight']))
+
+    # print(f"{plate_locations},{source_wells},{destination_wells},{spotting_volume}")
+    csv_parameters = collections.namedtuple("csv_parameters", ["plate_locations", "source_wells", "destination_wells", "spotting_volume", "agar_plate_weight"])
+
+    return csv_parameters(plate_locations, source_wells, destination_wells, spotting_volume, agar_plate_weight)
+
+def agar_height(agar_plate_weight, just_plate, agar_density,spotting_height):
+    bottom_area = math.pi*(83.5/2)**2
+    agar_weight = agar_plate_weight - float(just_plate)
+    agar_height = agar_weight/(bottom_area*agar_density)
+    spotting_height = agar_height + spotting_height
+    print(agar_weight)
+    print(spotting_height)
+
+    return spotting_height
+
+# run protocol
+def run(protocol: protocol_api.ProtocolContext):
+    """
+    Main function for running the protocol.
+    """
+    
+    params = get_parameters(parameters_json) # load the parameters from the json file
+    csv_params = read_csv_file(csv_file)
+
+    # loading hardware and labware
+    pipette_tipracks = [protocol.load_labware(load_name=params["pipette_tiprack_name"], location=i) for i in params["pipette_tiprack_slots"]]
+    pipette = protocol.load_instrument(instrument_name=params["pipette_name"], mount=params["pipette_mount"], tip_racks=pipette_tipracks) # p20 pipette
+    
+    # source plate located in the thermocycler
+    thermocycler_mod = protocol.load_module("thermocycler")  # thermocycler module, takes location 7,8,10,11
+    transformation_plate = thermocycler_mod.load_labware(params["transformation_plate_name"]) # plate where transformations take place, loaded onto  thermocycler module
+
+    # Extract the plate locations into a list
+    agar_plates = [protocol.load_labware(load_name=params["agar_plate_name"],
+                                         location=slot,
+                                         label=f"Agar Plate {str(i+1)}") 
+                                         for i, slot in enumerate(csv_params.plate_locations)]
+
+    # protocol.comment(f"{agar_plates}")
+    thermocycler_mod.open_lid()
+    ######### SPOTTING ##########
+    for plate, source, destination, volume, weight in zip(agar_plates, csv_params.source_wells, csv_params.destination_wells, csv_params.spotting_volume, csv_params.agar_plate_weight):
+        pipette.well_bottom_clearance.dispense = 1
+        pipette.pick_up_tip()
+        pipette.mix(repetitions=3, volume=5, location=transformation_plate[source], rate=2)
+        pipette.aspirate(volume=volume + params["dead_volume"], location=transformation_plate[source], rate=2)
+        pipette.well_bottom_clearance.dispense = agar_height(weight, params["plate_weight"], params["agar_density"], params["spotting_height"])
+        pipette.dispense(volume=volume, location=plate[destination], rate=4)
+        protocol.delay(seconds=5)
+        pipette.drop_tip()
\ No newline at end of file
diff --git a/OT2-setup/setup/protocol-templates/transformation-template.py b/OT2-setup/setup/protocol-templates/transformation-template.py
new file mode 100644
index 0000000..316fb09
--- /dev/null
+++ b/OT2-setup/setup/protocol-templates/transformation-template.py
@@ -0,0 +1,166 @@
+from opentrons import protocol_api
+import json
+import csv
+import collections
+
+metadata = {
+    "apiLevel": "2.13",
+    "protocolName": "E. coli heatshock transformation",
+    "description": "OT-2 protocol for standard E. coli heatshock transformation.",
+    "author": "Martyna Kasprzyk",
+}
+
+def read_csv_file(csv_file):
+
+    csv_data = csv_file.splitlines()[1:] # Discard the blank first line.
+    csv_reader = csv.DictReader(csv_data)
+
+    # if multi channel
+    seen_numbers = {}
+    result_rows = []
+        
+    for row in csv_reader:
+            well = row['dna_well']
+            letter, number = well[0], well[1:]
+
+            # Check if the number is already associated with a different letter
+            if number in seen_numbers and seen_numbers[number] != letter:
+                continue
+
+            result_rows.append(row)
+            seen_numbers[number] = letter
+
+    cells_source_wells = []
+    cells_volume = []
+    dna_source_wells = []
+    dna_volume = []
+    soc_source_wells = []
+    soc_volume = []
+    transformation_well = []
+
+    for row in result_rows:
+        cells_source_wells.append(row['cells_well'])
+        cells_volume.append(int(row["cells_volume"]))
+        dna_source_wells.append(row['dna_well'])
+        dna_volume.append(int(row["dna_volume"]))
+        soc_source_wells.append(row['soc_well'])
+        soc_volume.append(int(row["soc_volume"]))
+        transformation_well.append(row["transformation_well"])
+
+    csv_parameters = collections.namedtuple("csv_parameters", ["cells_source_wells", "cells_volume", "dna_source_wells", "dna_volume", "soc_source_wells", "soc_volume", "transformation_well"])
+
+    return csv_parameters(cells_source_wells, cells_volume, dna_source_wells, dna_volume, soc_source_wells, soc_volume, transformation_well)
+
+
+def get_parameters(json_file: str) -> dict:
+    """
+    This function parses the json file with the parameters for the experiment and returns them as a dictionary.
+    """
+    parameters = json.loads(json_file) # load and parse the paraemter json file
+    return parameters
+
+def run(protocol: protocol_api.ProtocolContext):
+    """
+    Main function for running the protocol.
+    """
+
+    params = get_parameters(parameters_json) # load the parameters from the json file
+    csv_params = read_csv_file(csv_file)
+
+    # loading hardware and labware
+    source_plate = protocol.load_labware(params["dna_plate_name"], params["dna_plate_slot"]) # plate containing dna to be transformed
+    thermocycler_mod = protocol.load_module("thermocycler")  # thermocycler module, takes location 7,8,10,11
+    transformation_plate = thermocycler_mod.load_labware(params["transformation_plate_name"]) # plate where transformations take place, loaded onto  thermocycler module
+
+    pipette_1_tipracks = [protocol.load_labware(load_name=params["pipette_1_tiprack_name"], location=i) for i in params["pipette_1_tiprack_slots"]]
+    pipette_1 = protocol.load_instrument(instrument_name=params["pipette_1_name"], mount=params["pipette_1_mount"], tip_racks=pipette_1_tipracks) # p20 pipette
+
+    pipette_2_tipracks = [protocol.load_labware(load_name=params["pipette_2_tiprack_name"], location=i) for i in params["pipette_2_tiprack_slots"]]
+    pipette_2 = protocol.load_instrument(instrument_name=params["pipette_2_name"], mount=params["pipette_2_mount"], tip_racks=pipette_2_tipracks) # p300 pipette
+
+    # loading liquid handling settings
+    pipette_2.flow_rate.aspirate = 10 # aspirate speed of the pipette
+    pipette_2.flow_rate.dispense = 10 # dispense speed of the pipette
+
+    ########## HEAT-SHOCK TRANSFORMATION ##########
+    protocol.comment("Starting heat-shock transformation.")
+    protocol.set_rail_lights(True)
+
+    # step 1: Preheat the module and open lid.
+    thermocycler_mod.set_block_temperature(temperature=params["init_temp"])
+    thermocycler_mod.open_lid()
+
+    # step 2: Transferring competent cells into the transformation plate.
+    protocol.pause("Put plate on the thermocycler module and click 'resume'.") # wait for operator to put the plate
+
+    pipette_2.distribute(volume=csv_params.cells_volume, # volume of competent cells to be transferred
+                    source=[source_plate.wells_by_name()[well] for well in csv_params.cells_source_wells], # transfer from the specified well in the resevoir containing competent cells
+                    dest=[transformation_plate.wells_by_name()[well] for well in csv_params.transformation_well], # transfer to transformation plate in the thermocycler
+                    mix_before=(1,50)) # resuspend the competent cells once before transfering into the transformation plate with the total volume to be trasfered, volume not specified sets the default to the max volume of pipette
+
+    # step 3: Transfer DNA into wells of the transformation plate.
+    pipette_1.well_bottom_clearance.aspirate = 0.5 # aspiration height of the pipette (when volume of DNA is low)
+    
+    for i in zip(csv_params.dna_source_wells, csv_params.transformation_well, csv_params.dna_volume, csv_params.cells_volume):
+        pipette_1.pick_up_tip()
+        pipette_1.well_bottom_clearance.aspirate = 0.5  
+        pipette_1.aspirate(volume=i[2], location=source_plate.wells_by_name()[i[0]])
+        pipette_1.well_bottom_clearance.aspirate = 1
+        pipette_1.dispense(volume=i[2], location=transformation_plate.wells_by_name()[i[1]])
+        mixing_volume = (i[2]+i[3])/2
+        pipette_1.aspirate(volume=mixing_volume, location=transformation_plate.wells_by_name()[i[1]])
+        pipette_1.dispense(volume=mixing_volume, location=transformation_plate.wells_by_name()[i[1]])
+        pipette_1.aspirate(volume=mixing_volume, location=transformation_plate.wells_by_name()[i[1]])
+        pipette_1.dispense(volume=mixing_volume, location=transformation_plate.wells_by_name()[i[1]])
+        pipette_1.blow_out(location=transformation_plate.wells_by_name()[i[1]])
+        pipette_1.move_to(transformation_plate.wells_by_name()[i[1]].bottom())
+        pipette_1.drop_tip()
+
+    # step 4: Close the thermocycler lid and cool the thermocycler down for specified temperature and time, deafult: 4 degrees celcius and 20 minutes
+    thermocycler_mod.close_lid()
+    thermocycler_mod.set_block_temperature(temperature=params["init_temp"], 
+                                           hold_time_minutes=params["init_time"])
+    
+    # step 5: Perform heat-shock transformation for specified temperature and time, deafult: 42 degrees celcius and 1 minute
+    protocol.comment("Starting heat-shock transformation.")
+    thermocycler_mod.set_block_temperature(temperature=params["heat_temp"], 
+                                           hold_time_seconds=params["heat_time"])
+    
+    # step 6: Cool down thermocycler for specified temperature and time, default: 4 degrees celcius and 2 minutes.
+    protocol.comment("Cool down thermocycler to 4C post heatshock")
+    thermocycler_mod.set_block_temperature(temperature=params["cool_temp"],
+                                           hold_time_minutes=params["cool_time"])
+    
+    pipette_2.flow_rate.aspirate = 15 # aspirate speed of the pipette
+    pipette_2.flow_rate.dispense = 15 # dispense speed of the pipette
+    
+    # step 7: Open the thermocycler lid and transfer SOC media to transformed cells.
+    thermocycler_mod.open_lid()
+
+    for i in zip(csv_params.soc_source_wells, csv_params.transformation_well, csv_params.soc_volume, csv_params.dna_volume, csv_params.cells_volume):
+        pipette_2.pick_up_tip()
+        pipette_2.aspirate(volume=i[2], location=source_plate.wells_by_name()[i[0]])
+        pipette_2.dispense(volume=i[2], location=transformation_plate.wells_by_name()[i[1]])
+        mixing_volume = (i[2]+i[3]+i[4])/2
+        for _ in range(3):
+            pipette_2.aspirate(volume=mixing_volume, location=transformation_plate.wells_by_name()[i[1]])
+            pipette_2.dispense(volume=mixing_volume, location=transformation_plate.wells_by_name()[i[1]])
+            
+        pipette_2.blow_out(location=transformation_plate.wells_by_name()[i[1]])
+        pipette_2.move_to(transformation_plate.wells_by_name()[i[1]].bottom())
+        pipette_2.drop_tip()
+
+    # step 8: Close the thermocycler lid and heat up both thermocycler block and lid for specified temperature and time, default: 37 celcius degrees and 60 minutes
+    thermocycler_mod.close_lid()
+    thermocycler_mod.set_lid_temperature(temperature=params["inc_temp"])
+    thermocycler_mod.set_block_temperature(temperature=params["inc_temp"], 
+                                           hold_time_minutes=params["inc_time"])
+    protocol.comment("Starting incubation.")
+    protocol.set_rail_lights(False)
+    
+    # step 9: Finish incubation and deactivate the thermocycler module.
+    protocol.comment("Incubation finished.")
+    thermocycler_mod.deactivate_lid()
+    thermocycler_mod.deactivate()
+
+    protocol.comment("Run complete!")
\ No newline at end of file
diff --git a/parameters.json b/parameters.json
deleted file mode 100644
index e69cae5..0000000
--- a/parameters.json
+++ /dev/null
@@ -1,43 +0,0 @@
-{
-    "transformations_n":24,
-    "dna_volume":2,
-    "cc_volume":20,
-    "soc_volume":178,
-    "competent_cells_well": "H12",
-    "init_temp":4,
-    "init_time":20,
-    "heat_temp":42,
-    "heat_time":1,
-    "cool_temp":4,
-    "cool_time":2,
-    "inc_temp":37,
-    "inc_time":60,
-    "spot_volume":5,
-    
-    "dna_plate_loadname":"armadillo_96_wellplate_200ul_pcr_full_skirt",
-    "dna_plate_slot":2,
-    "reservoir_loadname": "usascientific_96_wellplate_2.4ml_deep",
-    "reservoir_slot":3,
-    "transformation_plate_loadname":"armadillo_96_wellplate_200ul_pcr_full_skirt",
-    "agar_plate_loadname":"nunc_singlewell_plate_90ml_4x6_grid",
-    "agar_def_json": "nunc_singlewell_plate_90ml_4x6_grid.json",
-    "agar_max_wells_n":24,
-    "agar_slot":[1],
-    "p20_tiprack_loadname":"opentrons_96_tiprack_20ul",
-    "p20_tiprack_slot":6,
-    "p20_name":"p20_single_gen2",
-    "p20_mount":"right",
-    "p300_tiprack_loadname":"opentrons_96_tiprack_300ul",
-    "p300_tiprack_slot":9,
-    "p300_name":"p300_multi_gen2",
-    "p300_mount":"left",
-
-    "dispense_rate":60,
-    "aspirate_rate":60,
-    "agar_dispense_height":10.2,
-
-    "test_dispense_height":false,
-    "agar_incubation":false,
-    "temp_mod_slot":4,
-    "agar_incubation_temp":37
-}
\ No newline at end of file