Skip to content

Commit

Permalink
fix comments
Browse files Browse the repository at this point in the history
  • Loading branch information
@m-kasprzyk
m-kasprzyk committed Aug 13, 2024
1 parent 922de13 commit fa726b4
Show file tree
Hide file tree
Showing 13 changed files with 213 additions and 498 deletions.
38 changes: 18 additions & 20 deletions assets/instructions/protocol-1-instructions.Rmd
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
---
title: "Instructions"
title: "APEX Instructions"
output: pdf_document
params:
json_path: NULL
Expand All @@ -13,28 +13,26 @@ library(knitr)
json_data <- fromJSON(file = params$json_path)
```
\vspace{-1.5cm}
## Protocol 1: Heat shock transformations
## Protocol 1: Heat Shock Transformations in OT-2

### Overview
DNA is transferred to competent cells.
Pre heat-shock, the cells and added DNA are incubated at `r json_data$pre_shock_incubation_temp` °C for `r json_data$pre_shock_incubation_time` minutes.
Heat-shock is carried out at `r json_data$heat_shock_temp` °C for `r json_data$heat_shock_time` seconds.
Post heat-shock, the transformed cells are incubated at `r json_data$post_shock_incubation_temp` °C for `r json_data$post_shock_incubation_time` minutes.
The recovery medium is added and cells are incubated at `r json_data$recovery_temp`°C for `r json_data$recovery_time` minutes.
Competent cells are distributed into destination plate.
DNA is added to competent cells.
Pre heat shock, the cells and added DNA are incubated at `r json_data$pre_shock_incubation_temp` °C for `r json_data$pre_shock_incubation_time` minutes.
Heat shock is carried out at `r json_data$heat_shock_temp` °C for `r json_data$heat_shock_time` seconds.
Post heat shock, the cells are incubated at `r json_data$post_shock_incubation_temp` °C for `r json_data$post_shock_incubation_time` minutes.
The recovery medium is added and cells are incubated at `r json_data$recovery_temp` °C for `r json_data$recovery_time` minutes.

### 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.
Prepare the necessary reagents and labware as outlined in the layout provided below.
Listed volumes are in `r "$\\mu$L"` and indicate the amount of each reagent required.
Ensure to include an additional volume.

```{r import-labware-images, results='asis', echo=FALSE}
# Read all image files from the directory
image_files <- list.files(path = params$labware_images_dir, pattern = "\\.png$", full.names = TRUE)
# Sort files numerically and alphabetically
image_files <- sort(image_files)
# Print images in Markdown format, 2 per row
for (i in seq_along(image_files)) {
# Start a new line for every pair of images
if (i %% 2 == 1 && i > 1) {
cat('\\newline\n')
}
Expand All @@ -48,10 +46,10 @@ for (i in seq_along(image_files)) {
```

### Deck Loading
Check that `r json_data$right_pipette_name` is in the right mount and `r json_data$left_pipette_name` is in the left mount.
**Slot `r json_data$right_pipette_tiprack_slot`** load `r json_data$right_pipette_tiprack_name` for the `r json_data$right_pipette_name` pipette.
**Slot `r json_data$left_pipette_tiprack_slot`** load `r json_data$left_pipette_tiprack_name` for the `r json_data$left_pipette_name` pipette.
**Slot `r json_data$dna_plate_slot`** load `r json_data$dna_plate_name` containing DNA.
**Slot `r json_data$cells_plate_slot`** load `r json_data$cells_plate_name` containing competent cells.
**Slot `r json_data$media_plate_slot`** load `r json_data$media_plate_name` containing recovery medium.
**Slot 7,8,10,11** load a thermocycler and turn it on. Load `r json_data$transformation_plate_name` into the thermocycler when instructed on the screen.
Check that `r json_data$right_pipette_name` is in the right mount and `r json_data$left_pipette_name` is in the left mount.
**Slot `r json_data$right_pipette_tiprack_slot`** load `r json_data$right_pipette_tiprack_name` for the `r json_data$right_pipette_name` pipette.
**Slot `r json_data$left_pipette_tiprack_slot`** load `r json_data$left_pipette_tiprack_name` for the `r json_data$left_pipette_name` pipette.
**Slot `r json_data$dna_plate_slot`** load `r json_data$dna_plate_name` containing DNA.
**Slot `r json_data$cells_plate_slot`** load `r json_data$cells_plate_name` containing competent cells.
**Slot `r json_data$media_plate_slot`** load `r json_data$media_plate_name` containing recovery medium.
**Slot 7,8,10,11** load a thermocycler and turn it on. Load `r json_data$transformation_plate_name` into the thermocycler when instructed on the screen.
26 changes: 11 additions & 15 deletions assets/instructions/protocol-2-instructions.Rmd
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
---
title: "Instructions"
title: "APEX Instructions"
output: pdf_document
params:
json_path: NULL
Expand All @@ -13,28 +13,24 @@ library(knitr)
json_data <- fromJSON(file = params$json_path)
```
\vspace{-1.5cm}
## Protocol 2: Colony selection
## Protocol 2: Colony Selection in OT-2

### Overview
Transformed cells are spotted on the total of `r length(json_data$agar_plate_slot) ` agar plates.
Cells are spotted on the total of `r length(json_data$agar_plate_slot) ` agar plates.
The pipette aspirates additional `r json_data$additional_volume` $\mu$L of transformed cells.
The spotting height above the agar is set at `r json_data$spotting_height` mm.
The spotting height above the agar is set at `r json_data$spotting_height` (mm).
The agar height is calculated automatically per plate based on:
the plate weight without agar and with agar (g),
and agar density of `r json_data$agar_density`($g mm^{-3}$).
the plate weight without (`r json_data$empty_agar_plate_weight` g) and with agar (`r json_data$agar_plate_weight` g),
and agar density of `r json_data$agar_density` ($g cm^{-3}$).

### Preparation
The plates are spotted in uL according to the layout below.
The plates are spotted in `r "$\\mu$L"` according to the layout below.

```{r import-labware-images, results='asis', echo=FALSE}
# Read all image files from the directory
image_files <- list.files(path = params$labware_images_dir, pattern = "\\.png$", full.names = TRUE)
# Sort files numerically and alphabetically
image_files <- sort(image_files)
# Print images in Markdown format, 2 per row
for (i in seq_along(image_files)) {
# Start a new line for every pair of images
if (i %% 2 == 1 && i > 1) {
cat('\\newline\n')
}
Expand All @@ -48,7 +44,7 @@ for (i in seq_along(image_files)) {
```

### Deck Loading
Check that `r json_data$pipette_name` is in the `r json_data$pipette_mount` mount.
**Slot `r json_data$tiprack_slots`** load `r json_data$tiprack_name` for the `r json_data$pipette_name` pipette.
**Slot `r json_data$agar_plate_slot`** load `r json_data$agar_plate_name` containing agar.
**Slot `r json_data$source_plate_slot`** load `r json_data$source_plate_name` containing transformed cells.
Check that `r json_data$pipette_name` is in the `r json_data$pipette_mount` mount.
**Slot `r json_data$tiprack_slots`** load `r json_data$tiprack_name` for the `r json_data$pipette_name` pipette.
**Slot `r json_data$source_plate_slot`** load `r json_data$source_plate_name` containing cells to be spotted.
**Slot `r json_data$agar_plate_slot`** load `r json_data$agar_plate_name` with agar.
29 changes: 13 additions & 16 deletions assets/instructions/protocol-3-instructions.Rmd
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
---
title: "Instructions"
title: "APEX Instructions"
output: pdf_document
params:
json_path: NULL
Expand All @@ -16,25 +16,22 @@ json_data <- fromJSON(file = params$json_path)
## Protocol 3: Colony Sampling in OT-2

### Overview
The colonies are sampled using a pipette tip and transferred to destination plate containing fresh media supplemented with appropriate antibiotic.
The robot samples colonies from total of `r length(json_data$agar_plate_slot) ` agar plates.
The picking height into the agar is set at `r json_data$agar_pierce_depth` mm.
Media with supplemented antibtiotic is distributed into the destination plate.
The colonies are sampled using a pipette tip and transferred to destination plate.
Colonies are sampled from total of `r length(json_data$agar_plate_slot) ` agar plates.
The picking height into the agar is set at `r json_data$agar_pierce_depth` (mm).
The agar height is calculated automatically per plate based on:
the plate weight without agar and with agar (g),
and agar density of `r json_data$agar_density`($g mm^{-3}$).
the plate weight without (`r json_data$empty_agar_plate_weight` g) and with agar (`r json_data$agar_plate_weight` g),
and agar density of `r json_data$agar_density` ($g cm^{-3}$).

### Preparation
The colonies are sampled according to the plate layout below.

```{r import-labware-images, results='asis', echo=FALSE}
# Read all image files from the directory
image_files <- list.files(path = params$labware_images_dir, pattern = "\\.png$", full.names = TRUE)
# Sort files numerically and alphabetically
image_files <- sort(image_files)
# Print images in Markdown format, 2 per row
for (i in seq_along(image_files)) {
# Start a new line for every pair of images
if (i %% 2 == 1 && i > 1) {
cat('\\newline\n')
}
Expand All @@ -48,9 +45,9 @@ for (i in seq_along(image_files)) {
```

### Deck Loading
Check that `r json_data$right_pipette_name` is in the right mount and `r json_data$left_pipette_name` is in the left mount.
**Slot `r json_data$right_pipette_tiprack_slot`** load `r json_data$right_pipette_tiprack_name` for the `r json_data$right_pipette_name` pipette.
**Slot `r json_data$left_pipette_tiprack_slot`** load `r json_data$left_pipette_tiprack_name` for the `r json_data$left_pipette_name` pipette.
**Slot `r json_data$media_plate_slot`** load `r json_data$media_plate_name` containing fresh media with antibiotic.
**Slot `r json_data$agar_plate_slot`** load `r json_data$agar_plate_name` containing agar with developed colonies.
**Slot `r json_data$destination_plate_slot`** load `r json_data$destination_plate_name` where fresh media will be distributed and sampled cells propagated.
Check that `r json_data$right_pipette_name` is in the right mount and `r json_data$left_pipette_name` is in the left mount.
**Slot `r json_data$right_pipette_tiprack_slot`** load `r json_data$right_pipette_tiprack_name` for the `r json_data$right_pipette_name` pipette.
**Slot `r json_data$left_pipette_tiprack_slot`** load `r json_data$left_pipette_tiprack_name` for the `r json_data$left_pipette_name` pipette.
**Slot `r json_data$media_plate_slot`** load `r json_data$media_plate_name` containing fresh media with antibiotic.
**Slot `r json_data$agar_plate_slot`** load `r json_data$agar_plate_name` containing agar with developed colonies.
**Slot `r json_data$destination_plate_slot`** load `r json_data$destination_plate_name` where fresh media will be distributed and sampled cells propagated.
2 changes: 1 addition & 1 deletion assets/instructions/protocol-4-instructions.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ library(knitr)
json_data <- fromJSON(file = params$json_path)
```
\vspace{-1.5cm}
## Protocol 4: Protein Expression induction in OT-2
## Protocol 4: Protein Expression Induction in OT-2

### Overview
Fresh antibiotic media is distributed into the destination plate, followed by aliquoting and inoculating overnight cultures into this media.
Expand Down
Loading

0 comments on commit fa726b4

Please sign in to comment.