Skip to content

Commit

Permalink
readme and manual update
Browse files Browse the repository at this point in the history
  • Loading branch information
@m-kasprzyk
m-kasprzyk committed Aug 13, 2024
1 parent 9c669b8 commit 4dda6ee
Show file tree
Hide file tree
Showing 2 changed files with 10 additions and 93 deletions.
Binary file added APEX-manual.pdf
View file
Binary file not shown.
103 changes: 10 additions & 93 deletions readme.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,22 +4,14 @@
![](https://github.com/stracquadaniolab/apex-nf/workflows/build/badge.svg)

## Overview
APEX pipeline consists of a series of automated *E. coli* laboratory protocols for protein expression:
1. **Heat Shock Transformation**
2. **Colony Selection**
3. **Colony Sampling**
4. **Protein Expression Induction**

This manual provides instructions for using the Opentrons Protein Screening
Pipeline, which is written in Nextflow and shared on GitHub. The pipeline
consists of a seres of automated E. coli laboratory protocols including:
heat-shock transformations (Protocol 1), agar plate spotting (Protocol 2),
colony sampling (Protocol 3), and protein expression induction (Protocol4).

## Table of Contents
1. [System Requirements](#system-requirements)
2. [Installation](#installation)
3. [Protocol 1: Transformation](#protocol-1-transformation)
4. [Protocol 2: Spotting](#protocol-2-spotting)
5. [Protocol 3: Colony Sampling](#protocol-3-colony-sampling)
6. [Protocol 4: Induction](#protocol-4-induction)
7. [Running the Full Screening Pipeline](#running-the-full-screening-pipeline)
8. [Output](#output)
Manual providing detailed instructions for using APEX can be found here.
A comprehensive user manual detailing the setup, configuration, and operation of the APEX pipeline is available [here](./APEX-manual.pdf).

## System Requirements

Expand All @@ -42,8 +34,7 @@ This command downloads and sets up the `stracquadniolab/apex-nf` on your system.
After installing the `stracquadniolab/apex-nf`, a Docker image containing all
necessary packages, including the Opentrons runtime, will be downloaded. Docker
containers provide a consistent environment for the software to run, ensuring
that it works the same way on any system. This allows for the pipeline to run
the workflows effortlessly.
that it works the same way on any system.


## Run the pipeline
Expand All @@ -54,82 +45,8 @@ To run the pipeline execute this command in your CLI:
nextflow run stracquadaniolab/apex-nf
```

Before running the `stracquadaniolab/apex-nf`, you need to prepare JSON and CSV files corresponding to each protocol. Below, you can find the format for each file, and examples can be found in the "testdata" folder. Note that if a parameter is enclosed in quotation marks (e.g., `"p20_multi_gen2"`), you should include it exactly as shown. If a parameter is enclosed in brackets (e.g., `[2, 3]`), you should include it as a list, separated by commas if there are multiple values, even if there is only one value (e.g., `[2]`).

## Protocol 1: Heat-shock Transformation

### JSON Configuration File

| Parameter | Description | Example |
|----------------------------------|----------------------------------------------------------------------------------------|----------------------------------------------------|
| `right_pipette_name` | Defines the model of the right pipette. | `"p20_multi_gen2"` |
| `right_pipette_tiprack_name` | Defines the name of the right pipette's tip racks. | `"opentrons_96_tiprack_20ul` |
| `right_pipette_tiprack_slot` | Defines the slots on the deck where the right pipette's tip racks are placed. | `[2, 3]` |
| `left_pipette_name` | Defines the model of the left pipette. | `"p300_multi_gen2"` |
| `left_pipette_tiprack_name` | Defines the name of the left pipette's tip racks. | `"opentrons_96_tiprack_20ul` |
| `left_pipette_tiprack_slot` | Defines the slots on the deck where the left pipette's tip racks are located. | `[6, 9]` |
| `dna_plate_name` | Defines the type of plate containing DNA. | `"armadillo_96_wellplate_200ul_pcr_full_skirt"` |
| `dna_plate_slot` | Defines the deck slot for the plate containing DNA. | `1` |
| `cells_plate_name` | Defines the type of plate containing competent cells. | `"armadillo_96_wellplate_200ul_pcr_full_skirt"` |
| `cells_plate_slot` | Defines the deck slot for the plate containing cells. | `1` |
| `media_plate_name` | Defines the type of plate containing media. | `"armadillo_96_wellplate_200ul_pcr_full_skirt"` |
| `media_plate_slot` | Defines the deck slot for the plate containing media. | `1` |
| `destination_plate_name` | Defines the type of plate used for the transformation (compatible with thermocycler). | `"armadillo_96_wellplate_200ul_pcr_full_skirt"` |
| `init_temp` | Set the initial cooling incubation temperature (Celcius degrees). | `4` |
| `init_time` | Set the duration for the initial cooling incubation (minutes). | `20` |
| `heat_temp` | Set the temperature for the heat-shock (Celcius degrees). | `42` |
| `heat_time` | Set the duration for the heat-shock (seconds). | `30` |
| `cool_temp` | Set the temperature for the post heat-shock cooling incubation (Celcius degrees). | `4` |
| `cool_time` | Set the duration for the post heat-shock cooling incubation (minutes). | `2` |
| `inc_temp` | Set the temperature for the recovery incubation (Celcius degrees). | `37` |
| `inc_time` | Set the duration for the recovery incubation (minutes). | `60` |

### CSV Configuration File

| Parameter | Description | Example |
|---------------|---------------------------------------------------------------------------------|------------|
| `dna_id` | Identifier for the DNA sample. | `pUC19` |
| `dna_well` | Well location of the DNA sample on the plate specified in JSON file. | `A1` |
| `dna_volume` | Volume of DNA used for transformation (µL). | `1` |
| `cells_id` | Identifier for the competents cells sample. | `DH5a` |
| `cells_well` | Well location of the competent cells on the plate specified in JSON file. | `A2` |
| `cells_volume`| Volume of competent cells to be transformed (µL). | `10` |
| `media_id` | Identifier for the media used. | `SOC` |
| `media_well` | Well location of the media on the plate specified in the JSON file. | `A3` |
| `media_volume`| Volume of media used for recovery (µL). | `50` |


## Protocol 2: Agar plate spotting

### JSON Configuration File

| Parameter | Description | Example |
|----------------------------------|-------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------|
| `pipette_name` | Model of the pipette used for spotting. | `"p20_multi_gen2"` |
| `pipette_mount` | Specifies which side of the robot the pipette is mounted on (left or right). | `"right"` |
| `tiprack_name` | Name of the pipette's tip racks. | `"opentrons_96_tiprack_20ul` |
| `tiprack_slots` | Defines the deck slot where the pipette's tip racks are placed. | `[2, 3]` |
| `source_plate_name` | Specifies the type of plate containing the source material, i.e. transformed cells. | `"armadillo_96_wellplate_200ul_pcr_full_skirt"` |
| `source_plate_slot` | Defines the deck slot for the source plate. | `"thermocycler"` |
| `agar_plate_name` | Specifies the type of agar plate. | `"nunc96grid_96_wellplate_10ul"` |
| `agar_plate_slots` | Defines the deck slot for the agar plates. | `[1]` |
| `agar_plate_area` | The base area of the agar plate (mm<sup>2</sup>). | `9469.2` |
| `empty_agar_plate_weight` | The weight of the empty plate without agar (g). | `38.92` |
| `agar_density` | Density of the agar (g mm<sup>-3</sup>). | `0.0008975` |
| `spotting_volume` | Volume that is dispensed during the spotting process (&mu;L). | `5` |
| `additional_volume` | Specifies any additional volume that is added to the spotting volume but not dispensed (&mu;L). | `1` |
| `spotting_height` | Sets the height relative to the agar surface for spotting, where a negative value indicates pipette piercing the agar. | `0` |


### CSV Configuration File

| Parameter | Description | Example |
|------------------------|-------------------------------------------------------------------------------|---------------|
| `id` | Identifier for the sample. | `pUC19-DH5a` |
| `agar_plate_location` | Defines the deck slot for the agar plate specified in JSON file. | `1` |
| `source_well` | Well location on the source plate from which transformed cells are aspirated. | `A1` |
| `destination_well` | Well location on the agar plate where the transformed cells will be spotted. | `A1` |
| `agar_plate_weight` | Weight of the plate with agar (g). | `77.12` |
Before running the `stracquadaniolab/apex-nf`, you need to prepare JSON and CSV files corresponding to each protocol. Examples can be found [here](./assets/testdata/).



## Team
Expand Down

0 comments on commit 4dda6ee

Please sign in to comment.