apex-nf: Automated Protein EXpression in E. coli

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

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.

System Requirements

• Operating System: Compatible with Windows, macOS, or Linux.
• Software:
  • Nextflow: A workflow management system. Install it from Nextflow's website.
  • Access to a Command Line Interface (CLI).

Installation

To set up the stracquadniolab/apex-nf, open your Terminal or Command Prompt and execute:

nextflow pull stracquadniolab/apex-nf

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.

Run the pipeline

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. Examples can be found here.

Team

• Martyna Kasprzyk (Principal developer and Maintainer)
• Giovanni Stracquadanio (Principal Investigator)