ProtProtocols use Docker containers to distribute easy-to-use, reproducible bioinformatics workflows for MS/MS based proteomics approaches. This allows you to install complex bioinformatics workflows with a single command - or even at the click of a button through our docker-launcher application.
The docker-launcher tool is the simplest way to install and run ProtProtocol images. It is a lightweight Java application that provides a simple user interface to download and run ProtProtocols. It supports Windows, Mac OS X and Linux. Its only requirements are Java and Docker to be installed. For more information see our documentation pages.
A ProtProtocol to analyse isobarically labelled (iTRAQ / TMT) quantitative proteomics experiments. The IsoProt provides sophisticated statistical methods to analyse complex experimental designs at the click of a button. Like all ProtProtocols the protocol is run as a Jupyter notebook. Starting with peak list files as input (mgf format) it performs everything from the search of the spectra until the statistical analysis of the quantified proteins. The easiest way to use IsoProt is through our docker-launcher application.
The ProtProtocols template provides a basic docker image to start the development of a new ProtProtocol. It contains a system with Jupyter including an R kernel installed. To start a new ProtProtocol, simply clone the image and adapt it to your needs.