About ProtProtocols

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ProtProtocols was launched under the umbrella of the European Bioinformatics Community (EuBIC). The EuBIC initiative aims to bring together the bioinformatics community and tackle bioinformatics problems in proteomics collectively.

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What are ProtProtocol images?

ProtProtcol images are bioinformatic workflows encapsulated in Jupyter notebooks and installed in Docker containers.

Docker containers are lightweight virtual machines. If you download any Docker image, it is as if you were downloading a whole computer with all its installed software. Docker makes these images considerably smaller and more efficient to run than real virtual machines. As a prerequesite to running ProtProtocol images, you therefore have to install the Docker daemon to your system.

Jupyter notebooks is a software that allows you to combine text with analysis code in a single file. The, for example, resulting plots from your analysis code are automatically rendered with the text. Thereby, it creates an electronic notebook that contains both, the resulting plots and the code that generated them.

We use Jupyter notebooks to encapsulate all workflows in a reproducible fashion. All steps of a ProtProtocol protocol are executed within such a notebook. This gives us the advantage that we can leverage Jupyter’s inbuilt functions to, for example, download the whole notebook as a HTML file which contains the complete documentation of our results. Jupyter notebooks are web-applications. Therfore, they can be used on any operating system with a modern browser.


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This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 788042.