Sprinting with bio-imagers and how I learnt about NEUBIAS, EuBI, Elixir and tried out myBinder!


May 14-15, I was in Cambridge for a coding sprint jointly organized by bio- and medical- imaging infrastructures. The goal of the sprint was to capitalize on the infrastructure training experiences in order to provide online registries of training materials and create reproducible training environments.


We were a group of about 20 software engineers and research scientists from bio-imaging (microscopy), medical imaging (MRI) and bioinformatics.

The first morning, we introduced ourselves:

For the rest of the sprint we had two working groups:

  • WG1: Curation and vocabulary alignments
  • WG2: Reproducible training sessions using containers

In WG1, we started by representing various examples of training materials using the NEUBIAS model (as used in BISE). The following day, there was further effort to align this with Tess and bioschemas and to incorporate more examples directly in BISE.

On the second day, I joined WG2. I was very happy to find out about myBinder! Give it a GitHub repository with a Jupyter notebook and it will turn it into an interactive notebook hosted online!. We used mybinder at: https://github.com/dwaithe/model-training and further focused on providing a Docker file that could be run locally to launch the course (https://github.com/ac744/model-training). I've also tested it on one of my own repository: Software_Comparison#3!

I very much enjoyed meeting and working with members of the bioimage and bioinformatics communities!

I'd like to thank the organizers Perrine Paul-Gilloteaux from University of Nantes and Gabriella Rustici from the University of Cambridge as well as FLI for support to attend the event.

This event was covered using #trainhackcam on twitter.