Bio-IT Hackathon

Toby Hodges   2019-07-04   Comments Off on Bio-IT Hackathon

Date(s) - 2019-07-04
09:30 CEST - 17:00 CEST



The first Bio-IT Hackathon will give community members a chance to work collaboratively on a range of projects for a whole day.

The event is open to anyone, regardless of background and experience level. There are projects suitable for both newcomers to programming/computing and those with extensive experience.

Use this page to register your interest for a particular project. You can read short summaries of the projects below, and check out the Hackathon homepage for more information.

There’s still time to propose a project for the Hackathon. If you’ve got an idea that you’d like to work on during the event, please contact us at


1. Cluster stats dashboard

We’d like to make it easier for users of the EMBL compute cluster to access easy-to-understand summaries of their cluster usage and guidance for how they might improve the efficiency of their compute tasks. This will be achieved by developing an R-Shiny interface to the cluster Slurm database, which will allow EMBL users to view summary visualisations and statistics on their cluster jobs and receive advice on how they might improve the performance of their jobs in the future.

2. EMBL clubs app

There are a lot of clubs at EMBL, and many of these share some common challenges e.g. scheduling meetings, games, etc and finding out who’s planning to attend. This project team would develop an app to help clubs coordinate their activities.

3. EMBL groups directory

There is a great diversity of different research topics and methodologies spread across the six EMBL sites. When a researcher is getting started with a new approach and/or field, it would be helpful to be able to quickly find out who else at EMBL has experience with this. This project team would work to create a searchable directory of techniques/methods/analyses used by research groups across EMBL.

4. Expanding Bio-IT Git training material

We’d like to build on the excellent training material on Version Control with Git, originally developed by Genome Biology Computational Support (GBCS), incorporating some of the examples and material from recent Bio-IT courses on the topic.

5. Image analysis training resources

The project team would add to and improve the Image Analysis Training Resources project currently under development at These resources aim to provide a single interface for people to teach/learn important concepts in image analysis, regardless of the platform with which they want to do their image analysis (ImageJ/Fiji, Python, MATLAB, etc).

6. Create a short tutorial on an advanced programming skill

Bio-IT has been offering many beginners lessons on computing skills such as Python, R, Unix, git, etc. Our learners who finish these courses seek new and advanced skills that they can learn and apply in their work. With this project idea, I would like to invite the bioinformaticians to share one of their favorite skills by creating a small tutorial that can be taught by someone, or can be used for self-paced training.

7. Bio-IT interview blogs

Malvika has been interviewing members of the Bio-IT community over the past six months, talking about their career paths in computational biology/bioinformatics. Now that all of these interviews have been transcribed, we’d like to summarise them into stories where shared narratives exist and highlighting common advice that interviewees had for people in computational career paths.


Scientific figures, graphical abstracts, presentations. They’re all based on icons scientists spend hours on drawing or dealing with copyrights issues. How about saving researchers these hours by bringing EMBL community together, and a creating a visual library of high quality icons available in .eps format? Icons that once created, can be reused, modified and recycled again and again by anyone? This resource would include icons starting from simple objects through DNA strands, organelles and model organisms, to lab equipment, and much more!


Bookings are closed for this event.