NIAB Python Training,Ensembl Plants Workshop & Mini-Hackathon |28-29 October

Python Training, Ensembl Plants Workshop & Mini-Hackathon - 28–29 October 2025 Hosted by Niab and Ensembl Plants

Join us for a two-day event hosted at Niab HQ in Cambridge and online, bringing together researchers and students who want to strengthen their Python programming skills and learn how to access and work with genomic data using the Ensembl REST API. Whether you're new to scripting or looking to apply bioinformatics tools to real research problems, this event offers practical, hands-on learning and a chance to collaborate with others in the field.

Day 1: Python for Biologists – Processing Data with Python

Date: 28 October 2025 | Time: 9:00 AM – 5:00 PM

Trainers: Niab team (Ian Tsang, John Connell and Larry Percival-Alwyn)

The first day focuses on introducing participants to the Python programming language, with an emphasis on biological data analysis. This course is designed for biologists with little programming experience. We will cover key programming concepts such as loops, strings, and data types, as well as working with biological datasets using Biopython. Participants will also learn how to parse and manipulate text-based output from bioinformatics tools. By the end of the day, attendees should feel more confident using Python to automate data processing tasks common in research.

Day 2: Ensembl Plants Workshop & Mini-Hackathon

Trainers: Ensembl Plants team (Jorge Batista da Rocha, Jorge Alvarez and Sarah Dyer)

Date: 29 October 2025 | Time: 9:00 AM – 5:00 PM

On the second day, we’ll dive into the Ensembl REST API and explore how to programmatically access Ensembl’s rich biological data. The morning session will provide an overview of the REST API, including the structure of the data it provides, the different types of queries it supports, and the HTTP methods used to retrieve information. Participants will learn how to navigate the API documentation and write Python scripts that can fetch and manipulate Ensembl data. In the afternoon, attendees will be invited to take part in a mini-hackathon where they can begin solving predefined biological research problems using the tools and skills developed earlier in the day. This collaborative session will provide an opportunity to work through real challenges and explore how RESTful services can integrate into your research workflows.

Venues

The event will be hosted at:

• The Sophie Taylor Building, Niab HQ, Cambridge.
• Niab-EMR – venue details to be confirmed.
• For those unable to attend in person, we will also offer full participation via Zoom.

What You’ll Need

Participants should bring a laptop capable of running a modern web browser such as Google Chrome, Firefox, or Vivaldi. You’ll also need a Google Account in order to access and run notebooks on Google Colab, which will be used during both days of the training.

To get the most out of the second day, we ask that you have some basic familiarity with Python, as this will help you move quickly through the API scripting exercises. We also ask that you complete some prerequisite training in advance (either by attending an Ensembl Browser Training Course or by completing the free online course “Ensembl: Browsing Genomes” https://www.ebi.ac.uk/training/online/courses/ensembl-browsing-genomes/, which takes approximately 3 hours and is available on demand.

How to Register

To register for either or both days of the training, or to ask any questions about the event, please contact:

Larry (lawrence.percival-alwyn@niab.com) or Ian (ian.tsang@niab.com)

Spaces are limited, especially for in-person attendance, so we encourage you to register early to avoid disappointment.