The ‘Introduction to Jalview’ course is aimed at PhD students and post-doctoral researchers with little to no experience of the creation and analysis of multiple sequence alignments (MSAs) and their exploration in the context of predicted and observed 3D structures. It’s also a great opportunity for more experienced users to refresh their knowledge and learn about the latest features in Jalview 2.11.4. As an introductory level course, it is designed to be aligned with the needs of those completely unfamiliar with Jalview’s core capabilities. Advanced level courses will be advertised in the future - please keep an eye out on Jalview’s website.

This course takes place over two afternoons on the 2nd and 3rd October 2024 at the University of Dundee, in the Dalhousie Building on Day 1 and the Tower building on Day 2, in partnership with the School’s PhD program. The course is free of charge, but since spaces are limited, priority will be given to new PhD students affiliated with the University of Dundee and other Scottish universities.

Each of the two sessions consists of a brief introduction followed by a series of short talks and sessions based on Jalview’s hands-on exercises. On Wednesday, we will cover Jalview’s core capabilities: creation, editing, analysis and visualisation of alignments linked with phylogenetic trees, and Thursday will focus on using Jalview’s web services for protein secondary structure and disorder prediction, and visualising 3D structures from EMBL-EBI and AlphaFoldDB.

Date and Time: 2pm - 5pm on 2nd and 3rd of October, 2024

Who should attend: Research students and academics working on biomolecular sequence structure and function.

What you need to bring: This is a hands-on introductory course. You will need a laptop and the ability to connect to EduRoam in order to access Jalview, its web services, and the course materials.

Instructor: James Procter (Jalview Coordinator, Division of Computational Biology) and Khadija Jabeen (Outreach and Training Officer, Division of Computational Biology)

Before you come: You can save time during the workshop by downloading and installing Jalview on your laptop. We also recommend you familiarise yourself with Jalview by watching the following videos:

• Navigating the Jalview interface
• Loading sequences and alignments into Jalview
• Saving sequence alignments and projects in Jalview
• Jalview’s context menus

Relevant papers: The first session is focused on Jalview’s core workflow for creating multiple sequence alignments, analysing them and producing high-quality figures for publication. This was described in Procter et al. 2021). For background on Jalview’s capabilities, we also recommend reading the original Jalview 2 paper.