On Wednesday 29th April, the Jalview team ran their first online training workshops using Blackboard Collaborate. The team, Jim Procter, Suzanne Duce, Mungo Carstairs and Ben Soares were joined by 21 workshop participants from across the world. The course ran over three afternoons and involved practical exercises and presentations.
Edinburgh Genomics are hosting Jalview workshops on Monday 29th and Tuesday 30th April.
At the ‘Introductory workshop’ on Monday 29th April, participants will learn about multiple sequence alignments and how to create, analyse and visualise them with the Jalview Desktop. Participants will explore Jalview’s capabilities for working with phylogenetic trees, 3D structures and annotation from public databases.
BBSRC EastBio PhD students ran Jalview on their laptops as part of the ‘Visual and Verbal Bend to Science Communications’ DTP workshop held at the School of Life Sciences on 27th February. This was followed by a Do’s and Don’ts of Dataviz presentation by Jim Procter.
On Thursday afternoon on the 27th September and Friday morning on the 28th September, Jim Procter, Suzanne Duce and Ben Soares ran a Jalview workshop in the Tower Building IT Suite as part of the PhD Induction for Life Sciences students at the University of Dundee.
Great to see everyone loading, editing and aligning their protein sequences then going on to analyse the alignments, viewing the annotations and features as well as linking this to the 3D structure.
The Jalview YouTube channel started just over 4 years ago with the aim of helping our users to more easily learn to use Jalview.
Jim Procter and Suzanne Duce travelled to Liverpool to run a 2-day multiple sequence alignment, protein structure and function modelling workshop with Dr Dan Rigden. In Day 1, delegates learnt how to load data from public databases such as Uniprot, Ensembl and PDB into Jalview and then run multiple sequence alignment, conservation analysis and secondary structure and disorder prediction. Day 2 focused on protein structure visualisation, structure-based function predictions, homology modelling and ab inito modelling.
There are a few spaces left on the 2 day ‘Multiple Sequence Alignment with Jalview and Protein Structure and Function Modelling’ workshop in Liverpool on Monday 14th to Tuesday 15th May.
Day 1 is focused on creating, analysing and annotating sequence alignments (including cDNA/Protein) with Jalview. Day 2 involves 3D structure, we will explore the creation and use of protein 3D modelling for function prediction.
Registration for the course is free.
On Thursday 3rd May, 105 primary school pupils from St Clement's and St Francis Primary Schools visited the School of Life Sciences as part of the ‘Cell-ebration of Science’ event. As well as a drama workshop, the children could try out a variety of hands-on science activities. This included running Jalview and using our badge maker.
Pupils loaded the collagen protein sequence of Tyrannosaurus Rex from Uniprot database (P0C2W2) into Jalview. They used multiple sequence alignment analysis to compare this fragment of collagen to those of other species.
On Thursday 12th April, Alssundgymnasiet Sønderborg School from Denmark visited the School of Life Sciences. In the afternoon, 19 pupils took part in a workshop using Jalview to fetch DNA, RNA and protein sequences from a variety of biological databases. They aligned sequences, generated trees and viewed the 3D shape of myoglobin proteins.
On Thursday 30th November, Geoff Barton and Suzanne Duce ran the second Dundee Protein Sequence Analysis workshop of the year. The course considered the relationship between protein sequence and structure. It used JPred4 to predict protein structure from multiple alignments. Then used protein sub-family analysis in Jalview to identify functionally important regions.