• Jalview’s 1st online training workshop was a great success!

    in training news

    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. The first-afternoon session introduced Jalview and its capabilities, how to load, edit and save sequences, create and analyse multiple alignments (using trees and PCAs), and generate figures for publication. Read more →

  • Edinburgh Genomics host Jalview training course on 29-30 April 2019

    in training news

    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. At the ‘Advanced workshop’ on Tuesday 30th April, participants will work with genomic variant data from Ensembl and Gnomad, scripting Jalview with Groovy, and taking advantage of UCSF Chimera’s 3D structure analysis capabilities in Jalview. Read more →

  • BBSRC EastBio PhD students learn about Jalview

    in training news

    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.

  • Jalview PhD Induction Course

    in training news

    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. Read more →

  • Jalview YouTube channel passes 50,000 views

    in training news

    The Jalview YouTube channel started just over 4 years ago with the aim of helping our users to more easily learn to use Jalview. To date, we have published 36 videos, which are organised into playlists that cover 8 key Jalview themes. The videos have proved very popular, and we were very proud to see that this week the 50,000 views landmark was reached! Jalview’s YouTube channel has been watched by people from 146 countries, ranging from Afghanistan to Zimbabwe. Read more →

  • Jalview in Liverpool

    in training news

    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. Read more →

  • Last chance to sign up for the Jalview training course in Liverpool

    in training news

    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. Read more →

  • Primary school pupils viewed T Rex protein sequence in Jalview

    in training news

    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. Read more →

  • Jalview’s school worksheets tested

    in training news

    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.

  • Next Generation Bioinformatics User Group meeting

    in training news

    The School of Life Sciences hosted the Christmas Next Generation Bioinformatics User Group (NextGenBUG) meeting on 12 December. Jalview’s Kira Mourao spoke on ‘How to search and destroy spurious antisense reads in RNA-Seq experiments’ and Mungo Carstairs presented ‘Visualising variant data in Jalview’.

  • Dundee Protein Sequence Analysis Workshop

    in training news

    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.

  • Jalview Sequence Alignment and Analysis Workshop

    in training news

    On Thursday 23rd November, Jim Procter and Suzanne Duce ran the fourth Jalview workshop of 2017. Attended by Ph.D. students and researchers at University of Dundee and Glasgow. The picture was taken as Jim talked about the relationship between protein sequences and their structure.

  • New video added to Jalview's YouTube 'Analysis and Annotation' playlist

    in training news

    Protein disorder predictors in Jalview video has been added to the Jalview YouTube Channel in the Analysis and Annotation playlist, alongside Multiple Sequence Alignment and Analysis with Jalview, Principal components analysis of protein and nucleotide alignments in Jalview, Calculating and Displaying Trees in Jalview, 3D molecular structure Jmol and UCSF Chimera viewers in Jalview, Secondary structure prediction of proteins in Jalview.

  • Thanks to all attendees of the CBBU Jalview course at ANU!

    in training news

    Many thanks to Marcin Adamski of CBBU(and JCSMR) and Rob Lanfear for hosting a one day Jalview workshop at the ANU’s Sciences Teaching Building. Particants included delegates from John Curtin’s Medical School, the Research School of Biology, CSIRO (Canberra), and University of Canberra, and together represented a range of disciplines including mammalian ecology, parasite genomics, biological statistics and precision medicine.

  • Video added to the Analysis and Annotation playlist on the Jalview YouTube channel

    in training news

    A video on Secondary structure prediction of proteins in Jalview has been added to our YouTube channel. JPred predicts the location of secondary structure (α-helix and β-strand) and solvent accessibility from a single sequence of multiple alignment.

  • Three training workshops in one week

    in training news

    The Jalview team were busy last week. Jim Procter and Suzanne Duce ran the one-day Jalview training workshop at the University of Dundee on Wednesday 22th February and the University of St Andrews on Friday 24th February. Geoff Barton ran a protein sequence analysis and structure prediction workshop on Thursday with help from Stuart MacGowan and Fabio Maderia at the University of Dundee. Thanks to Rebeca Diaz Vazquez for the invitation and help setting up the St Andrews workshop. Read more →

  • Registration for St Andrews Jalview Workshop on 24th February is open!

    in training news

    The next Jalview training event is a one day course on 24th February, hosted by The University of St. Andrews' School of Medicine, and will take place in the Bute Building’s IT teaching room (A21). The day starts at 9.15am, and we’ll be covering essential Jalview skills (creating and analysing alignments, calculating trees, and working with features and annotation). We’ll also explore some of the more advanced features for working with 3D structures, linking coding and non-coding nucleotide alignments, and integrating annotation from Ensembl. Read more →

  • Last chance to sign up for the Jalview training course in Glasgow

    in training news

    There are just a handful of spaces left at the Jalview’s ‘Protein, RNA and DNA multiple sequence alignment and functional analysis’ workshop. The course is suitable for both Jalview novices and experienced users who would like to learn more about Jalview’s capabilities. The course will cover topic such as loading, editing and saving sequences, multiple sequence alignment, creating trees, viewing annotation and features, working with 3D structures. The 1-day course is on Friday 14th October from 9. Read more →

  • Register for the Glasgow Jalview workshop

    in training news

    Protein, RNA and DNA multiple sequence alignment and functional analysis workshop using Jalview On 9.15am - 5.00pm Friday 14th October At Strathclyde Institute of Pharmacy and Biomedical Sciences, Room CV309b, Coville Building, 16 Richmond Street, Glasgow G1 1XQ This one day computer based hands-on training course is designed for life sciences graduate students and researcher scientists who works with proteins, RNA and DNA sequence data. The course will involve presentations, hands-on exercises and demonstrations. Read more →

  • Protein Sequence Analysis Workshop- Afternoon 3

    in training news

    Geoff Barton runs the third part of the School of Life Sciences' Postgrad Computational Training on Multiple Sequence Alignment and Analysis. The afternoon workshop introduced the principles of sequence analysis and its relationship to protein structure and function. It highlighted common methods and tools for protein sequence analysis and multiple sequence alignment, it involved both talks and hands-on exercises. The hands-on examples applied methods that exploit evolutionary information to predict structural features from sequence and to identify functionally important residues by sub-family analysis. Read more →

  • New Jalview YouTube channel playlist

    in training news

    A new playlist has been added to the Jalview Online Training YouTube channel. The ‘Colour, Appearance and Figure Generation’ playlist contains 3 videos that described how to modify the appearance of the Jalview alignment window, colour sequence residues and alignments, and how to export data and save images for figure generation and publication.

  • New Jalview Videos

    in training news

    New videos have been uploaded to the Jalview YouTube Channel. View them on the Jalview Online Training channel.

  • Undergraduates test Jalview

    in training news

    As part of the science communication project Charlotte Campbell, a 4th year BSc Hons student in Molecular Genetics, prepared an undergraduate training booklet using Jalview to understand protein sequence alignment and tree generation. Today she tested it out on the undergraduate students.

  • Successful 3 day Jalview training course in Cambridge

    in training news

    With the help of David Judge and his team, the Jalview’s Cambridge workshop was very well received. Day One introduced how to use Jalview, by the afternoon students were editing and annotating their own sequences. Day Two focussed on using the different analysis tools available in Jalview, using Jalview to investigate proteins and RNAs structure and function. Several of Jalview’s newest features were presented such as the split DNA and protein window. Read more →

  • Sign up for the Cambridge Jalview workshop

    in training news

    A few places are still available on our Cambridge Jalview workshop (11-13 May 2015). For more information visit our training course web page. Come along, met the Jalview team and learn how to get the most from this powerful, easy to use, free protein and nucleic acid sequence analysis software. To register go to the University of Cambridge’s bioinformatics training web page.

  • Cambridge 2015 Jalview Training Course

    in training news

    We will be holding a 3 day Jalview and JPred hands-on workshop on Monday 11th May 2015 at University of Dundee, hosted by David Judge. Register via the University of Cambridge website. The main topics of the course is protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis. The course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. Read more →

  • Jalview YouTube videos have over 2,000 views

    in training news

    A new video ‘Selecting residues, sequences and columns in Jalview’ has been added to the Jalview Online Training YouTube channel. This video is the first in a new ‘Selecting and Editing Sequences’ playlist. Our first ‘Getting Started’ playlist has 5 videos, which have been viewed over 2000 times.

  • Jalview Online Training YouTube channel has 2 new videos

    in training news

    Loading sequences and alignments in Jalview and Saving sequence alignments and projects in Jalview videos have just be added to our other videos. All Jalview YouTube videos can be found at Jalview Online Training - YouTube channel.

  • London 2014 Jalview training course success

    in training news

    Jim Procter, Geoff Barton and Suzanne Duce travelled down to London to host the first London Jalview one-day training course at University College London’s Bloomsbury Campus. The workshop involved hands-on exercises using Jalview interleaved with talks about alignment algorithms, phylogenetic tree generation, 3D molecular visualisation, secondary structure and disorder prediction. The aim was to help both novices and more experienced users get the most from Jalview’s sequence alignment, editing, annotation and analysis capabilities. Read more →

  • Register for the Jalview London 2014 One Day Workshop

    in training news

    We will be holding a one-day Jalview hands-on workshop on Monday 15th December 2014 at University College London, hosted by the Orengo Group. This course is for anyone who works with biological sequences, it involves of a mixture of talks and hands-on exercises. The course will be held in IT Suite B29 in Foster Court (click for map), which is in University College London’s Bloomsbury Campus. Registration costs £15 for students and £25 for everyone else. Read more →

  • View our Jalview training video series on YouTube

    in training news

    Yesterday ‘What is Jalview multiple sequence alignment software?’ and ‘How to launch Jalview on your computer’ videos were uploaded on YouTube. They are part of a ‘Getting Going with Jalview’ series that helps users get started using Jalview.

  • Jalview and JABA update talk at ISMB 2014 in Boston

    in training news

    Follow the link to take a look at the slides for the Monday 14th July Jalview and JABA ISMB Technology track talk highlighting current and up-coming features in Jalview 2.8.2 and JABA 2.1. New features include New look JPred consensus secondary structure Display of secondary structure based on DSSP and RNAView analysis of sequences with 3D structure Prototype integration of UCSF Chimera

  • Jalview Lightning Talk

    in training news

    Suzanne presented Jalview at the Division of Computational Biology’s lightning talks here at College of Life Sciences, chaired by Geoff Barton. Marek G certainly had the the best slide, it was an Orwellian 1984 experience.

  • Jalview Hands-on Training Course

    in training news

    33 participants logged into their UoD computers at 9am on Friday 11th April to attend the Jalview Hands-on Day Training Course. The course was a combination of talks and hands-on exercises involving working through Jalview manual with help from Jim Procter. Course material can be found at: http://www.jalview.org/tutorial/training-materials/2014/Dundee/Apr/

  • Jalview at VIZBI 2014 EMBO conference

    in training news

    Both Jim and Suzanne attended VIZBI 2014 EMBO conference on Visualizing Biological Data in Heidelberg. Jim, with Seán O’Donoghue (below), organised the event. It is always a friendly and interesting meeting and this year was no exception. Jim gave a lightening poster presentation on Jalview (photo exactly 35 seconds in). Suzanne ran a workshop and chaired one of the informal break-out sessions about training.

  • Last Day to register for the 4th Jalview and JABA residential workshop!

    in training news

    Join us at the Medical Sciences Teaching Centre in Oxford for the fourth Jalview Residential Course and Hackathon, which we’ve now renamed to the Jalview and JABA residential workshop ! The workshop takes place from 9am on 12th December to 5pm on the 13th December 2013. It begins with a hands-on Jalview training course, followed by evening dinner at St Catherine’s College. The second day covers advanced Jalview topics for users and developers. Read more →

  • 4th Jalview and JABA Residential Workshop (Poster)

    in training news

    Download the PDF of the Jalview 2013 Oxford workshop poster

  • Registration now open for 3rd Jalview Residential Training Course and Hackathon

    in training news

    Join us for the third Jalview residential course and hackathon, which will be held from 21-22nd January 2013 at EMBL-EBI in Hinxton, UK. Registration costs £30 (excluding accommodation), and includes: Comprehensive hands on training to get the most out of the Jalview Desktop Lectures on multiple sequence alignment and analysis, and how Jalview is used at EMBL-EBI Jalview clinic and Jalview development hackathon Evening dinner at the Red Lion in Hinxton, and lunch and refreshments during the course The residential course offers the opportunity for new users to explore Jalview’s capabilities, and experienced users to try out its more advanced features. Read more →