Archived Jalview News Items (2011-2021)
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New minor release: Jalview 2.10.4
in development newsWe are very pleased to announce that the final release in Jalview’s 2.10 series is now available.
This minor release includes a number of critical patches to Jalview’s web service clients, sequence-to 3D structure mapping code and CDS/Protein cross- referencing system. It also fixes critical GUI and scroll-pad issues for Mac users running the latest versions of Java.
Jalview 2.10.4 also features new options in the Structure Chooser dialog, and a more efficient rendering pipeline that makes it easier to work with large alignments involving lots of hidden columns and sequence features.
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Last chance to sign up for the Jalview training course in Liverpool
in training newsThere 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.
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Primary school pupils viewed T Rex protein sequence in Jalview
in training newsOn 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.
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Jalview’s school worksheets tested
in training newsOn 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.
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Jalview on show at the Neglected Tropical Diseases festival
in community newsDelegates attending the International Society for Neglected Tropical Diseases festival in London on Tuesday 27th March got the opportunity to complete a Jalview jigsaw.
As well as speaking about Sci*Art and public outreach projects that she has been involved in, Suzanne (Duce) brought a mini exhibit to the festival. It was made up of artwork and outreach materials relating to malaria and kinetoplastid diseases.
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Jalview demonstration at Seaview Primary School
in community newsOn Friday 2nd February, Suzanne Duce visited Seaview Primary School in Monifieth, Angus. She had a question and answer session with a Year 7 class. Then talk about her research and gave practical demonstration of Jalview.
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New patch release: Jalview 2.10.3b1
in development newsWe are pleased to announce the first Jalview release of 2018!
The Jalview 2.10.3b1 bugfix release is distributed under a new Open Source codesigning certificate (“Open Source Developer, JAMES PROCTER”) and includes improvements to the web client for EnsemblGenomes, and fixes the following bugs in the Jalview Desktop:
- Only one structure is loaded when several sequences and structures are selected for viewing/superposing
- Alignment doesn’t appear to scroll vertically via trackpad and scrollwheel
- Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment
- Helix annotation has ’notches’ when scrolled into view if columns are hidden
- Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns
- User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
Jalview can be launched via Java Webstart (for anyone with an up to date java installation), downloaded as a locally installable package, and as a source tarball. You can also install Jalview on the command-line via Bioconda.
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Next Generation Bioinformatics User Group meeting
in training newsThe 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’.
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Dundee Protein Sequence Analysis Workshop
in training newsOn 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.
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Jalview Sequence Alignment and Analysis Workshop
in training newsOn 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.
