We are quite excited about the release of Jalview 2.11.0!
This major release introduces support for loading VCF files, and new
filters and shading models for sequence features. Under the hood, we've
addressed many bugs, and also made some important changes in the way the
Jalview desktop is installed and launched.
*
*The Jalview Launcher and Update System*. Jalview's new installation
model means you'll only need to download and install Jalview once.
After installation, Jalview will automatically keep itself up to
date. The launcher also sets Jalview's memory automatically, so
you'll never again have to manually configure Java's memory settings.
We are grateful to ej Technologies for providing a free open source
project license forinstall4j
<https://www.ej-technologies.com/products/install4j/overview.html>,
and also toThree Rings Design
<https://en.wikipedia.org/wiki/Three_Rings_Design>for Jalview's new
over the air update system:Getdown
<https://github.com/threerings/getdown>.
*
*VCF Support*. Proteins and genomic contigs with chromosomal
location annotation (such as protein coding genes retrieved from
Ensembl) can be annotated with variantsimported from a local VCF
file <http://www.jalview.org/help/html/features/importvcf.html>.
*
*Feature filters and attribute colourschemes*. A newFeature Display
Settings
<http://www.jalview.org/help/html/features/featureschemes.html>dialog
allows filters and feature attribute based colourschemes to be
constructed, and a new/filters/column added to theFeature Settings
<http://www.jalview.org/help/html/features/featuresettings.html>dialog.
Jalview's sequence feature datamodel has also been further
optimised, and is now maintained as a separate
library/IntervalStoreJ/(available
athttps://github.com/bartongroup/IntervalStoreJ)
*
*Alternative tables for CDS translation*. TheTranslate as cDNA
<http://www.jalview.org/help/html/menus/alwcalculate.html>option now
offers alternative amino acid coding schemes.
*
*PCA plots stored in Jalview Projects*. ThePCA viewer
<http://www.jalview.org/help/html/calculations/pca.html>user
interface has also been improved.
*
*Backup files*. Jalview will automatically create backups when
overwriting existing files, and - unlike with earlier versions -
should Jalview crash during a save, the original file will be
unaffected. TheBackups tab
<http://www.jalview.org/help/html/features/preferences.html#backups>in
Jalview's preferences dialog allows the number and format of backup
filenames to be configured.
The full list of bugs fixed in this release can be found in the2.11
Release Notes
<http://www.jalview.org/help/html/releases.html#Jalview.2.11.0>.
*Jalview and Java 11, and onwards*
The Jalview application comes bundled with its own independent Java
installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8 runtime
which will be kept up to date. A Java 11 based installation is available
from the Jalview development pages.
/Saying goodbye.../
Long time Jalview users will notice that this release no longer features
the/Vamsas/desktop menu, or a/Distributed Annotation System (DAS)/tab on
the feature settings dialog. DAS is no longer supported by major
bioinformatics databases, and we decided that it was no longer feasible
to maintain either JDAS or the VAMSAS client library which rely on
out-dated Java XML binding technologies.
/Next up.../
Keep an eye on the Jalview web site for news about JalviewJS - the web
based JavaScript implementation of Jalview. Whilst Jalview 2.11 has been
in development, we have also been working with Prof. Bob Hanson (Jmol
and JSmol) to enable Jalview to run as both a Java application and a
JavaScript app in a web page. To find out more,
open/http://www.jalview.org/jalview-js//in Chrome or Firefox.
Best wishes for 4th of July from Jim, Ben, Suzanne, Mungo, Geoff and
also Bob!
--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
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