</head>
<body>
<p>
- <strong>Jalview 2.11 - new installer and new capabilities</strong>
+ <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong><br/>
</p>
- <p>Jalview 2.11 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.</p>
- <ul>
- <li><strong>The Jalview Launcher and Update System</strong>.
- 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.<br />We are grateful
- to ej Technologies for providing a free open source project
- license for <a
- href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>,
- and also to <a
- href="https://en.wikipedia.org/wiki/Three_Rings_Design">Three
- Rings Design</a> for Jalview's new over the air update system: <a
- href="https://github.com/threerings/getdown">Getdown</a>.</li>
- <li><strong>VCF Support</strong>. Proteins and genomic contigs with
- chromosomal location annotation (such as protein coding genes
- retrieved from Ensembl) can be annotated with variants <a
- href="features/importvcf.html">imported from a local VCF file</a>.</li>
- <li><strong>Feature filters and attribute colourschemes</strong>. A new
- <a href="features/featureschemes.html">Feature Display
- Settings</a> dialog allows filters and feature attribute based
- colourschemes to be constructed, and a new <em>filters</em> column
- added to the <a href="features/featuresettings.html">Feature
- Settings</a> dialog. Jalview's sequence feature datamodel has also
- been further optimised, and is now maintained as a separate
- library <em>IntervalStoreJ</em> (available at https://github.com/bartongroup/IntervalStoreJ)</li>
- <li><strong>Alternative tables for CDS translation</strong>. The <a
- href="menus/alwcalculate.html">Translate as cDNA</a> option now
- offers alternative amino acid coding schemes.</li>
- <li><strong>PCA plots stored in Jalview Projects</strong>. The <a
- href="calculations/pca.html">PCA viewer</a> user interface has
- also been improved.</li>
- <li><strong>Backup files</strong>. 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. The <a
- href="features/preferences.html#backups">Backups tab</a> in
- Jalview's preferences dialog allows the number and format of
- backup filenames to be configured.</li>
- </ul>
+<p>Jalview 2.11.2.2 is the second patch release in the 2.11.2 series.</p>
+
<p>
- The full list of bugs fixed in this release can be found in the <a
- href="releases.html#Jalview.2.11.0">2.11 Release Notes</a>.
- </p>
+ This release series provides support for two popular 3D
+ structure visualisation tools, new features for discovery of 3D
+ structures, improved platform integration and a new command line
+ tool allowing Jalview to be more easily called from scripts.</p>
+
<p>
- <strong>Jalview and Java 11, 13, and onwards</strong>
+ <strong>View predicted protein structures via 3D-Beacons</strong> <br>
+ Jalview 2.11.2's <a href="features/structurechooser.html">Structure
+ Chooser includes a client for the 3D-Beacons Network</a>. Launched in
+ 2021, the 3D-Beacons network (<a
+ href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
+ provides a central point for the retrieval of predicted and observed
+ 3D structures for sequences in Uniprot, including homology models
+ from Swiss-model and deep learning based predictions from the EBI's
+ Alphafold database (Orengo et al. 2020, <a
+ href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
</p>
- <p>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.</p>
+
<p>
- <em>Saying goodbye...</em><br>Long time Jalview users will notice
- that this release no longer features the
- <em>Vamsas</em> desktop menu, or a <em>Distributed
- Annotation System (DAS)</em> 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.
+ <strong>Support for viewing structures with ChimeraX and
+ Pymol</strong><br> Jalview's 3D structure viewer system has been
+ re-architected to allow easier integration of external structure
+ viewers, and takes advantage of the strucViz2 Chimera communications
+ library developed by Scooter Morris (<a
+ href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).<br /> <br />
+ The <a href="features/preferences.html#structure">Structures
+ Preferences tab</a> provides new options allowing ChimeraX and
+ Pymol to be used for visualising external 3D structures. Views
+ from all structure viewers are saved in Jalview Projects, allowing
+ them to be shared with others using Jalview 2.11.2 or later,
+ providing they have the same viewer installed and configured to be
+ used with Jalview.<br/><br/>Jalview
+ 2.11.2 has been tested with <strong>Pymol 2.5.0 (community)</strong> and <strong>2.5.2
+ (incentive)</strong>. For <strong>ChimeraX, we recommend using v1.3 or later</strong>.
</p>
+ <p>Other highlights include:</p>
+ <ul>
+ <li>Import of annotated DNA and RNA loci via GenBank and EMBL
+ style flatfile</li>
+ <li><strong>Easier configuration of <a
+ href="features/preferences.html#startup">Jalview's memory
+ allocation</a></strong></li>
+ <li>Scripts for <a href="features/commandline.html">running
+ Jalview via the command line</a> on macOS, Linux/Unix and Windows.
+ </li>
+ </ul>
+
+
<p>
- <em>Next up...</em><br /> 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 <em>http://www.jalview.org/jalview-js/</em>
- in Chrome or Firefox.
- </p>
+ For the full details, see <a
+ href="releases.html#Jalview.2.11.2.1">the Jalview 2.11.2.1
+ release notes</a>.
+ </p>
+ <p>
+ <strong>Known Issues</strong> <br />The following known issues will
+ be addressed in a minor patch release.
+
+ <ul>
+ <li>Display of RESNUM sequence features are not suppressed when
+ structures associated with a sequence are viewed with an external
+ viewer (Regression from 2.11.1 series)</li>
+ </ul>
+ <p></p>
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git://source.jalview.org / jalview.git / blobdiff