X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=2bfed88900e97c7c1c04899126e9d1bb56ae1d94;hp=eb318f0dfcd1376ccbb535628a3060015d6e24f0;hb=a8e52ab26dc6d12c8c18844ed29b9e604f6f4522;hpb=a266ac9a0aff1686fd122fe60964f54b32cff59e diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html old mode 100755 new mode 100644 index eb318f0..2bfed88 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,81 +24,74 @@

- Jalview 2.11 - new installer and new capabilities + Welcome to Jalview Version $$Version-Rel$$ !!

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.

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 for install4j, - and also to Three - Rings Design for Jalview's new over the air update system: Getdown.
VCF Support. Proteins and genomic contigs with - chromosomal location annotation (such as protein coding genes - retrieved from Ensembl) can be annotated with variants imported from a local VCF file.
Feature filters and attribute colourschemes. A new - Feature Display - Settings dialog allows filters and feature attribute based - colourschemes to be constructed, and a new filters column - added to the Feature - Settings dialog. Jalview's sequence feature datamodel has also - been further optimised, and is now maintained as a separate - library IntervalStoreJ (available at https://github.com/bartongroup/IntervalStoreJ)
Alternative tables for CDS translation. The Translate as cDNA option now - offers alternative amino acid coding schemes.
PCA plots stored in Jalview Projects. The PCA viewer 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. The Backups tab in - Jalview's preferences dialog allows the number and format of - backup filenames to be configured.

19 April 2022

Jalview 2.11.2.2 is the second patch release in the 2.11.2 series.

- The full list of bugs fixed in this release can be found in the 2.11 Release Notes. -

+ 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.

- Jalview and Java 11, and onwards + View predicted protein structures via 3D-Beacons
+ Jalview 2.11.2's Structure + Chooser includes a client for the 3D-Beacons Network. Launched in + 2021, the 3D-Beacons network (www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/) + 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, doi:10.12688/f1000research.20559.1).

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. + Support for viewing structures with ChimeraX and + Pymol
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 (doi:10.1093/bioinformatics/btm329).

+ The Structures + Preferences tab 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.

Jalview + 2.11.2 has been tested with Pymol 2.5.0 (community) and 2.5.2 + (incentive). For ChimeraX, we recommend using v1.3 or later.

Other highlights include:

Import of annotated DNA and RNA loci via GenBank and EMBL + style flatfile
Easier configuration of Jalview's memory + allocation
Scripts for running + Jalview via the command line on macOS, Linux/Unix and Windows. +

+ +

- 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. -

+ For the full details, see the Jalview 2.11.2.1 + release notes. +

+ Known Issues
The following known issues will + be addressed in a minor patch release. + +

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)