From jalview-announce at jalview.org Mon Apr 30 10:38:14 2007 From: jalview-announce at jalview.org (jalview-announce@jalview.org) Date: Mon Apr 30 10:35:37 2007 Subject: [Jalview-announce] Jalview 2.3 Message-ID: <4635B906.2020403@compbio.dundee.ac.uk> Hello Jalview users, We are packaging together the latest new features added and issues resolved and writing documentation for the next Jalview release, which will be Version 2.3. New Features: Jmol 11 integrated in Application. * Jmol is an opensource structure viewer written in Java, so fits naturally with Jalview. The integration allows all the features from the original Jalview Structure viewer, such as colouring structures from alignment colours and mouse over structure / alignment highlighting. * For the first time you will be able to save the structure view along with your alignments within the Jalview file format. * Jalview 11 is not Java 1.1 compatible, but there are steps being made to allow Jmol to run in all browsers. For this reason, the Jmol applet will only run in Web Browsers with Java 1.4 plugin or greater. If the web browser uses Java 1.1 only, the original Jalview Structure viewer is still available. Slide sequences with cursor keys - very useful editing feature which has been missing from Jalview. Edit sequence in place - another highly requested editing feature, allows residues/sequences to be altered in place. Feature / Annotation editing in Applet - Previously only available in the application, but has proven to be very useful in web alignment editing tools. Sequence fetcher parses EMBL codon records - CDS regions marked on sequences retrieved using WsDBFetch sequence fetcher from EBI. Feature fetcher maps Uniprot features onto EMBL sequence. Feature display optimization - layering of features on the alignment can be optimized by a button on the Feature Settings window. Alignment Properties - View simple alignment statistics and predefined alignment properties. Annotation file - extensions have been made to add alignment properties and scores to sequence and alignment annotations. Sort by score - if scores exist in the alignment, Jalview will recognise them and allow the user to sort the sequences by the available scores. Issues Resolved : Headless state 2.2.1 - small bug in 2.2.1 prevented this release from running in a truely headless state. Applet 2.2.1 no transparency for features - compilation error lead to omission of feature transparency. DNA pairwise alignment will now run with non - GCTA symbols. Cut & paste of sequences with associated alignment annotation works Coming soon!!! From jalview-announce at jalview.org Thu May 10 11:49:18 2007 From: jalview-announce at jalview.org (jalview-announce@jalview.org) Date: Thu May 10 11:51:03 2007 Subject: [Jalview-announce] Jalview 2.3 Message-ID: <4642F8AE.3070806@compbio.dundee.ac.uk> Hello Jalview users, Jalview 2.3 is now ready and available to download from http://www.jalview.org New Features in the latest release: * Jmol 11.0.2 integration. Jmol is an open source structure viewer written in Java, so fits naturally with Jalview. The integration allows all the features from the original Jalview Structure viewer, such as colouring structures from alignment colours and mouse over structure / alignment highlighting. Jmol 11.0.2 is not Java 1.1 compatible so Jmol applet will only run in Web Browsers with Java 1.4 plug-in or greater. If the web browser uses Java 1.1 only, the original Jalview Structure viewer is still available. * For the first time you will be able to save the structure view along with your alignments within the Jalview XML file format. * Slide sequences with cursor keys - very useful editing feature which has been missing from Jalview. * Edit sequence in place - another highly requested editing feature, allows residues/sequences to be altered in place. * EMBL CDS features - CDS regions marked on sequences retrieved using WsDBFetch sequence fetcher from EBI. * DAS Feature mapping * Feature ordering - layering of features on the alignment can be optimized by a button on the Feature Settings window. * Alignment Properties - View simple alignment statistics and predefined alignment properties. * Annotation Scores * Sort by scores - if scores exist in the alignment, Jalview will recognise them and allow the user to sort the sequences by the available scores. * Feature/annotation editing in applet - Previously only available in the application, but has proven to be very useful in web alignment editing tools. * Annotation file - extensions have been made to add alignment properties and scores to sequence and alignment annotations. Issues Resolved : * Headless state operation in 2.2.1 * Incorrect and unstable DNA pairwise alignment * Cut and paste of sequences with annotation * Feature group display state in XML * Feature ordering in XML * blc file iteration selection using filename # suffix * Stockholm alignment properties * Stockholm alignment secondary structure annotation * 2.2.1 applet had no feature transparency * Number pad keys can be used in cursor mode * Jalview Structure Viewer mirror image resolved From jalview-announce at jalview.org Wed May 30 14:14:53 2007 From: jalview-announce at jalview.org (jalview-announce@jalview.org) Date: Wed May 30 14:15:47 2007 Subject: [Jalview-announce] Sayonara Message-ID: <1180530893.465d78cd40159@webmail.lifesci.dundee.ac.uk> Hello Jalview users, It has been a great honour to work on the Jalview Project over the past few years but my time is now up and I have already moved on so the current Jalview development team has now halved! It has especially been good to hear all your praise and suggestions for future development of Jalview. It is clear that you all find the software very important to your work with multiple sequence alignments, with all the new features of the desktop application and web services as well as the extensive development of the applet for web based alignment display and editing. The software will remain open source and freely available, it would seem that some people might have got the wrong impression from the recent questionnaire added to the launch of the application. The idea was to grab some thoughts on how to finance future Jalview development, hopefully a solution will be found in the coming months. Your comments on the future develpment of Jalview would be greatly appreciated! Please send them to the usual help at jalview dot org email address. Its goodbye from me, Andrew Waterhouse ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From jalview-announce at jalview.org Tue Jun 5 17:48:29 2007 From: jalview-announce at jalview.org (jalview-announce@jalview.org) Date: Tue Jun 5 17:48:40 2007 Subject: [Jalview-announce] Jalview Discussion List Message-ID: <466593DD.6080304@compbio.dundee.ac.uk> Hello Jalview users! We've had a number of requests for an open discussion list, so the people who use Jalview can talk to themselves as well as 'the jalview help'. We have now set up an open discussion list - jalview-discuss : http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss Feel free to post jalview related discussion - tricks and tips that you've found useful or ways that you've thought about or have improved jalview. It will be publicised on the web site shortly, so don't expect too much traffic yet. help@jalview.org will remain for specific technical queries and bugs. You should still use this if you're having problems with installation, or if you've discovered a bug, since we'll notice the message more quickly than if you sent it to jalview-discuss. All the best, and happy Jalviewing. Jim Procter.