From jprocter at compbio.dundee.ac.uk Thu Nov 5 09:05:32 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Thu, 05 Nov 2009 09:05:32 +0000 Subject: [Jalview-discuss] Jalview 2.4.0b2 bugfix release Message-ID: <4AF2955C.8000101@compbio.dundee.ac.uk> Dear Jalviewers. I'm pleased to announce that the Jalview applet and desktop application available from the Jalview download page (http://www.jalview.org/download.html) have been updated to the latest bug fix version, which was previously available from the 'release' branch of the jalview development version (http://www.jalview.org/versions.html). This release fixes a number of minor issues with the previous 2.4 release, including issues related to the applet's performance on java 1.6.0u12+, the retrieval of multiple records from a sequence data source in the application, and problems with launching the installAnywhere version from the command line. Please see the release history page for full details (http://www.jalview.org/releaseHistory.html). Usage Tracking with Google Analytics ------------------------------------ This bugfix release also introduces usage statistics tracking, via Google Analytics (GA). On first launch of the application, you will be asked if you would like to enable this feature. Please see the Jalview privacy statement for more information (http://www.jalview.org/help/html/privacy.html). We are very interested in recording when and how the Jalview desktop is used, and hope to use GA mechanism to record this information in an anonymous manner. This information, in addition to the www.jalview.org HTTP logs, will help us inform our funders - the BBSRC, and in the future, will inform our redesign of the Jalview user interface to make it even better. The next Jalview Release ------------------------ The development version of Jalview, available from http://www.jalview.org/versions.html now contains a number of new visualization features, including sequence logos, and score and label based sequence feature annotation colouring. I hope to incorporate these features into a new Jalview release scheduled for the last month of 2009, or early 2010. If you are interested in alpha/beta testing, please have a look at the latest version, and get in contact via jalview-discuss at jalview.org Happy Jalviewing! Jim Procter. -- ------------------------------------------------------------------- J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group http://www.jalview.org http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From paul.pillot at ac-nice.fr Sun Nov 8 20:09:54 2009 From: paul.pillot at ac-nice.fr (Paul Pillot) Date: Sun, 8 Nov 2009 21:09:54 +0100 Subject: [Jalview-discuss] A tutorial in french about Jalview, intended for undergraduate biology classes Message-ID: <23651BDC-DD0B-457C-8FAF-E130708948ED@ac-nice.fr> Dear Jalviewers, and especially dear Jalview developpers, I would like to let you know about a set of web pages I have just written. Despite being written in French, I thought they could be of interest as they show how Jalview could be use to teach certain aspects of evolution and of immunology to a secondary education audience. The link : http://www.ac-nice.fr/svt/productions/exploitations/jalview/index.html Thanks a lot for Jalview, keep up with this amazing software ! (looking forward i18n !) Paul Pillot From chica at embl.de Mon Nov 9 11:13:59 2009 From: chica at embl.de (Claudia Chica) Date: Mon, 9 Nov 2009 12:13:59 +0100 Subject: [Jalview-discuss] characters color in features Message-ID: dear all, i'm currently using Jalview to annotate an alignment with several features. is there a way to keep the color of characters in the features black instead of white? and additionally, can i define this in the parameters list of the Jalview Applet? thanks a lot for any hint you can give me Claudia From jprocter at compbio.dundee.ac.uk Mon Nov 9 12:57:02 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Mon, 09 Nov 2009 12:57:02 +0000 Subject: [Jalview-discuss] characters color in features In-Reply-To: References: Message-ID: <4AF8119E.3070908@compbio.dundee.ac.uk> Hello Claudia, thanks for the email. Claudia Chica wrote: > is there a way to keep the color of characters in the features black > instead of white? > and additionally, > can i define this in the parameters list of the Jalview Applet? > I'm afraid there isn't any way to do this at the moment, but it is on our TODO list (as both a bug and a feature request ;) ). If you are interested, I can let you know when it gets implemented so you can try it out. Jim. -- ------------------------------------------------------------------- J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From jprocter at compbio.dundee.ac.uk Mon Nov 9 16:30:27 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Mon, 09 Nov 2009 16:30:27 +0000 Subject: [Jalview-discuss] A tutorial in french about Jalview, intended for undergraduate biology classes In-Reply-To: <23651BDC-DD0B-457C-8FAF-E130708948ED@ac-nice.fr> References: <23651BDC-DD0B-457C-8FAF-E130708948ED@ac-nice.fr> Message-ID: <4AF843A3.3020409@compbio.dundee.ac.uk> Hi Paul.. Paul Pillot wrote: > The link : > http://www.ac-nice.fr/svt/productions/exploitations/jalview/index.html > These pages are really great! A very nice example of online teaching material. If you'd like, I can discuss with you off-list about a couple of new command line features in the development version that might be of use to make things even easier for the students (if that's what you'd like to do ;) ). > Thanks a lot for Jalview, keep up with this amazing software ! > (looking forward i18n !) > Thanks ! I'm hoping we can make the jump to i18n after the next major release next year. Is it still OK to enlist your help for the French translation ? ;) cheers.. Jim. From jprocter at compbio.dundee.ac.uk Tue Nov 10 12:19:55 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Tue, 10 Nov 2009 12:19:55 +0000 Subject: [Jalview-discuss] Last Call For Registrations for EMBO Visualizing Biological Data Workshop Message-ID: <4AF95A6B.2030108@compbio.dundee.ac.uk> Hello Jalviewers - apologies for the blatant propaganda, but some of you, or your colleagues may be interested in the meeting below: Dear colleagues, we would like to remind you that November 16 is the deadline for registration and abstract submission for the first EMBO Workshop on Visualizing Biological Data (VizBi, http://www.vizbi.org), 3-5 March 2010, at EMBL Heidelberg, Germany. The goal of the workshop is to bring together, for the first time, researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). The workshop program includes high-profile speakers from each of these areas, as well as keynote talks by Ben Fry (Seed Visualization), Bang Wong (Broad Institute) and Chris North (Virginia Tech) - for details, see http://tinyurl.com/vizbi10Speakers. We are pleased to announce that we have a limited number of student travel fellowships provided by the European Science Foundation - see http://vizbi.org for details on how to apply. Furthermore, a 15% discount on the registration fee is available to members of the International Society for Computational Biology (ISCB). To apply to join the workshop, please go to http://vizbi.org and submit an abstract and image related to your work. In addition to the program of speakers, participants are normally required to present a poster and to give a 'fast-forward' presentation (limited to 30 seconds and 1 slide). If several people are working on the same project they may use the same abstract to apply. However, we encourage registrants to submit work that reflects their own interests - and not necessarily new or unpublished work. But, since places are limited, we will use submissions to select participants whose work is most relevant to the goals of the workshop. Notifications of acceptance will be sent within three weeks after the close of submissions. You may also submit your image for consideration for the VizBi Scientific Art prize. This prize will be awarded to the submitted image that best conveys a strong scientific message in a visually compelling manner. Please forward this announcement to anyone who may be interested. We hope to see you in Heidelberg next spring! Se?n O'Donoghue, EMBL Jim Procter, University of Dundee Nils Gehlenborg, European Bioinformatics Institute Reinhard Schneider, EMBL If you have any questions about the registration process please contact: Adela Valceanu Conference Officer European Molecular Biology Laboratory Meyerhofstr. 1 D-69117 Heidelberg Tel: +49-6221-387 8625 Fax: +49-6221-387 8158 Email: valceanu at embl.de -- ------------------------------------------------------------------- J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From dwrice at indiana.edu Wed Nov 11 03:04:18 2009 From: dwrice at indiana.edu (Danny Rice) Date: Tue, 10 Nov 2009 22:04:18 -0500 Subject: [Jalview-discuss] rearranging sequences not working correctly Message-ID: <4AFA29B2.2000708@indiana.edu> When I open a fasta file like: $JAVA -Djava.ext.dirs=$JALVIEW_HOME/lib -cp $JALVIEW_HOME/jalview.jar jalview.bin.Jalview -open $file and click on the sequence name I can't move the sequence up or down with the arrow keys. If I go to Tools->Preferences and then Cancel I am then able to move the sequence with the arrow keys. I have noticed this on all versions I have tried and also on the current version I just installed yesterday. I am using the Linux version and am using the jre provided with Jalview. -Danny From dwrice at indiana.edu Wed Nov 11 03:20:00 2009 From: dwrice at indiana.edu (Danny Rice) Date: Tue, 10 Nov 2009 22:20:00 -0500 Subject: [Jalview-discuss] feature request - default Above Identity Threshold Message-ID: <4AFA2D60.1000705@indiana.edu> It would be efficient to be able to set the Above Identity Threshold "on" and to set the Threshold "value" in preferences. I often go through a large number of alignments and I have to manually set these each time. -Danny From jprocter at compbio.dundee.ac.uk Wed Nov 11 10:23:24 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Wed, 11 Nov 2009 10:23:24 +0000 Subject: [Jalview-discuss] rearranging sequences not working correctly In-Reply-To: <4AFA29B2.2000708@indiana.edu> References: <4AFA29B2.2000708@indiana.edu> Message-ID: <4AFA909C.5070008@compbio.dundee.ac.uk> Danny Rice wrote: > When I open a fasta file like: > > $JAVA -Djava.ext.dirs=$JALVIEW_HOME/lib -cp $JALVIEW_HOME/jalview.jar > jalview.bin.Jalview -open $file > > and click on the sequence name I can't move the sequence up or down with > the arrow keys. If I go to Tools->Preferences and then Cancel I am then > able to move the sequence with the arrow keys. I have noticed this on > all versions I have tried and also on the current version I just > installed yesterday. I am using the Linux version and am using the jre > provided with Jalview. > There may be a couple of issues here. Occasionally, the GoogleAnalytics usage tracking dialog box and the Jalview splash screen 'interact' - leaving the desktop window without input focus. I found that if you respond to the prompt (rather than cancel it), and then quit (using the dropdown menu) and restart Jalview, the Desktop window should behave normally (ie. you can select seuqences and move them up/down). You could also provide the -nousage option to prevent the dialog box launching. If you find you get the same problem as me - and can't even click on the menu items, then try starting Jalview via the -jar parameter: $JAVA -Djava.ext.dirs=$JALVIEW_HOME/lib -jar $JALVIEW_HOME/jalview.jar -open $file This really shouldn't make any difference, but for some reason it did in my case (it may have been simply luck that the input focus race condition described above didn't happen). let me know what architecture/distro you are running if you are still having problems. Jim. From jprocter at compbio.dundee.ac.uk Wed Nov 11 10:23:32 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Wed, 11 Nov 2009 10:23:32 +0000 Subject: [Jalview-discuss] feature request - default Above Identity Threshold In-Reply-To: <4AFA2D60.1000705@indiana.edu> References: <4AFA2D60.1000705@indiana.edu> Message-ID: <4AFA90A4.6050202@compbio.dundee.ac.uk> Danny Rice wrote: > It would be efficient to be able to set the Above Identity Threshold > "on" and to set the Threshold "value" in preferences. I often go > through a large number of alignments and I have to manually set these > each time Duly noted. These preferences will be added in future releases. Jim. From eroshkin at burnham.org Sat Nov 14 01:41:04 2009 From: eroshkin at burnham.org (Alexey Erohskin) Date: Fri, 13 Nov 2009 17:41:04 -0800 Subject: [Jalview-discuss] cDNA codon alignments Message-ID: <066801ca64cb$87148c90$953da5b0$@org> Helloo: I just subscribed to the group and found this old message related to cDNA codon alignments rquiroga at fcq.unc.edu.ar wrote: > I am having three problems. > > One is the Translation of cDNA, which seems to not handle gaps > correctly sometimes, > (ATAAAG---GTTCCT) translates to (IKVP) > (ATAAAA---GTTCCA) translates to (IKVP), missing the gap. Jim's answer: The translate cDNA function will exclude any gapped columns from the translated protein alignment. Otherwise, gaps are introduced when codons intersect but are misaligned. e.g. A-TAAAG AATAA-G becomes -I-K N-K- > Also I get a "Please select at least three bases in at least one > sequence in order to perform a cDNA translation." when I try to > translate my entire cDNA codon alignment to protein. (Sequences: 154 > Minimum Sequence Length: 314 Maximum Sequence Length: 365 Average > Length: 351). Maybe too big? Jim's answer was: My guess is that you have one or two Ns in the region you are translating. The translate cDNA routine complains when the effective number of *defined* bases that have been selected for translation is not divisible by three. This is partly because it doesn't know how to use an N or an X (or ?) in a codon. My experience: 1. Gaps in translation are kept correctly 2. I have the same error message "Please select at least three bases . " when I select the whole alignment for translation and this has nothing to do with N, X or "?" in a codon. 3. This very useful option is unfortunately not working for entire sequences or large chunk of positions. If some trick is known for fixing this problem? Thanks Alexey Eroshkin, Burnham Institute for Medical Research -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20091113/1f6a1e3e/attachment.html From eroshkin at burnham.org Sat Nov 14 02:04:19 2009 From: eroshkin at burnham.org (Alexey Erohskin) Date: Fri, 13 Nov 2009 18:04:19 -0800 Subject: [Jalview-discuss] cDNA codon alignments In-Reply-To: <066801ca64cb$87148c90$953da5b0$@org> References: <066801ca64cb$87148c90$953da5b0$@org> Message-ID: <067601ca64ce$c6d4b5f0$547e21d0$@org> Now I am trying development version of the program and I see that the whole alignment translation works just fine. Jim and others, thanks for quick fix of this bug. And the connection between two windows - cdna and protein - is just great. Thanks. Alexey From: jalview-discuss-bounces at jalview.org [mailto:jalview-discuss-bounces at jalview.org] On Behalf Of Alexey Erohskin Sent: Friday, November 13, 2009 5:41 PM To: jalview-discuss at jalview.org Subject: Re: [Jalview-discuss] cDNA codon alignments Helloo: I just subscribed to the group and found this old message related to cDNA codon alignments rquiroga at fcq.unc.edu.ar wrote: > I am having three problems. > > One is the Translation of cDNA, which seems to not handle gaps > correctly sometimes, > (ATAAAG---GTTCCT) translates to (IKVP) > (ATAAAA---GTTCCA) translates to (IKVP), missing the gap. Jim's answer: The translate cDNA function will exclude any gapped columns from the translated protein alignment. Otherwise, gaps are introduced when codons intersect but are misaligned. e.g. A-TAAAG AATAA-G becomes -I-K N-K- > Also I get a "Please select at least three bases in at least one > sequence in order to perform a cDNA translation." when I try to > translate my entire cDNA codon alignment to protein. (Sequences: 154 > Minimum Sequence Length: 314 Maximum Sequence Length: 365 Average > Length: 351). Maybe too big? Jim's answer was: My guess is that you have one or two Ns in the region you are translating. The translate cDNA routine complains when the effective number of *defined* bases that have been selected for translation is not divisible by three. This is partly because it doesn't know how to use an N or an X (or ?) in a codon. My experience: 1. Gaps in translation are kept correctly 2. I have the same error message "Please select at least three bases . " when I select the whole alignment for translation and this has nothing to do with N, X or "?" in a codon. 3. This very useful option is unfortunately not working for entire sequences or large chunk of positions. If some trick is known for fixing this problem? Thanks Alexey Eroshkin, Burnham Institute for Medical Research -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20091113/396ddf8f/attachment-0001.html From chica at embl.de Tue Nov 17 11:00:55 2009 From: chica at embl.de (Claudia Chica) Date: Tue, 17 Nov 2009 12:00:55 +0100 Subject: [Jalview-discuss] GWT and jalview Message-ID: <40E9D530-9D9A-4253-83B4-A54A3BB0CAFF@embl.de> dear all, i'm currently trying to run the Jalview applet from within a GWT project. not being very successful, though. anybody with experience who could give me a hint? thanks a lot!! c. -- Claudia Chica Post doctoral fellow Structural and Computational Biology Unit Toby Gibson Group EMBL Meyerhofstrasse 1 69 117 Heidelberg Germany Tel. +49 6221 387 8451 From jprocter at compbio.dundee.ac.uk Tue Nov 17 13:29:50 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Tue, 17 Nov 2009 13:29:50 +0000 Subject: [Jalview-discuss] GWT and jalview In-Reply-To: <40E9D530-9D9A-4253-83B4-A54A3BB0CAFF@embl.de> References: <40E9D530-9D9A-4253-83B4-A54A3BB0CAFF@embl.de> Message-ID: <4B02A54E.7010204@compbio.dundee.ac.uk> Hi there Claudia. I've been meaning to try out the applet under GWT, but have not gotten around to it yet. Andrew Waterhouse did consider this a while back when GWT was released, but he had a suspicion there would be a fair few issues to fix before the applet would play nicely. I'd be very interested in hearing how you are getting on! One of the plans for the next year is to unify the applet and the application's UI model to allow alternate UI implementations to be used - I've already got you down as an interested party for one feature - perhaps you'd like me to keep you in the loop with these developments too ? (esp. if you can evaluate GWT for the applet!). Cheers Jim. On Tue, 17 Nov 2009 12:00:55 +0100 Claudia Chica wrote: > dear all, > > i'm currently trying to run the Jalview applet from within a GWT > project. > not being very successful, though. > anybody with experience who could give me a hint? > > thanks a lot!! > > c. > > -- > Claudia Chica > Post doctoral fellow > Structural and Computational Biology Unit > Toby Gibson Group > EMBL > Meyerhofstrasse 1 > 69 117 Heidelberg > Germany > Tel. +49 6221 387 8451 > -- ------------------------------------------------------------------- J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From veronica.xiaoyu at gmail.com Thu Nov 19 21:25:49 2009 From: veronica.xiaoyu at gmail.com (Xiaoyu Liang) Date: Thu, 19 Nov 2009 16:25:49 -0500 Subject: [Jalview-discuss] Jalview install problems Message-ID: Hi, I'm installing Jalview, but it pops out an error said " Installer User Interface Mode Not Supported". I added the option "-i Console" as it suggested, but it still doesn't work. Does anybody know how could I fix the problem? Thank you very much, Xiaoyu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20091119/d89f757e/attachment.html From jprocter at compbio.dundee.ac.uk Fri Nov 20 07:11:59 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Fri, 20 Nov 2009 07:11:59 +0000 Subject: [Jalview-discuss] Jalview install problems In-Reply-To: References: Message-ID: <4B06413F.7020903@compbio.dundee.ac.uk> Hello Xiaoyu. It sounds like you are installing on a unix or linux box, and the Flexera installAnywhere system cannot find any X libraries on your system. This could be because you have logged in to a non-X enabled console (try starting an xterm and see if that works) or that you have configured your machine purely as a server, i.e. X is not installed. When running Jalview in headless mode it still has some dependencies on the Java GUI implementation to access fonts and other graphical resources, so even if you want to run it in batch mode only, you'll still need to have a basic X install. Hope this helps Jim. Xiaoyu Liang wrote: > Hi, > > I'm installing Jalview, but it pops out an error said " Installer User > Interface Mode Not Supported". I added the option "-i Console" as it > suggested, but it still doesn't work. Does anybody know how could I > fix the problem? > > Thank you very much, > Xiaoyu > ------------------------------------------------------------------------ > > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss at jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss > -- ------------------------------------------------------------------- J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From m.simon at har.mrc.ac.uk Mon Nov 23 09:10:35 2009 From: m.simon at har.mrc.ac.uk (michy) Date: Mon, 23 Nov 2009 09:10:35 +0000 Subject: [Jalview-discuss] NGS data Message-ID: <4B0A518B.4080502@har.mrc.ac.uk> Hello, I am new to jalview. Can you open and view NGS from jalview? Kind Regards, Michy -- Michelle Simon Bioinformatics, MRC Mammalian Genetics Unit, Harwell, Oxon, ox11 0rd, U.K. E-mail: m.simon at har.mrc.ac.uk Telephone: +44 (0)1235 841031 www: http://www.har.mrc.ac.uk/ This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm From jprocter at compbio.dundee.ac.uk Mon Nov 23 11:11:44 2009 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Mon, 23 Nov 2009 11:11:44 +0000 Subject: [Jalview-discuss] NGS data In-Reply-To: <4B0A518B.4080502@har.mrc.ac.uk> References: <4B0A518B.4080502@har.mrc.ac.uk> Message-ID: <4B0A6DF0.2070903@compbio.dundee.ac.uk> Hello Michy I remember your email from back in January 2009, when you asked about tools to convert .ace files to any NGS format. None of the current versions of Jalview will cope perfectly with NGS scale data, although it is possible to read in a whole reference genome + aligned reads, you will need a machine with considerable amounts of RAM (6G at the very least) to work with jalview projects containing such alignments, and some operations (e.g. sequence selection and group creation) will be very slow. I hope to devote a whole development period to improving this situation next year, including the introduction of support for some of the common NGS formats (such SAM and BAM which can be manipulated using SAMtools). If there are specific formats that your institute works with, then do let me know and I'll see if I can incorporate them. Until then, I can only suggest you explore some of the existing NGS readers. One that I know of is Tablet (http://bioinf.scri.ac.uk/tablet/) written by Iain Milne, who also developed the TOPAli application for evolutionary analysis (one of the tools that was supported by the VAMSAS project). All the best, Jim Procter. michy wrote: > Hello, > I am new to jalview. Can you open and view NGS from jalview? > > Kind Regards, > Michy > > -- ------------------------------------------------------------------- J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096.