The jalview applet is now available in the Mobyle Pasteur website

Dear Jalviewers,

This e-mail is both an announcement and a call for comments. We have installed the new version of the Mobyle framework (v1.0RC1) on the Pasteur website (http://mobyle.pasteur.fr).

Among other improvements, it includes the possibility to visualize your multiple alignments with the Jalview Applet. To do so, once you have run any program that produces a multiple alignment (muscle, clustalw...), just click on the "View with Jalview" button below the result, and it will display the multiple alignment using Jalview. Any comment would be welcome, especially coming from users familiar with Jalview or Jalview authors ;).

Cheers,

Hervé, for the Mobyle Development team

Hi there, Hervé... Mobyle 1.0RC1 is looking great, and all normal functions work fine with firefox 4!

I do have a couple of comments (of course). One thing that confused me was the version number given after the title - e.g. Jalview 1.011, and Archeopteryx 0.955 beta. It might be better to include 'Mobyle' somewhere there to make it clear that the version number is associated with Mobyle rather than the embedded tool (which has its own version number given in the 'about' menu.

I also ran in to some oddness whilst trying something obscure. I've been doing lots of work on the JalviewLite javascript api related to running multiple applet instances on the page (e.g. two applets, structure views, tree views, etc), and so I tried to launch both archeopteryx and jalviewLite on the same alignment, just to see what happens. Mobyle currently doesn't allow this directly, of course, so I did this by opening each viewer, then clicking the 'view in own tab' icon at the top right of each viewer's iframe.
The strange thing is that only one of the applets will run at once when they are in different tabs. I could eventually get both working in separate windows (carefully refresh/reloading each one), but they both seemed to crash easily, and when one crashed, the other would too. I'm not quite sure what's going on here, but I do know that there are some problems with the way JalviewLite responds to signals from the browser, and it'd be nice to track them down.

Jim.

···

On 25/01/2011 09:31, Hervé Ménager wrote:

Dear Jalviewers,

This e-mail is both an announcement and a call for comments. We have
installed the new version of the Mobyle framework (v1.0RC1) on the
Pasteur website (http://mobyle.pasteur.fr).

Among other improvements, it includes the possibility to visualize your
multiple alignments with the Jalview Applet. To do so, once you have run
any program that produces a multiple alignment (muscle, clustalw...),
just click on the "View with Jalview" button below the result, and it
will display the multiple alignment using Jalview. Any comment would be
welcome, especially coming from users familiar with Jalview or Jalview
authors ;).

Cheers,

Hervé, for the Mobyle Development team
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://lists.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.

Thank you very much for your extremely quick feedback, Jim!

I'll take your comments into account to correct the interface.
Regarding the "strange bug", it really seems very odd, but I'll try to reproduce it, and give you some data about it.

Hervé

···

On 01/25/2011 10:55 AM, Jim Procter wrote:

Hi there, Hervé... Mobyle 1.0RC1 is looking great, and all normal
functions work fine with firefox 4!

I do have a couple of comments (of course). One thing that confused me
was the version number given after the title - e.g. Jalview 1.011, and
Archeopteryx 0.955 beta. It might be better to include 'Mobyle'
somewhere there to make it clear that the version number is associated
with Mobyle rather than the embedded tool (which has its own version
number given in the 'about' menu.

I also ran in to some oddness whilst trying something obscure. I've been
doing lots of work on the JalviewLite javascript api related to running
multiple applet instances on the page (e.g. two applets, structure
views, tree views, etc), and so I tried to launch both archeopteryx and
jalviewLite on the same alignment, just to see what happens. Mobyle
currently doesn't allow this directly, of course, so I did this by
opening each viewer, then clicking the 'view in own tab' icon at the top
right of each viewer's iframe.
The strange thing is that only one of the applets will run at once when
they are in different tabs. I could eventually get both working in
separate windows (carefully refresh/reloading each one), but they both
seemed to crash easily, and when one crashed, the other would too. I'm
not quite sure what's going on here, but I do know that there are some
problems with the way JalviewLite responds to signals from the browser,
and it'd be nice to track them down.

Jim.

On 25/01/2011 09:31, Hervé Ménager wrote:

Dear Jalviewers,

This e-mail is both an announcement and a call for comments. We have
installed the new version of the Mobyle framework (v1.0RC1) on the
Pasteur website (http://mobyle.pasteur.fr).

Among other improvements, it includes the possibility to visualize your
multiple alignments with the Jalview Applet. To do so, once you have run
any program that produces a multiple alignment (muscle, clustalw...),
just click on the "View with Jalview" button below the result, and it
will display the multiple alignment using Jalview. Any comment would be
welcome, especially coming from users familiar with Jalview or Jalview
authors ;).

Cheers,

Hervé, for the Mobyle Development team
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://lists.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss