VIZBI 2011 call for participation - early registration deadline 31st Jan 2011

We are delighted to invite you and your colleagues to register for VIZBI 2011, the 2nd workshop on ‘Visualizing Biological Data’, to be held at the Broad Institute, Cambridge-MA (USA), March 16-18, 2011.

VIZBI 2011 brings together scientists actively using or developing computational visualization to study a diverse range of biological data. We have assembled a list of high-profile speakers (see end of email) who will review the state-of-the-art and challenges of visualization within their field. VIZBI 2011 also features an ‘art & science’ evening (Thursday) during which we will be joined by medical illustrators, graphic designers, and artists interested in biological visualization. On Saturday, March 19, immediately after the workshop, participants can choose to attend one of a range of tutorials and take part in a hands-on ‘bring-your-own-data’ session.

All workshop participants are encouraged to submit a poster on their work, plus an image for the art & science evening. A limited number of participants will also be offered the opportunity to be part of an authoritative book co-authored with the VIZBI speakers, essentially an expanded version of the Nature Methods focus issue (http://www.nature.com/nmeth/journal/v7/n3s); the book will be the first to comprehensively review this topic and will be distributed by a major scientific publisher.

Please see http://vizbi.org for more information.
We hope you can join us for this exciting event!

We would also be grateful if you consider forwarding this call to colleagues who may be interested.

The VIZBI 2011 chairs:

Seán O’Donoghue, EMBL
Bang Wong, Broad Institute
James Procter, U. Dundee
Larry Hunter, U. Colorado

VIZBI 2011 Speakers (in order of appearance):
Manuel Lima Microsoft, UK. (Keynote: Visual Complexity).
Robert Kuhn, UCSC, USA…
Bradley Bernstein, Harvard, USA.
Erez Lieberman-Aiden, Harvard, USA.
Eric Westhof, U. Strasbourg, France.
John Quackenbush, Harvard, USA.
Yoseph Barash, U. Toronto, Canada.
Tamara Munzner U. British Columbia, Canada. (Keynote: Human-Computer Interfaces).
John Westbrook, Rutgers, USA.
Arthur Olson, Scripps, USA.
Gaël McGill, Harvard Medical School & Digizyme, USA.
Trey Ideker, UCSD, USA.
Anne-Claude Gavin, EMBL, Germany.
Minoru Kanehisa, U. Kyoto, Japan.
Yannis Kalaidzidis,MPI-CBG Dresden, Germany.
Drew Berry, Walter & Eliza Hall, Australia. (Keynote: Communicating science, Visually).
Willy Supatto, U. Paris Diderot, France.
David Shattuck, UCLA, USA.
Rob MacLeod,U. Utah, USA.
Des Higgins, U. College Dublin, Ireland.
Rod Page, U. Glasgow, UK.
Hervé Tettelin, U. Maryland, USA.
Martin Wattenberg & Fernada Viegas, Google, USA. (Keynote: Visual Design)

VIZBI training day topics:
Blender, Cytoscape, Circos, Jalview, Processing, VTK & ParaView.

Dear Jalview developers,
I have been encountering problems with the PDB model viewing since September. At first it was no more possible to color the model according to the alignments. I tried again today and it looks like it's not possible at all to fetch or view the PDB files linked to sequences.
-Paul

further to my last email it occured to me you might be talking about problems with JalviewLite. The major change with version 2.6.x is that I upgraded the version of Jmol used by Jalview to series 12 - and so Jalview needs this new version of Jmol to run. Please check you have updated the JmolApplet jar reference included in the applet tag to this one: http://www.jalview.org/examples/JmolApplet-12.1.13.jar

You can also test the applet on your machine via www.jalview.org/examples/applets.html

Jim.

···

On 12/01/2011 22:29, Paul Pillot wrote:

Dear Jalview developers,
I have been encountering problems with the PDB model viewing since September. At first it was no more possible to color the model according to the alignments. I tried again today and it looks like it's not possible at all to fetch or view the PDB files linked to sequences.

--
-------------------------------------------------------------------
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.

Thanks Jim for your answer and the links you provided.
I made several trials today.
The example you provided works well.
I tried to fetch sequences and structures from the PDB, and it worked well too.
In fact the concern arises when I load projects made with previous versions of jalview. In one case, the color chain command has no effect, and in the other case, no model can be linked to a structure and displayed.
Except if it is of any specific interest to your team to try to debug that incompatibility, I think I'll just rebuild these projects with the newer Jalview version.
Thanks again,
Paul

----- Message d'origine -----

···

De: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Jeudi, Janvier 13, 2011 12:30 pm
Objet: Re: [Jalview-discuss] Problem with PDB model display
À: Paul Pillot <Paul.Pillot@ac-nice.fr>
Cc: jalview-discuss@jalview.org

On 12/01/2011 22:29, Paul Pillot wrote:
> Dear Jalview developers,
> I have been encountering problems with the PDB model viewing since
September. At first it was no more possible to color the model
according to the alignments. I tried again today and it looks like
it's not possible at all to fetch or view the PDB files linked to sequences.
further to my last email it occured to me you might be talking about
problems with JalviewLite. The major change with version 2.6.x is that
I
upgraded the version of Jmol used by Jalview to series 12 - and so
Jalview needs this new version of Jmol to run. Please check you have
updated the JmolApplet jar reference included in the applet tag to
this
one:

You can also test the applet on your machine via
www.jalview.org/examples/applets.html

Jim.

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764
The University of Dundee is a Scottish Registered Charity, No. SC015096.

It is of interest - because it is important that we maintain backwards compatibility with previous Jalview versions, so if you are willing, I'd be interested in taking a look at the files.

I've created a bug on our issue tracker - here:http://issues.jalview.org/browse/JAL-747

If you would like to register, you can then upload one or more of your files onto this bug. Furthermore, if the contents of the files are sensitve then just drop me a line once you've registered and I'll make the issue private to just you and me so you can keep your data confidential (or you could just email me the files and I'll do all that for you !).

Jim.

···

On 13/01/2011 12:15, Paul.Pillot@ac-nice.fr wrote:

Thanks Jim for your answer and the links you provided.
I made several trials today.
The example you provided works well.
I tried to fetch sequences and structures from the PDB, and it worked well too.
In fact the concern arises when I load projects made with previous versions of jalview. In one case, the color chain command has no effect, and in the other case, no model can be linked to a structure and displayed.
Except if it is of any specific interest to your team to try to debug that incompatibility, I think I'll just rebuild these projects with the newer Jalview version.