Post-ISMB ping: Jalview integration in Genomespace

Forwarding to list for posterity:

The University of Dundee is a registered Scottish Charity, No: SC015096


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Jim and all,

Thanks so much for staying in touch - we’re glad to help with this. I’m adding our software developer Marco Ocana to the thread. Looking forward to continuing the discussion,


On Thu, Jul 25, 2013 at 9:39 AM, Dr JB Procter <> wrote:

Hi Ted and Michael.

A bit later than promised, but here’s the ping re Jalview. After we
talked, I sat down with Hervé Menager - who does, and did come
to your tech track. He had already spun up a private genomespace account
to try and hook in Mobyle, so we had a bit of a play. As far as I can
see, there are some minor hurdles we need to deal with, but nothing

It looks like step 1 - ‘launch Jalview with some data from the
genomespace web GUI’ is nearly straightforward, but we will ideally need
to hook up with the genomespace auth model. The problem is getting
Jalview to do Single Sign On (SSO), to avoid repeated logins. Section 4.1 (the GSLogin
Dialog) is the only section that mentions SSO, but from the
documentation it looks like SSO happens only between applications using
the CDK… can it also be made to happen if the user launches a tool from
the website (ie propagate session id/auth cookie from browser to JVM
launced via jnlp) ?

Regarding step 2… ‘login to access data from my genomespace account’ -
it looks like the CDK provides all the magic, and seems to already have
been decorated with OSGI metadata. So, providing the best example is the
cytoscape app, then I guess all we need to do is follow that pattern to
create some jalview specific genomespace glue.

If there’s anything we should be looking at for future steps, do let us
know. Otherwise, something will most likely happen in the next few
months - particularly when we get some new folk on the project.

It was good to meet you in Berlin !

The University of Dundee is a registered Scottish Charity, No: SC015096

Michael Reich <>
Director of Cancer Informatics Development
Broad Institute of MIT and Harvard
7 Cambridge Center, Cambridge, MA 02142, USA (617) 714-7467

Subject: Re: Post-ISMB ping: Jalview integration in Genomespace
Date: Thu, 25 Jul 2013 09:43:01 -0400
From: Michael Reich
To: Dr JB Procter
CC: Ted Liefeld, Jalview Development List, Marco Ocana