[DAS] Question about das development.

Mon, 19 Aug 2002 15:44:09 -0400

I've responded inline and have added Foo Cheung to the CC list as he contacted me about using our browser (the SVG Open link) as the basis for a DAS system.

Chris Lewis
Bioinformatics Programmer
Saskatoon Research Center
Agriculture and Agri-food Canada
lewisCT@em.agr.ca
phone: 306-956-7693

>>> "Kulp, David" <david_kulp@affymetrix.com> 08/19/02 11:41am >>>
>From the whizbang angle, I've been thinking about a DAS-SVG viewer.  The
"problem" is typical for genome browser displays: too many features
significantly slows down display, both in terms of data transmission and SVG
client rendering.  

We found the load tolerable for our purposes.  As you start adding additional data it becomes necessary to think about the difference views you need.  We opted for a chromosome view, a BAC view, a gene view, a sequence view and a annotation view.  Each of these opens in an SVG 'window' inside the browser.  As long as you don't try to jam everything into one display, and your client has a decent amount of processing power, it seems to be ok.

I looked a little into how one might deal with dynamic
content and semantic zooming.  It turns out that the Adobe viewer provides
two non-standard hooks which allow you to make URL calls and to parse the
returning document into a DOM.  

This is what we've done, we've used the postURL and parseXML methods to fetch and dynamically display data in our browser.

Thus, Javascript callbacks could be attached
to zoom levels, hidden tracks, or objects, which caused the server to be
queried for additional SVG which was then attached to the existing DOM.
Sounds very cool!

Haven't done anything with zoom levels, but what you describe is certainly possible.

But another problem is that SVG (at least with Adobe's viewer) has a
hard-limit of 8 levels of zoom, i.e. a 256X zoom, but unless you're fancy,
it's really just 4 levels of zoom in and 4 out.  That's not enough to go
from nucleotide to chromosome.

Have decided not to use the mouse-click zoom with our browser for two reasons:

1) The 8 zoom levels that you mention
2) There is no way (that I found) to restrict the mouse-click zoom to a specific portion of the document (though you could work around it).

Instead I modify the transform attribute for the elements...  Each SVG 'window' in our framework has a transform object associated with it, and this is adjusted to scale and translate the content within the window.

We're working to get a public version of our browser out on the web.  I would be quite interested in working with people on other SVG based projects.  One thing worth mentioning is that text handling in SVG, especially text entry, is awkward in SVG and might pose a problem for a DAS system.

cheers,
Chris

-d

-----Original Message-----
From: David Block [mailto:dblock@gnf.org] 
Sent: Monday, August 19, 2002 10:33 AM
To: Chris Lewis
Cc: Bill Gooding; das@biodas.org; Lincoln Stein
Subject: Re: [DAS] Question about das development.

So close - the author of the first link was at BOSC!

Chris - this Bill Gooding wants to collaborate on an SVG viewer starting 
from XML and using XSLT - you guys should be collaborating.

Go for it!
Dave

On Tuesday, August 13, 2002, at 05:51 AM, Lincoln Stein wrote:

> Search for "SVG" and "genome browser" on google.  Here's one:
>
> http://www.svgopen.org/abstracts/lewis_et_al__bioviz_genome_viewer.html 
>
> Here's another:
>
> http://www.labbook.com/ 
>
> Here's a third (ruby):
>
> http://gb.bioruby.org/ 
>
> There's also a commercial java based browser that uses XML as its data
> transport and SVG for its UI, but for the life of me I can't find the 
> name or
> URL (it's in development).
>
> Lincoln
>
> On Monday 12 August 2002 03:12 pm, Bill Gooding wrote:
>> Hi,
>>
>> Although I am new to the mailing list, I have been looking at
>> bioinformatics information for a while and had a simple question.  From
>> what I have seen it appears that in order to access the XML information
>> from various servers people use a downloaded java program which 
>> implements
>> a GUI (Swing/AWT) for displaying information.  I was wondering if 
>> anyone
>> had considered using an XML based server that tranforms the data into 
>> SVG
>> for display on a browser.  That is, something similar to Cocoon.  That 
>> way,
>> differing XML format could be handled in a more comprehensive way.  I 
>> have
>> begun writing code to implement this idea (although it is not Cocoon 
>> based
>> - I use jave xml api's) and am perfectly willing to donate it to 
>> biodas.org
>> as open source as a start to developing such a system.
>>
>> So with that background my question is:
>>
>> 1.  If a system such as I have proposed has been developed, where is 
>> it ?
>> I just need a specific link.
>>
>> 2.  If such a system does not exist, is anyone interested in the idea 
>> or
>> want to discuss it ?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Bill Gooding
>>
>>
>>
>> ---------------------------------
>> Do You Yahoo!?
>> HotJobs, a Yahoo! service - Search Thousands of New Jobs
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--
David Block                                  dblock@gnf.org 
GNF - San Diego, CA             http://www.gnf.org 
Genome Informatics / Enterprise Programming
Weblog:      http://radio.weblogs.com/0104507/ 

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