[Gmod-ajax] Similie

[Aanensen, D. <d.a...@im...>]

Hi,
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have you by any chance seen MIT's Similie project -   Timeline widget?=20
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http://simile.mit.edu/timeline/
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It struck me that this could be utilised in a gmod-ajax type fashion but =
with the timescales converted to sequence co-ordinates for displaying =
sequence annotation.
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this is a very quick (and apologetically shoddy)  thrown-together =
example that I have done for parsing an EMBL file into XML and using the =
'days' in the timeline to display CDS positions based on annotated =
sequence start and end points -=20
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http://www.mlst.net/chr/chr.html
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click on the gene to view homolog details from a database (probably best =
to ignore the details!).=20
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the scale labels  need changing and the iframe at the bottom needs =
replacing with a DIV and results AJAX'd in but you can see the kind of =
thing I mean.
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The scales can quite easily be changed, various levels added and custom =
graphics added (bioperl glyphs for eg) but I don't know how well it =
would scale.
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one of their examples is here - =
http://simile.mit.edu/timeline/examples/dinosaurs/dinosaurs2.html=20
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all the best

David
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________________________________

From: gmo...@li... on behalf of Steve Taylor
Sent: Fri 01/06/2007 14:11
To: Mitch Skinner
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Openlazlo



Hi,

>
>>perhaps a Google Maps-type widget is lurking out there that's
>>exactly what we need (though I doubt any available toolkit can do the
>>scary things that Mitch is currently trying with tracks built entirely
>>out of DIVs)
>
>
> I've been experimenting with this over the last few weeks, which is =
part
> of the reason I've been so quiet lately.  This is still in an =
extremely
> sketchy state, but there's enough there to get the idea:
> http://genome.biowiki.org/test/divbrowser/genome2.html
>
> The features are exons from D. melanogaster chromosome 3R.  There are
> about 16,000, of which Firefox is able to show a few thousand on my
> hardware before it starts to bog down.  If you zoom out beyond about 3
> megabases the zooming gets to be quite slow, but that's above the =
point
> where we're currently switching to a feature density histogram for =
that
> track, anyway.
>
> There's still some low-hanging fruit performance-wise, so I'm =
optimistic
> that it'll scale to a full set of tracks, especially if we're smart
> about interval search and attaching and detaching things from the DOM.
> And adjusting the threshold where we switch to a density histogram
> should accommodate hardware differences.
>
> The rationale for using divs is:
> 1. reduces server side processing/storage for image tiles
> 2. allows for a nice client-side feature creation/editing UI
> 3. zooming is cool, but it's more than just eye candy--it helps you =
keep
> an intuitive sense of where you are
> 4. client can cache an entire chromosome worth of features (at least =
for
> some tracks)--given where firefox and WHAT-WG are going this may =
enable
> offline use in the future.
> 5. more cross-browser than SVG (I've been testing in firefox and IE =
6/7
> and I'll be trying for Safari as well)
>

Hey that is really cool! Reminds me of the Integrated Genome Browser =
zooming functionality.

I would be surprised if OpenLazlo could do the hardcore stuff but was =
wondering if it would be worth looking into using the components for =
other parts of the interface such as popups, menus, search
forms, sidebars, annotation editing etc.

Cheers,

Steve
------------------------------------------------------------------
Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University

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