Re: [Gmod-ajax] Similie

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

Dear Ann Loraine

It certainly is,  you can focus the window using a call to a =
centerTimeline(xxx) function using the href tag in the html - where xxx =
is a date (ie the sequence base position)

have a look at this - =
http://simile.mit.edu/timeline/examples/religions/religions.html  (I =
can't be responsible for the subject matter!)

all the best

David

-----Original Message-----
From: Ann Loraine [mailto:alo...@gm...]
Sent: Fri 01/06/2007 16:32
To: Aanensen, David
Subject: Re: [Gmod-ajax] Similie
=20
This is nice!

Is it possible to focus the zooming at a single position or selection, =
so
that the item you want to examine in detail doesn't scoot off the screen =
as
you zoom in?

Yours,

Ann Loraine

On 6/1/07, Aanensen, David <d.a...@im...> wrote:
>
>  Hi,
>
> have you by any chance seen MIT's Similie project -   Timeline widget?
>
> http://simile.mit.edu/timeline/
>
> 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.
>
> 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 -
>
> http://www.mlst.net/chr/chr.html
>
> click on the gene to view homolog details from a database (probably =
best
> to ignore the details!).
>
> 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.
>
> 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.
>
> one of their examples is here -
> http://simile.mit.edu/timeline/examples/dinosaurs/dinosaurs2.html
>
> all the best
>
> David
>
>
>
> ------------------------------
> *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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--=20
Ann Loraine
Assistant Professor
University of Alabama at Birmingham
http://www.transvar.org
205-996-4155