Re: [Gmod-ajax] Feature Mark Up

[Andrew U. <and...@gm...>]

Hi Steve (et al)...

This sounds like excellent news, thanks!  But, I'm getting timed-out
loading both pages you linked to... can you let us know when they're
back up?  I would love to take a look.

You should commit the code to CVS... I've also made a few changes
across the server-side code (including generate-tiles) to test
on-demand tile rendering, which will be useful for large genomes, and
to fix some stupid bugs left in TiledImage, etc. from back in the day
(e.g. database connections not hanging up), which you probably noticed
and fixed by now also.  Once your code is in, I'll merge in my
changes.

Just to let everyone know about the "render on demand" stuff... the
idea is that we still fill a database with primitives, but only render
tiles as they are request by user (they are also saved, so no need to
re-render unless the underlying data changes, so we'll have some sort
of "dirty tile" flag or some such).

This will enable people to put up large genomes without pre-rendering
all the tiles.  Currently, the rendering step is the major limiting
factor (my benchmarks show around 90% of the actual generate-tiles.pl
time is spent on database lookup of primitives).  For example, Dmel
arm 4 takes a full day to render on our 24-CPU cluster, but only an
hour of that time is spent filling the database.

I'm trying a few things to optimize this right now, including the
on-demand rendering, and I'll keep the list updated once I get
somewhere (the things I'm trying can be found on
http://biowiki.org/view/GBrowse/WishList under the "rendering
optimizations" sublist).  I think we could seriously reduce the
fill/access time, but until then, on-demand rendering will at least
make large genomes feasible.

Cheers,


Andrew


On 11/13/06, Steve Taylor <st...@mo...> wrote:
> Hi,
>
> I thought I'd send this to open up the discussions on the new list!:-)
>
> I haven't checked in this code yet but I have modified generate-tiles.pm and BatchTilesImage.pm to allow marking up of the features in each of the tiles using client side image maps. We may want to
> change this later to do CSS maps but that would be only a small code modification. It basically generates an html file per tile with an inlined image and the appropriate map coordinates. The browser
> XMLHttpRequests the data over when it needs to using Ajax.Updater (from the js library Prototype).
>
> You can see what it looks like on:
>
> http://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrowse.html
>
> Try dragging and clicking on features.
>
> Advantages of current implementation
> -----------------------------------
> - should work on all browsers and doesn't require any fancy javascript
> - will support polygons, ellipses etc
> - allows distribution on different servers for tiles
>
> Disadvantages of implementation
> -------------------------------
> - all html per tile currently generated server side (not sure if this is an advantage or disadvantage at this stage) but may be a pain to do updates
>
> Obviously where javascript:alert('Active image map') you should have the relevant details of the feature and a nicer pop up. The js alerts are pretty annoying at the moment when dragging! I intend to
> put js pop ups similar to the ones we have at http://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=U00096%3A1..10000.
>
> Let me know what you think. I will check it in if people think it is worthwhile at this stage.
>
> Regards,
>
> Steve
> ------------------------------------------------------------------
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