Re: [Gmod-ajax] rendered larger chromsome

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

Good work improving the rendering time!  It's great to see we can do a
large chromosome in a good amount of time.

Yeah, we definately need some sort of heuristic where we compact
features above some threshold.  Suzi's suggestion to turn them into a
feature density plot or some such was a good idea, but would require a
bit of work... maybe for now we can just drop the smaller features
out, or turn them off completely (e.g. how GBrowse stops displaying
features above the 1MB zoom level) or do something smarter than that,
where we have a "max track height" above which feature display would
shut off.

Andrew

On 3/22/07, Mitch Skinner <mit...@be...> wrote:
> I've put up Dmel 3R here:
> http://genome.biowiki.org/gbrowse/dmel51/prototype_gbrowse.html
>
> It rendered in less than 8 hours on one CPU, and the tiles and HTML take
> up around 13 gigabytes on disk.  Memory usage maxed out at 342 MB.  The
> 3R chromosome arm is the largest Dmel one at 28 Mb, or about 20 times
> the size of chromosome 4.  So to do human we just have to scale another
> order of magnitude; it's CPU bound and we've got a fair amount of CPU to
> throw at it, but if memory usage grows linearly with the amount of
> sequence then we may start running into problems.  We could do some more
> work on rendering on demand, and that would help, but you've still got
> to have all the features in memory at the same time to do layout, so we
> may not be able to reduce max memory usage very much that way.  Maybe we
> can partition the layout job if there are empty regions of the chromosome.
>
> One problem with the current approach is that the HTML files get quite
> large for the lower (more zoomed-out) zoom levels.  For the Genes track
> the entire_landmark HTML file is 1.6 megabytes; for CDS it's 7.7
> megabytes.  The HTML for entire_landmark for all tracks totals 24
> megabytes, which is how much you would have to download to actually view
> the entire_landmark zoom level.  Maybe we should have some kind of limit
> above which we turn off the HTML.  Also, if we had a way of lazily
> loading feature information then the HTML could be a lot smaller.
>
> With a large number of features the browser starts to slow down; for me
> this starts to be noticeable around the 1Mbp zoom level on Windows.  On
> other platforms firefox starts to bog down at higher (less dense) zoom
> levels.  Again, if we turn off the html above some feature density
> threshold this should be less of a problem.
>
> Mitch
>
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