[GSoC] GSOC project: improve SegAnnDB interactive DNA copy number analysis

[Peter Cock]

On Mon, Mar 3, 2014 at 10:13 PM, Toby Hocking <tdhock5 at gmail.com> wrote:
> Hey Eric thanks for your input -- these are really valuable comments!
>
> It would be nice to integrate with Galaxy, but do you think the interactive
> features would be possible? Can you recommend the relevant part of the
> Galaxy manual to read?

I've not tried this, but see
https://wiki.galaxyproject.org/VisualizationsRegistry
and for a (slightly out of date) overview, Jeremy's slides from BOSC 2012:
http://www.slideshare.net/jandot/j-goecks-the-galaxy-visual-analysis-framework

> I agree that it should be very nice to have a more robust genome viewer to
> view other tracks such as RefSeq genes or SNP allele frequency data, but
> again I wonder if the interactive annotation would be possible? By the way,
> what is "paging GMOD?"

I guess Eric meant paging as in calling (for some reason pagers
were very popular in the USA before mobile phones took off).
http://en.wikipedia.org/wiki/Pager

The verb is also used in large buildings for Tannoy announcements
via ceiling speakers ("Could Mr Jones please come to reception").
Although they probably don't use Tannoy as a noun in the USA?
http://en.wikipedia.org/wiki/Tannoy

> By the way, the reason why I decided to draw the signal using PNG
> scatterplots is because it is very fast -- at first I tried using
> JavaScript/D3 to draw it as SVG <circle> elements, but that is really slow
> when there are a lot of points on screen (as in the genome-wide plots).
>
> There is some SegAnnDB code for reading bedGraph files from disk before they
> are loaded into BerkeleyDB --- do you think that reader is suitable for
> inclusion in BioPython?
>
> Finally, there are indeed some Python extension modules (PrunedDP and
> SegAnnot) for efficiently calculating the displayed segmentation models, so
> those could definitely be included in BioPython if you like. Their source
> code is in SVN here
> https://r-forge.r-project.org/scm/viewvc.php/python/?root=segannot

Interesting - a Python module written entirely in C code (not sure
but I suspect for Python 2 only at the moment). Is there some end
user documentation to help understand the intended usage?

Regards,

Peter