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

[Toby Hocking]

Thanks for the ideas and the link to the Galaxy information, Peter. For now
it looks difficult to implement interactively defining and saving annotated
regions as a Galaxy Visualization, but I added Galaxy integration the list
of TODOs, and to the list of possible improvements that the GSOC student
could implement.

About the Python/C/C++ segmentation modules, they are indeed only Python 2
at the moment, and I just created some end user documentation

https://r-forge.r-project.org/scm/viewvc.php/*checkout*/python/00_README.html?revision=32&root=segannot


On Tue, Mar 4, 2014 at 5:13 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> 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 and for a (slightly out of date) overview, Jeremy's slides from BOSC 2012: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
>