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

[Eric Talevich]

Hi Toby,

The project idea looks good to me so far. If you feel confident in the
proposal now, would you mind posting it on the OBF wiki page under the
"cross-project" section?
http://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas

Thanks,
Eric

On Tue, Mar 4, 2014 at 9:16 AM, Toby Hocking <tdhock5 at gmail.com> wrote:

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 and for a (slightly out of date) overview, Jeremy's slides from BOSC 2012: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