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

[Toby Hocking]

Great, thanks for the encouragement, Eric. I posted it under the
cross-project section so I will be hoping to hear from some interested
students in the coming weeks.


On Tue, Mar 4, 2014 at 3:45 PM, Eric Talevich <eric.talevich at gmail.com>wrote:

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 and for a (slightly out of date) overview, Jeremy's slides from BOSC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