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

[Toby Hocking]

Thanks for the input and the links to related work, Peter and Raoul.

About BioPython, I have used it in previous projects, but its current
features do not really help for this SegAnnDB project. As I understand,
BioPython is best for things like sequence analysis and downloading data
from GenBank, but for SegAnnDB I was doing something quite different:
interactive visualization and storing user-specific annotations using a web
server/database.

About GenomeDiagram, it definitely could be used to plot DNA copy number
profiles, but it is currently neither interactive nor linked to a database,
and I really needed both of those features for SegAnnDB. GenomeDiagram
could have been used to make some of the static PNG plots on SegAnnDB, but
instead I used PIL directly since that is faster.

About R, thanks for the link to the Java implementation of fastR, but I
haven't used R at all in SegAnnDB since I wanted to just depend on 1
language on the server side (Python).

Finally about BioJS, I also wrote them, but now I realize that SegAnnDB is
a better fit for the cross-language nature of OBF. BioJS is focused on
developing web client-side JavaScript visualizations, which SegAnnDB does
for DNA copy number profiles, so perhaps I could work with the BioJS guys
on porting my existing JS code for their uses. However, my SegAnnDB project
is also tightly integrated with a server-side Python component, which I
would like a student to develop in GSOC.

So again thanks for the encouraging comments and I will go ahead and post a
more detailed project proposal on the wiki.


On Mon, Mar 3, 2014 at 10:47 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Mon, Mar 3, 2014 at 3:07 PM, Toby Hocking <tdhock5 at gmail.com> wrote:
> > Hey OBF developers, I am a bioinformatics researcher and long-time
> > developeR (admin and mentor for R's participation in GSOC). Using
> > JavaScript and Python, I have developed SegAnnDB, a web site for
> > visualization and interactive annotation of DNA copy number profiles
> >
> http://bioinformatics.oxfordjournals.org/content/early/2014/02/03/bioinformatics.btu072.shortand
> > I want to get a GSOC student to implement some improvements. Would it
> > be possible for me to propose this as an OBF project and possibly be a
> > mentor for GSOC?
> >
> > I think SegAnnDB fits into the main theme of OBF: writing open-source
> code
> > for analysis and visualization of biological data. The student would need
> > to write Python code for the server side and JavaScript code for the web
> > client side so I think it would fit best into the "cross-project ideas"
> > section.
> >
> > Anyway, if it is OK with you guys, can please I post my project proposal
> to
> > the OBF GSOC ideas wiki page?
>
> Do you see any natural links to Biopython on the server side (an OBF
> project which would be good for the GSoC link) or BioJS on the client
> side (not an OBF project, but also participating under GSoC directly)?
>
> See also Leighton's outline Biopython proposal on interactive graphics:
>
> http://biopython.org/wiki/Google_Summer_of_Code#Interactive_GenomeDiagram_Module
>
> Peter
>