[Biopython] GSoC 2015: Interactive visualisations for GenomeDiagram

[Peter Cock]

Hi Lucas,

On Thu, Feb 26, 2015 at 10:30 PM, Lucas van Dijk <info at lucasvandijk.nl> wrote:
> Hi all!
>
> I don't know if you guys already have a contender, but I'm really interested
> to be part of the Google Summer of Code this year, and especially doing the
> interactive visualisations for GenomeDiagram project!
>
> A little bit about myself:
> - I'm 24 years old and from the Netherlands, currently studying at Delft
> University of Technology.
> - Electrical (Computer) Engineering background
> - Started this year with the master Bio-informatics
> - Very experienced in Python, and I also have done a lot of webdev work so
> Javascript is no problem.
> - Currently have a small side job (1 day/week) as python software engineer
> where I create tools and webservices to visualise GIS related data.
>
> Why this project:
> - I'm really excited for the field of Bio-informatics, and I want to get
> more experience with the existing toolkits
> - I like making visualisations
> - This looks like something I can handle :)

Great :)

Another idea if you prefer something web-based might be Galaxy
visualisations, perhaps with BioJS. For instance I'd like to offer a way
view NCBI BLAST+ output graphically like the NCBI webserice or
better. Galaxy are also hoping to be accepted for GSoC:
https://wiki.galaxyproject.org/Develop/GSOC/2015Ideas

> About the project:
> You mention the library Bokeh, which looks very awesome, but it may depend
> on a lot of other libraries which are not necessary for the rest of
> BioPython. Some possibilities:
> - Make bokeh and all its dependencies optional: display a nice error message
> if the dependencies aren't installed when using trying to create a
> visualisation

That's roughly what we do do with "soft dependencies", for example
Bio.Graphics requires ReportLab but the rest of Biopython does not.

> - Put it the other way around: Create a separate python package which
> depends on BioPython for creating the visualisations.

Also possible.

> By the way, any particular reason for the choice of Bokeh, besides
> looking awesome? Any thoughts on Vispy or other libraries?
>
> Hope to hear from you guys!
>
> With kind regards,
> --
> Lucas van Dijk

The obvious choice of mentor here would be Leighton Pritchard,
if he can spare the time. I've not looked at Vispy or Bokeh myself.

Regards,

Peter