[BioRuby] GSoC - project "Represent bio-objects and related information with images"

[Christian Zmasek]

Hi, Michał:

You timeline is much better now!

I put some comments/question into your text (see below).



>     Week 1:
>     Goal: choose one  representative type of BioRuby object and develop class
> that would convert  its data to proposed format. That should come along with
> unit  tests.


This is a good idea -- to deliver a proof of concept first!

Did you think about how exactly the image(s) will be produced?

Which library (if any) do you plan to use?


Also do you plan to produce (interactive) graphics on the fly and/or create 
(static) image files (such as .png) to be viewed with other software?




>     Week 2:
>     Goal: develop graphical  module that would create image files based on
> data in unified format and  provide user interface, write unit tests.
> 
>     On this point it  should be possible to fully visualize chosen BioRuby
> object.
> 
>      Weeks 3 to 8:
>     Goal: basing on first weeks work, prepare  similar classes for all of the
> remaining BioRuby objects. Each class should  have unit tests.
> 
>     Week 9:
>     Goal: develop  mechanism of browsing images in shell. It should include
> simple search and a  way of opening images.
> 
>     Week 10:
>     Goal:  write integration tests.
> 
>     Weeks 11 and 12:
>      Goal: write documentation.
> 
> I would like to be more specific about what  should be done from weeks 3 to
> 8, though. It would be nice to plan some time  for every object that needs
> visualization, but I don't know which that would  be exactly. Could you give
> me a hand with this?

I think Raoul can answer this better.


I guess a good candidate would be sequence objects with features, such as 
intron/exon, mutations, etc.


I have doubts about this "develop  mechanism of browsing images in shell. It 
should include simple search and a way of opening images."

What about anticipated problems? Can you propose alternatives for things which 
might not work as planned?

Christian