[BioRuby] GSoC - project "Represent bio-objects and related information with images"
Christian Zmasek
cmzmasek at yahoo.com
Wed Apr 6 18:48:32 UTC 2011
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
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