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

[Michał Koziarski]

2011/4/6 Christian Zmasek <cmzmasek at yahoo.com>

> 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?
>

I thought about using Rubyvis to produce images.

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

I've read a little about the Rubyvis and it seems like a fine solution, so I
would like to go with that, but I am open for suggestions.

>
>
> 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?
>

I think that since one of the purposes of the project is to prepare images
for use in web, they should be static from the beginning. It would be great
to create an interactive version too, so that you could modify data on the
fly and perhaps change data by modifing a graphic, but I don't think that I
would make it in time.

>
>
>
>
> >     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."
>

 Could you explain why?

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

 Yes, I am working on that right now, but strangely I can't come up with
many problems to anticipate. Perhaps you have some suggestions about this?
Anyway, I will most certainly update that.

>
> Christian
>
>