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

[Raoul Bonnal]

Hi Michal,
the time line is more detailed now.
As Francesco suggested and also reported on our page we suggest RubyVis library, Claudio the coder of the binding offers his help and this is a very good news for us.

Week 9: what do you mean for browsing images in shell ? I can't grasp the benefit now, but we can discuss. The main problem is how to control the application which displays  the image; for web browsers there are techniques but are not so easy.
I'm just thinking to an add-on for this week: if we have different types of data that we can display quite easily  on the web(done in the previous weeks) , why not spending this time to enrich the images with controls (bars, check boxes, interaction in general). This part requires a skill in javascript. http://vis.stanford.edu/protovis/ex/cartogram-full.html
Or another interesting feature would be: adding layers of information to the standard image.
Note: perhaps these ideas are a bit complicate for 1 week but it would be interesting to evaluate the feasibility. 

I forgot to mention, in some case I think that if there are web services which produce images that services could be used. Consider the possibility to display Venn diagrams Google has one service http://code.google.com/intl/it-IT/apis/chart/docs/gallery/venn_charts.html or another one is http://bioinfogp.cnb.csic.es/tools/venny/index.html.
Sets are a kind of data type that in my daily work I have to display with a high frequency, specially when the boss needs to make reports :-)

So we arrived to the which bioruby objects we want to display. This is a quite complex question because some are there and other are not.
This library as been always sequence/feature centric (please correct me if I'm wrong), because we were used to demand to R tasks more statistics.
Main areas are 
* NGS: display create coverage alignemnt for a region with the possible annotation that are accessible from bioruby
* Matrix: display heatmaps, scatter plots, bars ( I wrote a very alpha lib for handling real time PCR  and gene expression datasets -not images-) 
* Sets: a seq could be generated from any kind of analysis, enrichment, annotation, reports
 ** reports could be meta-objects for instance the results of an allignment or mapping or gene quantification when you need to compare multiple populations or technical replicates 
* Phylo (i'm not an expert)

with the idea to produce high quality images ready to be published.

These are a bunch of ideas and words.
About tomorrow IRC meeting, @work they scheduled a meeting for (my) afternoon, I'll do my best to be on IRC. Feel free to contact who is around.

Regards.

  _____  

From: Christian Zmasek [mailto:cmzmasek at yahoo.com]
To: Michał Koziarski [mailto:michalkoziarski at gmail.com], Chris Fields [mailto:cjfields at illinois.edu], bioruby at lists.open-bio.org
Cc: Raoul Bonnal [mailto:bonnalraoul at ingm.it]
Sent: Wed, 06 Apr 2011 20:48:32 +0200
Subject: Re: [BioRuby] GSoC - project "Represent bio-objects and related information with images"

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