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

Raoul Bonnal bonnal at ingm.org
Thu Apr 7 22:26:46 UTC 2011 

Hi Michal,
On 07/apr/2011, at 22.27, Michał Koziarski wrote:

> 2011/4/7 Raoul Bonnal <bonnal at ingm.org>
> 
> On 07/apr/2011, at 19.39, Michał Koziarski wrote:
> 
>> 2011/4/6 Raoul Bonnal <bonnal at ingm.org>
>> 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 thought about whether to implement that shell browser or work on images enrichment, and I am quite confused. Generally, I would agree that your idea seems to be better, but right now I can't come up with specific ways of enriching them. I guess it should be more obvious once images itself are created, but then there may be not enough time to implement everything.
> Those were just ideas and were not mandatory. I think, as you wrote, when the images will be ready and you'll be more familiar with bioinformatics problems, the enrichment will be more clear. What about the possibility to evaluate how to "fuse"/enrich and image with data coming from slightly different objects ? Like tagging data sets etc... (today american football training, I hope to find inspiration ^_^ )
> 
> Yeah, I realize that they were not mandatory, I just would like to make the best of this time. Anyway, I guess I will just stick to the file browsing idea for now, and later on reevaulate which one will be better at the time. 
> 
>> 
>> 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-)
>> 
>> Is that lib public now? And if so, could you provide me with repo url?
> Did you mean  R? http://www.bioconductor.org/developers/package-guidelines/
> this library is voted to bioinformatics + statistic 
> note that Claudio Bustos (RubyVis) has coded another great library for R http://ruby-statsample.rubyforge.org/rserve-client/
> and this is for statistics http://ruby-statsample.rubyforge.org/
> 
> Sorry, I wasn't very specific. I ment your lib for handling real time PCR.
It's not yet on github, was/is quite experimental, but is't a good candidate for a new plugins :-D when I'll have time to reopen it, however basically the data are managed like matrices ( in the latest version i was using statsample).

>>  
>> * 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)
>>  
>> That seems to be the most complicated one of those to visualize (or am I wrong?), it would be great to hear some specifics.
> If you mean phylo, I think Christian is an expert .
> 
> Yes, I ment Phylo. 
Ok wait some hint from Christian.
> 
>> 
>> Out of those, I think that Matrix would be a good place to start. They could be generated only with Rubyvis, and as I believe are used quite often. Would you agree?
> 
> Yeah at low level I think that most of the problems could be reduced to matrices.
> Another great tool for visualizing data and I love it, coded in perl, is http://mkweb.bcgsc.ca/circos/  we could you is to find inspirations.
> and http://vizbi.org/2011/Posters/List/?poster=D10
> 
> Indeed, Circos looks really great. Have you used it? How about the readibility? 
Yeah for some projects mostly on visualizing feature on circular genome, some time ago I was working on assembling bacterial genome which are circular

> 
> 
> Ciao.
> 
>> 
>> 
>> 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
>> 
>> 
> 
> 
> --
> Ra
> 
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> 
> 
> 
> 
> 
> 
> 

--
Ra

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