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

Thu Apr 7 20:27:44 UTC 2011

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.htmlor 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.

>
>
>> * 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.

>
>
> 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?

>
>
> 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
>
> linkedin: http://it.linkedin.com/in/raoulbonnal
> twitter: http://twitter.com/ilpuccio
> skype: ilpuccio
> irc.freenode.net: Helius
> github: https://github.com/helios
>
>
>
>
>
>
>