[GSoC] Bionode project at GSOC 2014

[Pjotr Prins]

Maybe we can ask Rob Buels to be a co-mentor on this project. Rob is
the most JS savvy of all of us.

Pj.

On Fri, Mar 14, 2014 at 10:50:26PM -0700, Eric Talevich wrote:
> Hi Chris,
> 
> To add to what you and Bruno already have, here are a couple more sub-ideas:
> 
> 1. In addition to the object designs you see in BioJS and the other Bio*
> projects, there are couple of database schemas bionode could be made
> compatible with: BioSQL and CHADO.
> http://www.biosql.org/wiki/Main_Page
> http://gmod.org/wiki/Chado_-_Getting_Started
> 
> These schemas are already designed to encapsulate the types of information
> that appear in a variety of different file formats, so they can be a guide
> for designing your objects in bionode. Plus, compatibility.
> 
> 2. For supporting genome browsers and NGS-type data sets, notice that VCF,
> GFF, BED, and a few other formats have some useful similarities. These
> formats are supported together by tools like tabix and bedtools and can be
> queried similarly:
> http://samtools.sourceforge.net/tabix.shtml
> http://bedtools.readthedocs.org/en/latest/
> See also:
> http://genome.ucsc.edu/FAQ/FAQformat.html
> 
> Cheers,
> Eric
> 
> 
> 
> On Mon, Mar 10, 2014 at 1:21 PM, Christoph Neuroth <
> christoph.neuroth at gmail.com> wrote:
> 
> > Hi everyone,
> >
> > I am interested in working on the bionode project for GSOC and would
> > like to shortly introduce myself and ask for any thoughts on my
> > proposal.
> >
> > My name is Chris, or c089 on both Github and Twitter. I have a B.Sc.
> > in computer science from Munich University of Applied Sciences and
> > plan to start a master's degree at University of Leipzig in April (not
> > yet enrolled, but will be on April 21, which the FAQ states as the
> > decisive date, if nothing goes wrong with the paperwork). This masters
> > course allows to specialize in either bioinformatics or medical
> > informatics and while I've not yet decided on which to chose I would
> > like to use GSOC to get a good understanding of bioinformatics as well
> > as contribute to open source. I don't have an existing bioinformatics
> > background, but currently supplement my high school biology knowledge
> > by taking a genetics online course and will probably take both the
> > bioinformatics class at uni and the Coursera one mentioned on the
> > project idea page to acquire the required knowledge during the GSOC
> > period.
> >
> > As for my open source background, I've been contributing to various
> > open source projects for years. I am currently a maintainer of
> > rendrjs, which might be relevant for the bionode project because it is
> > a library that focuses on rendering Backbone.js apps on the client and
> > server from the same code.
> >
> > For my project plan I would really like some input and especially
> > don't know how much detail up-front is required for a successful
> > proposal, but the following possible tasks came to mind after reading
> > the project rationale:
> >
> > 1) Learn about the needs of the bioinformatics community. This should
> > be achievable by enhancing knowledge on the domain itself, discussions
> > with mentors and evaluating strengths and weaknesses of the
> > implementations available for other languages by using them and
> > reading about them on the mailing lists
> > 2) Extend the existing project infrastructure to run the test suite in
> > targeted browsers as well as node.js environment using the karma
> > runner and Browserstack or SauceLabs cloud services for cross-browser
> > infrastructure
> > 3) Identify good JavaScript API design for the requirements identified
> > earlier and implement new features in bionode using test-driven
> > development. If possible and desired, I might also work on
> > cross-implementation test suites for the different language projects.
> > 4) detect duplications/overlaps of code in BioJS and the other JS
> > libraries mentioned on the wiki and extract those to bionode
> > 5) If there's time left for side-projects, I'm also interested in
> > contributing a bit to the visualization projects listed on the
> > projects page of the BioJS project to see how well the APIs in bionode
> > work.
> > 6) Given a successful project, I also plan on presenting the project
> > at node.js/JavaScript meetups and conferences at the end of the summer
> > as well.
> >
> > Looking forward to any feedback on these thoughts!
> > _______________________________________________
> > GSoC mailing list
> > GSoC at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/gsoc
> >
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