[GSoC] Bionode project at GSOC 2014

[Eric Talevich]

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
>