[GSoC] Bionode project at GSOC 2014

[Christoph Neuroth]

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!