[GSoC] Bio JavaScript/Node.js idea (bionode)

[Bruno Vieira]

Hi,


Can we still submit this idea for OBF projects?



bionode - A Node.js JavaScript library for client and server side
bioinformatics.

=================================================================================

**Rationale**

During the development of a web front-end or software with a web-interface,
it often becomes clear that a component implemented for the server-side
must be performed on the client side, or vice-versa. This generally
requires functionalities implemented in one language to be reimplemented in
another. Recent developments in Javascript make this unnecessary. Indeed,
JavaScript has become a “write once run everywhere” full stack programming
language that can be executed in the browser as well as on the server
(thanks to Node.js). The web-development community is enthusiastically
embracing this technology. In the last year, Node.js modules increased
2.6-fold to a total of 61656. The average growth rate is 175 modules per
day, which means that it will quickly surpass Java (71906) and Ruby (71446)
having already surpassed all the other languages (e.g., Perl: 29097;
Python: 40455). [1]

Consistent with this, web applications for visualizing or interacting with
biological data increasingly rely on javascript (e.g. [2-4]). Surprisingly
however, no generic javascript bioinformatics library yet exists, leading
independent projects to redundantly implement basic functionality. Here, we
propose to develop bionode a core javascript library for handling and
analyzing bioinformatics data - mirroring the core functionality of
established bio* libraries (e.g. bioperl, bioruby).

This will be done in close collaboration with the developers of BioJS (who
build reusable components for visualization of biological data) and of
WebApollo/Afra (a gene prediction curation software) for immediate
short-term applications. Importantly, we expect the long-term interest for
a bioinformatics javascript library to be huge.

**Approach**

We already seeded this project: bionode[5] is a Node.js module with some
bioinformatics methods that work on the client and server side.

Under the supervision of the mentor(s), the GSoC student will add more
methods/algorithms to the bionode project. The student could take
inspiration from other similar libraries in other programming languages,
such as bioperl or bioruby. Methods for input/output and wrangling basic
data types should be given a higher priority at the beginning of this
projects. For example, implementing some of the functions of
biopython.SeqIO could be a project. Another source for inspiration could
come from Massive Open Online Course, such as the “Bioinformatics
Algorithms” from the University of California, San Diego.

**Challenges**

Methods provided should be able to run on a server environment (via
Node.js) or browser environment (via webpack or browserify). Thus, the
module pattern used should be the one used by Node.js (CommonJS).

Good programming practices should be used, the code should be clear, well
documented and unit tested. Furthermore, relevant examples should be
provided for novice users (i.e. biologists who are just learning to
program).

**Difficulty and needed skills**

The student should ideally have an very good knowledge of JavaScript and
basic knowledge of bioinformatics/biology.

Experience using GitHub for collaboration would be a big plus.

**Mentors**

Bruno Vieira (@bmpvieira), Yannick Wurm (@yannick__)

[1]: modulecounts.com

[2]: jbrowse.org

[3]: apollo.berkeleybop.org

[4]: biodalliance.org

[5]: bionode.io


Regards,
Bruno Vieira
PhD Student at the Queen Mary, University of London