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

[Raoul Bonnal]

Hi Bruno,
I am personally fine with this and please go ahead and add the project in the cross section on the wiki.
 Just a minor suggestion when you are citing modules from other projects please provide links to projects and specific modules so people can smoothly surf.

Raoul

On Mar 3, 2014, at 11:46 AM, Bruno Vieira <mail at bmpvieira.com> wrote:

> 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
> 
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