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

[Peter Cock]

Devil's advocate: Would this not be a better match to BioJavaScript
which was accepted as a GSoC organisation in its own right? What
do they think?

http://www.google-melange.com/gsoc/org2/google/gsoc2014/biojs

Regards,

Peter



On Mon, Mar 3, 2014 at 11:10 AM, Raoul Bonnal <bonnal at ingm.org> wrote:

> 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
> >
> > _______________________________________________
> > GSoC mailing list
> > GSoC at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/gsoc
>
>
>
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