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

Tue Mar 4 13:03:17 UTC 2014

Dear Eric et al,

Thanks for the interesting and very valid discussion. For what its worth,
let us provide some more info/thoughts regarding some of the specific
points that have been raised:

We had already contacted the BioJS team and they are indeed interested in
working in close collaboration with us regarding the development of core
bio* functionality in javascript (both within and without gsoc). However,
they are a new GSoC host organization applying to only three slots & thus
prefer to focus these slots on extending graphical client-side
functionalities. We strongly agree that efforts should be made to avoid
redundancy.

> Re: Eric’s 1.

We clearly agree that biogems.info-type portals can be very helpful. Once
we really start seeing a lot of bioinformatic package on npm this could be
relevant as well. However, it is likely that the npm portal will soon
improve (e.g. with better tagging and scoring of
https://www.npmjs.org/search?q=bioinformatics). Thus a bio-specific npm
portal could rapidly become obsolete.

> Re: specific project details.

In the "Approach" section of our proposal we state: "Methods for
input/output and wrangling basic data types should be given a higher
priority at the beginning of this projects." This is voluntarily vague - we
hope that an ambitious student would consider what the highest priority
aspects should be and make their proposal based on this. Obviously we (and
hopefully other members of the OBF community) would additionally feed into
this.

There are different ways we can embrace the modular nature of node/npm. One
approach could be to have "bionode" as the core of common methods and then
for specific topics like microarrays, have "bionode-microarray" that has
bionode as an obligatory dependency for core functionality. This sounds
like what Eric is suggesting; it is similar to the
https://www.npmjs.org/search?q=voxel packages; or specific bio-gems
depending on bio-ruby. Our intuition is that this would indeed be the best
approach. Alternatively, bionode could act as a common framework that would
have "plugin" modules to extend its functionality (like
https://www.npmjs.org/search?q=gulp, which is a build system and works like
a unix pipeline). This is a popular pattern but has drawbacks (e.g., it
consists in building yet another plugin-system. We agree that deciding
which way to go will need to be done maturely. We definitely want to avoid
building a monolithic platform - apologies if that was unclear. At present,
the most basic functionality doesn’t exist - we thus also want to avoid
over-engineering at such an early stage.

In any case we will be happy with whatever decision you guys make - whether
or not its possible this year we will be happy to propose one or several
projects next year.

Thanks & all the best,

Yannick and Bruno

On Tue, Mar 4, 2014 at 6:28 AM, Pjotr Prins <pjotr2014 at thebird.nl> wrote:

> I agree with the intent and reasoning.
>
> One word of caution, however, it is easier to discourage people than
> to encourage them. My most important suggestion is to try and say YES
> more often. We can't have enough project proposals - the actual
> application process will leave us with the ones we really want
> (student, mentor and/or content-wise). If members of the community
> (that community remember) is enthousiastic about an idea I think we
> ought to embrace it as an org. People come to OBF/GSoC for a reason.
> So, I'd turn that argument around.
>
> A lively list of projects will look good with Google too. The key
> thing is enthusiasm. The next key thing is talent. Being open may
> surprise us. Let us be surprised.
>
> Pj.
>
> On Mon, Mar 03, 2014 at 08:31:02PM -0500, Hilmar Lapp wrote:
> > Well said, Chris.  -hilmar
> >
> >
> > On Mon, Mar 3, 2014 at 12:27 PM, Fields, Christopher J <
> > cjfields at illinois.edu> wrote:
> >
> > > Pjotr, Peter,
> > >
> > > In the end I think this has to be a decision that Eric and Raoul make,
> as
> > > they are running the show.  We wouldn't have any GSoC 2014 w/o their
> hard
> > > work.  My feeling is, in the end, openly discussing these will suss
> out the
> > > ones that seem to fit best overall.
> > >
> > > My 2c, if it's worth anything: I tend to agree with Pjotr, in that we
> > > should not limit ourselves to the various Bio*.  If anything, what I
> > > personally would like to see at the end of the day is a very good set
> of
> > > projects overall that we can pick from.
> > >
> > > However, I also think a balance needs to be struck, and that whatever
> we
> > > accept has to (in the end) benefit OBF.  That, to me, is the purpose of
> > > GSoC.  If it means we can get a new Bio* started up or we can (even
> > > tangentially) add functionality to one of the Bio* projects, all the
> > > better.  But I do think this has to feed back to OBF somehow.
> > >
> > > The reality is, we simply can't take every project from other related
> but
> > > non-accepted orgs.  In some instances, other accepted orgs might
> simply be
> > > a better fit, such as BioJS.  It doesn't mean we won't accept
> > > Javascript-based projects, but all alternatives need to be explored
> > > (particularly when there are a finite # of slots for a lot of
> projects).
> > >
> > > chris
> > >
> > >
> > > On Mar 3, 2014, at 5:56 AM, Pjotr Prins <pjotr2014 at thebird.nl> wrote:
> > >
> > > > BioJS is browser oriented. It may or may not fit there. See also
> > > > earlier E-mails on this ML by Chris and myself (Feb 27th).
> > > >
> > > > Even so, can we please be open to new project ideas and get rid of
> the
> > > > discriminatory programming language notion?  The bioinformatics
> > > > community is growing rapidly. Way faster than before. We should cater
> > > > for community needs as is represented by project ideas coming out of
> > > > the community.
> > > >
> > > > I think, as long as the project is about bioinformatics and FOSS, it
> > > > will fit GSoC/OBF.  We should only filter on the quality of students
> > > > and mentors.
> > > >
> > > > Note also that Yannick is a respected member of BioRuby.
> > > >
> > > > Pj.
> > > >
> > > > On Mon, Mar 03, 2014 at 11:39:04AM +0000, Peter Cock wrote:
> > > >> 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
> > > > _______________________________________________
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> > > > GSoC at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/gsoc
> > >
> > >
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> > >
> >
> >
> >
> > --
> > Hilmar Lapp -:- lappland.io
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