[GSoC] [GSoC2012] BioRuby

[Saket Choudhary]

Hi Pjotr,

Thanks !

I have been using BioRuby and BioPython for 6 months now to solve the
"Protein Loop Closure" problem. I use it mainly to manipulate the atom
positions in a given PDB file, thus perturbing their positions.

I went through the discussion that happened on the mailing list last month:
Here are my notes about the same

1.http://lists.open-bio.org/pipermail/bioruby/2012-February/002087.html

Even I am a big fan of Jruby homepage. Here are my suggestiosn :
1. Ruby is simple, clear , intutitve and this makes Biouby intutive to
everyone. This needs to be emphasised the very first time a user comes to
the webpage : Instead of giving them examples on Wiki[
http://bioruby.open-bio.org/wiki/SampleCodes] to "read" through a tutorial
in the form of a short writeup/description about Ruby/BioRuby foolwed by a
challenge would be more appealing and intuitive to the user even though he
is being exposed to Ruby/BioRuby for the first time. Say some tutorial on
the lines of http://www.codecademy.com/ , a short tutorial followed by your
Scratchpad. !


2. Calendar/Tweet/Conference widget:

Something again on the lines of Jruby website.


3. Favicon missing ?

Though a very trivial issue , but just wanted to know why isn't there a
favicon for bioruby.org ?

These are the stuff I gathered , I am still digging the old threads, will
post here if something relevant comes up !


Saket Choudhary
IIT Bombay
github.com/saketkc



On 26 March 2012 19:07, Pjotr Prins <pjotr2012 at thebird.nl> wrote:

> Hi Saket,
>
> Welcome!
>
> It would be good if you also introduce yourself to the BioRuby ML, and
> post your ideas. We are working on the website (should I say
> web 'experience'), and I like what you propose. Also check out the ML
> archive of the last months, you'll find a lot of information.
>
> Pj.
>
> On Mon, Mar 26, 2012 at 02:10:51PM +0530, Saket Choudhary wrote:
> > Hi !
> >
> > I am Saket Choudhary, a third year undergraduate student at IIT Bombay,
> > India.
> >
> > Ruby has been my first love for programming. My last project[internship]
> > was at SlideShare <http://www.slideshare.net>, one of the biggest Ruby
> on
> > Rails website in the world. I had developed the Admin interface for
> > SlideShare which could enable suspending users, reconversion/deletion of
> > SlideShows , and user deletion/suspension.
> >
> > My hack at Yahoo! Open Hack India -2011 qualified among the Top 50 hacks
> ,
> > I built a Sinatra app for fetching a defined file from a Dropbox account
> > and sending it to a specified email address , just on a SMS.[
> > https://github.com/saketkc/dropbox_on_sms]
> >
> > I went through the GSoC idea page and "Adding social networking
> > functionality to BioRuby.org", is of my special interest. I have an
> > experience working on the Rails platform. My plans for making the website
> > more "Social" is as follows:
> >
> > 1. Provide an online 'Scratchpad' for Ruby/BioRuby enthusiasts that not
> > only allows them to run their codes online but also provides them a
> > facility to store it online in the form of an archive so that they an
> acess
> > it later.
> >
> > 2. Include sharing facility on "Scratchpad" so  that one user can share
> his
> > code online with other users/community and get feedback/comments. On the
> > lines of "Sage <http://www.sagenb.org/>" notebooks.
> >
> > 3. Develop an Online Board on the lines of "Quora <https://www.quora.com
> >"
> > Boards  so that users can pin certain codes/algorithms on to their own
> > boards for their reference this would reduce the overhead of searching
> for
> > a particular algorithm again and again .
> >
> > Let me know you views on these ideas. I would send a mockup of the same
> > incase these ideas seem feasible to you.
> >
> > Thanks
> >
> >  Saket Choudhary
> > IIT Bombay
> > _______________________________________________
> > GSoC mailing list
> > GSoC at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/gsoc
>