[BioRuby] [GSoC] [GSoC2012] BioRuby

[Pjotr Prins]

To all GSoC applicants: be sure to start on your proposal and share it
with your project mentors. It is a surprisingly thorough and
competitive selection process, and if you want to succeed, the plan
and presentation has to be good. Every year we see students who start
too late. We can give feedback now, do use that to your advantage. We
want you to succeed.

Pj.

On Mon, Mar 26, 2012 at 09:02:40PM +0530, Saket Choudhary wrote:
> 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
> >
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>