[BioRuby] Welcome to the 2010 Phyloinformatics Summer of Code (BioRuby/duplications)

[Christian M Zmasek]

Hi, Sara:

Congratulations to having been selected as a student to the 2010 Google 
Summer of Code!

The next several weeks until May 24 are called the "community bonding 
period." Although you won't be spending your full time on your project 
yet during that time, you get comfortable with setting aside several 
hours each week to get the most out of the summer, with a focus on the 
following.


1) Please subscribe yourself to the BioRuby mailing list at the 
following URL: http://lists.open-bio.org/mailman/listinfo/bioruby
and introduce yourself and the project.
This is your first action item, and the sooner you can accomplish it the 
smoother we can get the rest set up and communicated. You can use your 
favorite email (it need not be your gmail address).

2) Familiarize yourself with the Git distributed version control system, 
as well as GitHub.
See:
http://git-scm.com/
http://github.com/

3) If you haven't done so yet, set yourself up with the BioRuby code 
base. You need to set up your own GitHub repository and clone the 
BioRuby main trunk (from http://github.com/bioruby/bioruby), for an 
example of a cloned fork, see (from Diana): 
http://github.com/latvianlinuxgirl/bioruby/

4) Install the Archaeopteryx tree viewer, in order to display phyloXML 
formatted evolutionary trees (Archaeopteryx also allows to directly 
execute the SDI algorithms), available at:
http://www.phylosoft.org/archaeopteryx/

5) Obtain the forester Java source which contains an implementation of 
the SDI algorithms, instructions for this can be found at (for the 
Eclipse IDE):
http://aptxevo.wordpress.com/2010/04/19/importing-forester-into-eclipse-ide/
Also see:
http://www.phylosoft.org/forester/applications/sdi/

6) I strongly recommend you to set up a blog (blogger? wordpress?) where 
you can report your progress and discuss issues and problems.
For a very good example (again, from Diana) see:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby

7) Reading, reading, reading...
Please obtain the papers listed at:
http://evogsoc2010.wordpress.com/2010/03/25/references-for-gene-duplications-proposal/
(needless to say, you don't need to bother with the paper written in 
German).

Also, obtain copies of:

"Programming Ruby 1.9: The Pragmatic Programmers' Guide (Facets of Ruby)"
(http://www.amazon.com/Programming-Ruby-1-9-Pragmatic-Programmers/dp/1934356085/)

and

"The Ruby Programming Language"
(http://www.amazon.com/Ruby-Programming-Language-David-Flanagan/dp/0596516177/)

and

"Ruby Best Practices"
(http://www.amazon.com/Ruby-Best-Practices-Gregory-Brown/dp/0596523009/)
Strangely, this is available for free at: http://rubybestpractices.com/

8) Finally, update yourself on the details of your project and related 
efforts. As you do this, together with your mentor review and revise 
your project plan to become what you will actually be working off of 
come the week of May 24. This will probably be the part that requires 
the most time. There'll be more communication on this in the near future.


*You should be completely done with these tasks* and ready to go and
commit code by May 24.


Again, congratulations, welcome to our Summer of Code, and I'm looking
forward to working with you!

Christian


PS: Parts of this text are copied from Hilmar's instructions. Thank you!