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

[Sara Rayburn]

Hello all,

Thank you for selecting me to participate in Google Summer of Code with BioRuby! I'm looking forward to working with the BioRuby community and to getting involved with open source development. 

This summer I'll be implementing a gene duplication inference algorithm for both binary and non-binary species trees. My first steps are going to be those in the list below, starting with this email introducing myself. 

Again, thanks, and I'm looking forward to working on the project.

Sara Rayburn

On Apr 26, 2010, at 11:47 PM, Christian M Zmasek wrote:

> 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!