[BioRuby] Google Summer of Code project ideas

[Michael Barton]

Excuse my late reply to your emails Pjotr and Naohisa. I
wanted to find the time to reply in detail.

> > I think "Restyling BioRuby.org" is very difficult for
> > Google Summer of Code 2012 because the FAQ says that
> > documentation-only work cannot be accepted.

I agree with this. I think if our aim is to attract new
people to BioRuby then giving out tasks to update
documentation is not very exciting.

I would like to offer a suggestion that BiorUby GSOC
projects could also push scientific problems with new ruby
code. As we are scientists in addition to coders we could
coach on the scientific investigative side as well as on
coding.

I also think encouraging GSOC students to publish their
projects, such as a bioinformatics application note could be
a good way demonstrate the success of BioRuby GSOC projects
as a concrete outcome. I think this would demonstrate
BioRuby is an exciting community where "open source work
leads to publications" which I think is primary barrier to
scientists committing time. I speak for myself in this case
as I'm at the point in my career where publications are
becoming critical to finding a new position when my current
one ends.

I've never been involved in a GSOC project however so please
correct my ignorance if I am wrong.

Perhaps somewhere on the redesigned site we could list
publications that have directly come form BioRuby projects.
Concretely, rather than "we used BioRuby in this project" it
would be "I wrote this for BioRuby and published it." I
think recent BioGems paper is a good example of this.

> Depends on the programming component. If we use
> staticmatic and HAML to generate the site, with
> coffeescript to interact with github and others, I think
> it becomes a very interesting programming job.

I've used nanoc to generate the scaffolder documentation
here: http://next.gs. The github repo for the site is here:
https://github.com/scaffolder/scaffolder-website. The static
site generator "stasis" also looks interesting and follows a
rails centric theme: http://stasis.me. As Pjotr wrote these
could generate the static HTML which is uploaded to
BioRuby.org.

> Also the 'documentation' could consist of real example
> scripts, which execute. Possibly showing results online. I
> don't think students should be documenting, but they can
> put software together to make creating tutorials easier.

I strongly agree with this. Documentation code should be
executable to ensure that it works as expected. I've read
somewhere in the past about gems that allow this.

Mike