[BioRuby] Restyling BioRuby.org

[Pjotr Prins]

On Fri, Feb 17, 2012 at 06:25:18PM +0100, Pjotr Prins wrote:
> What would you like to a fresh BioRuby.org to be?
> 
> Myself, I am thinking we need to retool the site for inexperienced
> programmers. That means accentuating Tutorials and examples, as
> Michael Barton suggested.
> 
> What do you think?
> 
> And please, also let some respond that have not mailed to this list
> before! We are here to hear you!

With an embarrassing 0 (zero) responses, I can conclude there is
either no interest in this matter, or no one considers it his/her
business. That is sad. Open source software matters. Web presence
matters.

So let me take you by the hand and draw a vision :). I think
programming for Biology (which I call big B) is important for the
future of humanity, and the broader world we live in. We are the ones
that have to unlock the potential of big data. 

As I see it around me, scientists are generating data at an incredible
rate. Now the data analysis is the bottle neck, there are plenty of
indications. For example, we have a programming course here at our
biology university which was never really popular. This year the
attendance tripled, and includes a number of Ph.D. students! I.e. the
research groups are feeling the pinch. There are not enough people to
analyse the data.

It gets worse. What I see is that the universities train people to the
level they can script a bit, and use existing tools. For example for
genome assembly. The problem is that these tools work for the general
case.  With different experimental design and setups the data may
contain more valuable information, i.e. there is often opportunity for
harvesting more information - which never gets done.

And we do not scale. Each of us is too busy, even to write to a
mailing list and participate in mentoring students in the Google
Summer of Code (GSoC).

Are we being responsible scientific citizens here? I think not. Are
most of us true participants in Bio*. I think not.

This ML and GSoC is about all Bio* projects (BioRuby, Biopython,
BioPerl, Bioconductor...).  The programming languages are tools that
we should use to not only analyse our own data, but also to give back
to others so we can maximize the scientific potential. You are using
open source software (OSS). I bet you have benefited from Bio*.

We are asking to give back some of your time. Everyone can do it in a
different way. Ben Woodcroft has created many small plugins of his
coding efforts. That is greatness in my opinion. Raoul spent many
weeks of his free time to create the Biogems tool and make it possible
for people to share code. That is greatness in my opinion.

So how can you participate and be great? First by discussing ideas on
the mailing list. Discuss what you want out of the BioRuby web
presence.  Any idea will do. An active mailing list will help young
developers find us.  Adding projects to GSoC will help young
developers find us. I don't think mentoring GSoC students necessarily
leads to long term committers, but that is not the point. The point is
to move science as a whole forward. The universities train people to
use tools and maybe script them together. We here, are the select
crowd of real software afficiendos in Biology. I think there is only
one conclusion possible, if we are not to sink in a cynical mire.

If you understand and benefit from *our* OSS, don't go the way alone.
Don't just take and not give.  Help us materialize that potential of
young developers. They are out there, and we need them to find us.

I am asking: What do you think? How can we accommodate this goal using
the tools we have.

Pj.