[BioRuby] New age BioRuby

Fri Feb 24 22:34:48 UTC 2012

Hello Pjotr,

I felt your recent statements sent to me and on this list were not fair.
I believe everyone naturally has rights and freedom to try any changes on
the code base. You can propose it when you implemented. You can also propose
new web site candidate when it is ready. I have been a web maintainer
for the historical reasons (as I paid for past 10 years and maintained
the computer resources in my institution and on the open-bio.org).
I tried to cover all aspects of the BioRuby related web resources when
I designed the current site. I can admit we need to update the site and
happy to see the alternative candidates, but I personally think what actually
we need is not that superficial but the contents which kindly describes
the usage of the BioRuby for scientific purposes (and future plans, maybe).

The founder of the BioRuby had been responsible on the functionality and
stability of the BioRuby over 10 years and have never been non-democratic.
We welcomed contributors like you and gave privileges as a committer.
However, you had never committed the process of the release management which
actually is a hard and sometimes painful task. Dr. Goto has been done a great
job on this as a release manager for many years as he understand all modules
in the BioRuby code base so that he could pay careful attention to keep
the library very stable and also to keep backward compatibilities.
I respect him as he has been an only person who dedicated on this procedure
because no one else have volunteered for the task until now.

We invited you to Japan and discussed many aspects of the BioRuby
which finally resulted as the Biogem system. Before we get there,
we started from open CVS repository then moved to SVN but both still had
some barrier to join the development process, therefore we moved to
the GitHub so that everyone can fork and contribute without any privileges
given in advance. (Other Open Bio* groups followed the same way.)
This means real democracy had been maintained as much as we can.
Finally, with Biogem, anyone can develop and release bioinformatics modules
without bothered by the release cycle of the stable core. I believe that
this system was a milestone where most democratic development process had
been firstly introduced among the Open Bio* projects.

Given said that, I don't intend to block your motivations to make the BioRuby
better. Rather, I hope you to push your plans in a fruitful way.

I just wish that people on this list won't misunderstand the founders of
this project wrongly. We had paid tons of efforts to cross the chasm
as innovators. We may already have reached the early majority stage with
the help of early adopters like you and good others on this list.
If so, now is the time to change the scene as you described.

I may have missed several mails recently posted on this list or sent personally
to me as I had been quite busy. Sorry about that.

Despite the long message of this mail, it is easy for me to catch up
with short e-mails, basically. Thanks. ;)

P.S.
I have several plans to develop (Bio)Ruby/Rails or Node.js based semantic DB
applications starting from this spring. Is there anyone who are interested
in to work with us in Japan? We may be able to employ some developers.

Regards,
Toshiaki Katayama

On 2012/02/25, at 1:11, pjotr.public14 at thebird.nl wrote:

> Hi everyone,
> 
> We are happy to announce a new age BioRuby. This is BioRuby in the
> broadest sense, which includes gems and web presence. As a group, we
> have decided to take BioRuby into a new age, and change the way we
> approach community and newcomers. This we will do at four levels:
> 
> 
> (1) Democracy
> 
> First of all, for new age BioRuby the decision making process will be
> transparent and democratic. To guard the democratic process we are
> forming a panel of active major BioRuby committers, including Pjotr,
> Raoul and Francesco. The panel will act as a monitor. Other active
> major BioRuby and biogem committers are welcome to join the panel.
> 
> 
> (2) Web presence
> 
> The web presence needs to change to appeal to a new generation of
> coders. We are committed to changing that.
> 
> 
> (3) BioRuby gems
> 
> The recently published Biogem system has introduced the plug-in
> approach and we think has a natural evolving process that BioRuby
> needs to be adapted for the new generation of tools. We will take on
> moving functionality into gems, creating a modular setup, and reducing
> the existing BioRuby source to a skeleton framework. The old BioRuby
> will continue to exist for reasons of backward compatibility. Until
> someone else is elected by the community, the panel will be
> responsible for the new BioRuby code base, and Pjotr will be in charge
> of coordinating the effort.
> 
> 
> (4) New talent
> 
> The new age of BioRuby is really about nurturing new talent. This
> means giving away responsibilities to the next generation. We will
> rotate leadership for projects on a regular basis.
> 
> To achieve our ends we will put together a VISION statement for
> BioRuby, as well as a road map.
> 
> 
> Pj, Ra & Fra 
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