[BioRuby] New age BioRuby

[Pjotr Prins]

On Sat, Feb 25, 2012 at 07:34:48AM +0900, Toshiaki Katayama wrote:
> 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. 

I think no one on this list disagrees with the above. I would be the
last one not to recognize your and Naohisa's inputs and achievements.
I thank you for inviting us to Japan, for encouraging plugins. And
basically I thank you for being you. I hope that is clear enough.

> 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.

We as BioRuby have been innovative, and attract some really good
people. We should continue pushing for innovation, including the
processes that encourage innovation. Also, it is very important that
people who put in a lot of energy get the right credit for their work,
and get encouraged to keep putting in a lot of work.

We have erected a panel to ascertain that we continue the line of
innovation, including total encouragement to new comers and old hands.
That takes a lot of time and energy, and needs total commitment. By
erecting the panel we have *committed* ourselves. Together with you we
can define the exact remit of the panel. In fact, you should be on the
panel.

In my opinion the remit of the panel is to ascertain the code base,
chosen technologies, website, web presence etc. represent the
interests of the community. I am not saying it was not handled
properly before, but I am saying it can be improved. By having a body
of dedicated people, and open discussion, we can move forward.

We also have to think about developing leadership. You have been doing
this job for over 10 years. I don't expect you to think you will be
project leader in another 10 year's time. Personally I think no one
should be leading for a really long time. People get very busy - which
is a natural progression in science. The panel should put the
processes in place to nurture new leadership.

The first job of the panel is to exactly define its remit for the
coming years.  We have made a start in that earlier announcement.

Thanks for response Toshiaki. We all have the interest of BioRuby at
heart, so let's keep on innovating and keep BioRuby going as the most
exciting Bio* project!

Pj.