[BioRuby] Restyling BioRuby.org

[Raoul Bonnal]

Hi Pjotr, Hilmar and others,

On 20/02/12 10.51, "Pjotr Prins" <pjotr.public14 at thebird.nl> wrote:

> On Sun, Feb 19, 2012 at 06:27:00PM -0500, Hilmar Lapp wrote:
> 1. Where is our leadership?
> 
>   This is not unique to BioRuby. The other projects suffer similar
>   problems. Perhaps, in bioinformatics (the small b), people get too
>   busy too quickly, and sitting leadership starts being the cause of
>   inertia.
> 
> 2. Is this the time fork the BioRuby project?
> 
>   I have been thinking this for many years ;). Forking the code is one
>   thing - as noted before, we can and should strip out modules into
>   Biogems. Forking the project is not possible, unless the domain gets
>   released. Do we want a bioruby2.org?
At this time forking is not a solution, like creating another Bio language
(as suggested by Mic with D) which is just used by a niche of developers.
Why is not a solution ?
A) Because I supposed we have no time to support a whole library from zero.
B) It's not a founded project, so I can not spend time on it. Now I can
justify the effort because I use it daily or for specific tasks but if I
must spend time supporting people on things which are not relevant to my own
work, that would be a real problem. In Boston (BOSC) (Apache talk) we
discussed about the chance to be founded, but I can imagine is not easy.
C) I think that extending or hacking bioruby with plugins is a good way to
introduce new concept/design keeping compatibility when needed and most
importantly publishing papers to be cited = Ruby more widespread in
bioinformatics. Unfortunately bioruby by itself is not enough so we must
provide support and contribute to SciRuby (just an example).
C.1) everyone will contribute to its own field and is normal.
D) WE NEED A ROAD MAP (is connected to point 3)

I would put a link ( Ruby for Science Alliance ) to friend projects like
SciRuby :-)

> 3. How are we going to revamp our web presence?
> 
>   With Biogems.info we show that a change in this can have real
>   effect on contributions. Here we have raised that we can take the
>   web presence to a new level.
Publications, ML activities, IRC meetings, ROAD Map is the only way I see.
So in a new BioRuby site, as Francesco suggested, calendar/events etc.. Is
more than welcome. 

> 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio*
>    projects? 
>    
>   It is appears to me that sitting leadership is reluctant to
>   give away their positions. I have discussed this with Chris Fields
>   last year. We agreed that there are also few to take over the helm.
>   So...
I don't see how OBF could push the projects, in case of founds they would be
distributed equally? We are good people so we are working together promoting
our language helping the others. During the last BioHackathon the most
astonishing things was seeing Bio Perl/Ruby/Python/Java working (really)
together, it was great.

 
> 5. how do we nurture future leadership?
> 
> I am old and cynical enough to know people mostly work for their own
> direct benefit (their itch, so tho speak) in OSS, or anywhere else.
> Still, I am going to poke and prod for some time, to see if we can
> make change. I believe Bio* projects are at fork in the road. Which
> one are we going to take?

> Should BioRuby exist as it is, or should we
> use it as a breeding ground for young developers. Same question really
> for BioPython and BioPerl.
Not very clear, at least to me.
 
> The BioRuby community is almost in a coma, I think. Despite 180
> readers of the ML. I see the same people engaging, and interestingly,
> a significant number of messages from Biopython and BioPerl
> leadership. Thank you for that. BioRuby is just coming out of its
> shell, and you are helping.

 
> 6. What is needed to get BioRuby out of the comatose state?
> 
>   With BioRuby we have had lively discussions before, but they tend to
>   peter out. We can reason about this, but I think it goes back to
>   leadership again.
I don't know how to solve this issue... The democratic process you suggested
some time ago ? Which is the workload, which is the coding power we have ?
Which are the languages we can rely on for performances (it means which is
the knowledge of the people around here )? Do we want to support Jruby?
Suppose we now need a new feature in BioRuby, which one ? Do we want to
participate to GSoC ? YES and we MUST there is no doubt and we NEED to write
good proposals but everything should be made as a community not only as a
group of passionate developers.


LANGUAGES:
D or Scala, I don't know that I'm just curious and eager to learn. Most of
my work is managing large scale data and interconnecting them extracting
information etc... I would say, why not Hadoop ?
We are just a piece of a bigger ecosystem, the problem is that most of the
time "setting up" each piece is a pain in the ass.

WEBSITE Proposals:
Why not create and post images, an image per page. Is a usual approach for
proposing new layouts.


We are growing and this kind of discussions are a natural process.
--
Ra