[BioRuby] Fork => suggestions

Tue Mar 27 05:24:14 UTC 2007

Trevor, Jan,

Thank you for all of your discussions to make our bioruby community better.
And, Pj, thank you for your kind personal mail.

I'm very sorry that I couldn't spare enough time for the release management,
but I'll work on bioruby extensively starting from tomorrow until April 1
to make the next release.

Trevor, could you suspend your fork plan until my attempt fails?
One more thing, do you think your modules are ready for the next release?

Jan, your board plan (1) sounds nice as I'm not good in release management.
I think face-to-face meeting will accelerate to make it possible,
so if we could have BoF meeting during the BOSC 2007, it would be great.
Everyone who wish to involved in the bioruby development and future planning,
please consider to gather there.

These days, I slowly worked on brushing up the bioruby shell to use with rails.
I wish to figure out how it can be integrated with rails smoothly.
I hope to provide repository which stores bioinformatics related rails plug-ins,
rake tasks, models etc. so that user can develop your-own databases, web services
and workflows easily utilizing the functionality of bioruby.
This might also serve as Jan's plan (2).

But I still not sure how it should be shaped.
Switching towards svn may solve the part of technical problems,
but, personally I want to wait until OS X includes svn by default.
Does anyone know whether Leopard includes svn?

I'll respond to mails stacking in my mail box as much as possible
during this week.

(3) future reqests + bugs
I agree with utilizing rubyforge. Last year, I added some todo list there.
Trevor, do you think Trac is better?

(4) missing? :)

(5) blog
Writing English blogs must be a burden for me, but I'm happy to create
links to yours at bioruby.org

(6) manuscript
Your draft was excellent but I want to rewrite it to cover various aspects
that bioruby offers, and want to include future plans which may stand out
the difference with other Open Bio* projects.

Regards,
Toshiaki Katayama

On 2007/03/26, at 21:59, jan aerts (RI) wrote:

> Trevor,
>
> I must admit that I stopped mailing the list months ago after not
> getting much response... I'm afraid that also included answering to
> other people's questions.
>
> Was thinking about some suggestions for a project like bioruby to keep
> people informed and make clear (or sure?) that it's very much alive. I
> believe I mentioned some/most of these in earlier posts way back, and
> many/most of these will be completely stupid (copyright: myself), but it
> might get people thinking a bit. Note that the _last_ thing I want to do
> is step on the toes of the real developers.
>
> Just read this as some thoughts during your coffee....
>
> (1) bioruby board
> -----------------
> As English is only my x-th language, I can't think of another word than
> 'board'. Wouldn't it be nice if there was a limited group of people (3
> to 5) that would act as a central authority so to speak to represent
> bioruby. This 'board' would preferably consist of people from different
> continents. Some things that this group could do is:
> * make sure that questions on the mailing list get answered or at least
> directed to the right people for answering
> * make the end-decision on which new modules (from BiorubyExtensions,
> see below) should be added
> * discuss releases
>
> (2) BiorubyEdge aka BiorubyExtensions
> -------------------------------------
> Purpose: to make clear what's in store for bioruby in the near future
> and to allow for preparing new classes for inclusion in bioruby.
>
> I suppose that more people will have ruby classes defined locally that
> are not really ready to be included in an 'official' repository like
> bioruby, but that could become candidates later on. I know I have. How
> about creating something like BiorubyExtensions, which would be like a
> waiting room for classes before they get into bioruby. If a class gets
> polished enough and ends up fitting into the official bioruby structure,
> it could be 'upgraded' to the main bioruby. On the other hand: it can
> also be removed from BiorubyExtensions instead if not supported or
> well-developed enough, of course.
> An example would be Bio::Graphics. Someone asked about that a while ago
> on the mailing list, and some people (including myself) might actually
> have a working class for this. It's just not polished enough and misses
> some functionality. And therefore a candidate for such an 'extensions'
> waiting room.
>
>
> (3) feature requests + bugs
> ---------------------------
> How about using the rubyforge system for bugs and feature requests?
> (This mainly means making it clear on the bioruby website to submit them
> on rubyforge...)
>
>
> (5) blog
> --------
> I don't want to sound like trying to follow latest trends nilly-willy,
> but a bioruby blog by the board-thingy (see above) and/or developers (a)
> would make really clear to the community that people are working on
> bioruby, (b) give more background on the development and/or (c) could
> give additional examples on how to use it.
>
>
> (6) manuscript
> --------------
> I believe bioruby needs a reference in a journal read by a large
> cross-section of bioinformaticians (Bioinformatics? BMC
> Bioinformatics?). I've actually worked on this about year ago with
> Toshiaki, but it kind-a got stranded in the end...
>
> Just to get some discussion started... Comments welcome.
>
> jan.
>
>
>
>> -----Original Message-----
>> From: bioruby-bounces at lists.open-bio.org 
>> [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of 
>> Trevor Wennblom
>> Sent: 25 March 2007 07:27
>> To: bioruby at lists.open-bio.org
>> Subject: [BioRuby] Fork
>>
>> Judging by the overwhelming response that I've received over 
>> the past year (2006-2007) compared to the previous year 
>> (2005-2006) does this mean that's it's time for a fork?
>>
>> If it's time let's do it.
>>
>> Wake.  Up.
>>
>> Trevor
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
>
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