[BioRuby] bioruby docs

Tue Oct 23 04:08:44 UTC 2007

Hi,

I've just read through this thread and the saaientist blog (too long for me... :-)
and added links to the following blogs at http://bioruby.org/

As for the site integration,

* Top page needs refactoring.

Pretty cool icons were contributed from Okamoto-san, and
I made a draft version of the new site but never finished.
Hisotically, the site is hosted at my office (University of Tokyo)
but now might be the time to migrate to open-bio.org.

http://bioruby.org/
http://bioruby.org/tmp/site_design.png

* Wiki sites needs to be transfered.

I can't keep control over the wiki site anymore, so the contents in the current wiki
pages should be transfered to the other site and updated by the user community.

I thought that to use the Media Wiki at open-bio.org is the best solution,
but using rubyforge's Wiki page is the another option as Jan was suggested.
Any way, I'll forward wiki.bioruby.org to the new site when the migration is done.

http://wiki.bioruby.org/ - obsoleted by spam
http://dev.bioruby.org/wiki/ja/
http://dev.bioruby.org/wiki/en/

* How about API documentations?

Trevor has been kindly provided bioruby-doc.org for the API documentation site.

1. just link to the site from the new bioruby.org
2. put the contents under the new bioruby.org site (http://bioruby.org/rdoc/)
3. radically integrate it with Trac and SVN system at open-bio.org?!

For any of the above, I need volunteers.

Thanks,
Toshiaki Katayama

On 2007/10/13, at 4:40, jan aerts (RI) wrote:

> Just a little suggestion: what if we would start with trying to get an idea of who blogs about ruby and bioinformatics? We could then put that list on the bioruby website for example. There is Propeller Twist (http://fjossinet.u-strasbg.fr/), the new bioinforuby by Francesco (http://bioinforuby.blogspot.com/), my own SaaienTist (http://saaientist.blogspot.com), and if possible the Japanese ones as well. I suspect that Mitsuteru has one: http://bioruby.g.hatena.ne.jp/nakao_mitsuteru/.
>
> What do you think?
>
> jan.
>
>
> -----Original Message-----
> From: bioruby-bounces at lists.open-bio.org on behalf of jan aerts (RI)
> Sent: Fri 12/10/2007 13:40
> To: Pjotr Prins; Shameer Khadar
> Cc: bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] bioruby docs
>
> Hey Pjotr.
>
> You're absolutely right. The last thing I wanted to do was to criticize the management (I hope you don't read the blog post in that way). They've done a great job and it's not easy to put a lot of effort in an open source project (as I've experienced myself as well). Believe me: I have the greatest respect. As I mentioned in that post, what I proposed was actually to have part of the load lifted from upper echelon's shoulders. That way, they probably would feel less pressure as well about being in charge of bioruby. Where I mentioned "getting organized", I didn't mean that _they_ should get organized (as a way of pointing a finger), but that we should find a way to distribute the responsibilities more. It's *us*, the community, that has to get organized as well. As you say, until there is a group of people that can say "We'll put a lot of time in this and make it a great success", we all favour running with the people who gave birth to bioruby. At the same time, we could he
 l!
>  p them more if some simple things would be organized in a slightly different way (e.g. making it easy to give people the opportunity to add to the wiki).
>
> What I wanted to call for in addition, is to have bioruby put a bit more in the spotlights. We all know that bioruby is relatively unknown compared to other projects like bioperl (obviously), biojava and biopython. Of course that has a lot to do with the fact that ruby is less known than the other languages, but I think that 'getting the word out' is not a bad thing. Hence my call for a blog or something where we (the developers) could organize our thoughts on what we would like to add to or change in bioruby as well as explain the rationale behind some decisions. The more bioruby is mentioned everywhere, the more we can create a buzz, the more people will get interested, the more developers we'll get, the better bioruby will become.
>
> So in the end, you're right if you say "who has the time or energy". What we could try to do is find a way to distribute the efforts, so less time and energy is needed from single individuals.
>
> I'll try to rephrase some things on the blog to make sure it's clear that it's meant as some suggestions rather than criticism. (The title now seems like a bad choice as well...)
>
> jan.
>
>
> -----Original Message-----
> From: bioruby-bounces at lists.open-bio.org on behalf of Pjotr Prins
> Sent: Fri 12/10/2007 12:20
> To: Shameer Khadar
> Cc: bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] bioruby docs
>
> On Thu, Oct 11, 2007 at 02:48:32PM +0530, Shameer Khadar wrote:
>> Here is an excellent article about the status of BioRuby
>> http://saaientist.blogspot.com/
>> (NB: Not official but an excellent personal perspective)
>
> Criticism is good and Jan is a respected contributor to BioRuby.
> Nevertheless with open source projects we have to take great care at
> giving people their due respect and it is easier to criticise the
> management side of this type of project than actually fixing stuff. I
> have seen to many opensource projects where people don't actually
> commit themselves fully after lengthy discussions on 'how to do
> things'.
>
> So, until a number of individuals steps up and says "WE WANT TO RUN
> WITH THIS PROJECT AND MAKE IT A GREAT SUCCESS", I will favour the
> idea of running with the people who have made it a success, so far.
>
> Otherwise, it is unfair on the guys who have put in a lot of their
> free time and energy to get where we are.
>
> Almost all open source project hinge on a few individuals - and
> BIORUBY could do better (I agree), but who has the real time and
> energy and has the proven coding track record? Both Jan and Trevor
> belong in the last category - but I know they don't have time.
>
> Pj.
>
>
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