[BioRuby] bioruby development process / real life usage / visions?

Toshiaki Katayama ktym at hgc.jp
Fri May 26 02:39:45 UTC 2006

On 2006/05/25, at 11:13, Isaac Xin Pei wrote:

> Dear All,
> I am very curious of the development process of bioruby, especially what the
> vision for bioruby project among the open bio projects?
> According to my understanding,
> - bioperl has the largest users community due to the history reason, rather
> than the languate itself
> - biopython solved the OOP issue in bioperl,  and I like the language itself
>    however, the biopython project in particular seems to have a rather loose
> developing process
>    I am just not sure if I decide to pick it for everyday usage / long term
> programming project, it will help
> - bioruby:
>   the library/class seems comprehensive
>   the codes looks very clean
>   first impression of programming using bioruby is that it does follow KISS
> principle
>   : yet questions
>           - the devloping process

What do you mean?

We have a CVS repository on open-bio.org as well as the other projects
and contributions or enhancements discussed in this mailing list
will be accepted to the repository by core developers.

We also have a documentation on the development guideline:


>          - does it have a large user community (or a large
> community/bioinformatics/biologists in Japan?)

I suspect there are >300 users in the world from the download counts in apache's log.
(maybe half of them are in Japan) and the number is steadily increasing even the
actual number might still be smaller than other projects.  We can't count users
of Linux or BSD-like distribution having BioRuby bundled.

The number of the developer is about 10, and the number of core developers are around 5.

I had BioRuby tutorials and hands-on seminars in Japan for several years.

>          - the vision of the project?

Now we are forcusing on

- to expand user community
  - adding documentations and unit tests
- to enhance ability of the BioRuby library
  - web services
  - post-genomic analysis
  - cheminformatics
  - integration with Rails

> sorry for so many questions.
> in my research I have come to the point to using a programming language to
> investigage possible hypothesis in the genome, as well as a programming
> language to ease everyday bench work design ...

If you are not sure, you should try some of the above libraries to choose
your favorite.  If you choose BioRuby after the consideration,
could you let us know what point of the BioRuby you feel better or worse
than other project. :)

> hope to get some insights from you
> thanks!
> -- 
> Best ,  Isaac
> - "A word fitly spoken Is like apples of gold in network of
> silver. " Proverbs 25:11
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

Toshiaki Katayama
Human Genome Center, Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
tel://+81-3-5449-5614, fax://+81-3-5449-5434
BioRuby project     http://bioruby.org/
GenomeNet/KEGG      http://www.genome.jp/
Human Genome Center http://www.hgc.jp/

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