[BioRuby] Guidelines for writing bioruby plugins

George Githinji georgkam at gmail.com
Sat Oct 9 12:46:11 UTC 2010

Hi Pjotr
Thank you very much for the explanation.

On Sat, Oct 9, 2010 at 12:05 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Hi George,
> The plugin system is in a conceptual stage. I intend to write an
> 'Anatomy of a BioRuby plugin' soon.  Some quick responses
> On Fri, Oct 08, 2010 at 09:21:29PM +0300, George Githinji wrote:
>> Hi Bioruby developers,
>> I have heard of bioruby plugins and also seen two such plugins from github
>> http://github.com/pjotrp/bioruby-gff3-plugin and
>> http://github.com/helios/bioruby-plugin-graphics
>> 1. Is  the plugin system supposed to open development methods? (helios
>> uses unit testing while pjotrp uses r-spec for testing)
> You are free to choose
>> 2. Will the core developers concentrate on making bioruby core more stable?
> That is the goal
>> 3. What constitutes Bioruby core?
> Anything we agree on that belongs in core and can be stable and
> maintained.
>> 4. Are there plugin development guidelines?
> Planned
>> 5. How is the plugin system supposed to work?
> The first stage is by simply adding a search path. We can make it
> more sophisticated in time - i.e. plugins that can get loaded by
> BioRuby core, etc. Some of it has already been done by us, but needs to
> solidify.
>> More practically I have created a library for calculating the
>> isoelectric point of a protein using Ruby
>> (http://github.com/georgeG/isoelectric_point_4_R).
>> Using shoulda as the testing framework. I would like to turn it to a
>> bioruby plugin while adhering to a 'bioruby plugin development
>> standard' if it exists.
> Cool. For now, make sure it has ./lib/bio/xxx, use BioRuby module
> naming conventions and name your project like bioruby-xxxx-plugin, so
> it is clear it can work that way.
>> Please advise
> Pj.

KEMRI/Wellcome-Trust Research Program
Skype: george_g2
Blog: http://biorelated.wordpress.com/

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