[BioRuby] Guidelines for writing bioruby plugins

Pjotr Prins pjotr.public14 at thebird.nl
Sat Oct 9 09:05:26 UTC 2010

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

> 4. Are there plugin development guidelines?


> 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

> 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


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