[BioRuby] Bio-projects comparison

Pjotr Prins pjotr2006 at thebird.nl
Tue Nov 28 06:04:54 UTC 2006

On Mon, Nov 27, 2006 at 04:13:53PM -0800, Moses M. Hohman wrote:
> community. I think it would be cool if bioruby could leverage more of  
> what ruby has to offer to build a more compelling platform than  
> bioperl, biopython and biojava offer.

A few years ago I wrote that it would be a good idea to be able to
call into the BioPerl or BioPython libraries from Ruby.  That would
leverage existing technology strengthened by Ruby and what is
implemented in BioRuby. This can actually be done by firing up a Perl
XML/RPC or SOAP server from Ruby with a dedicated BioPerl adapter.
When certain functionality from the other BioProducts proves to be
popular and the mapping a bottleneck (speed and memory use will be
significant) it provides a clear incentive to implement it in pure

I think it will help people move to BioRuby from the other Bio
projects once they realise they get the same functionality, but with
a nicer (read more productive) language.

It should be reasonably straightforward to do this. What you need is
some Perl support (going for BioPerl first) to respond to invocation
with a new listener. Next you need some Perl introspection to expose
mappings (automatically). Then you need to tell the Ruby client how to
access these classes/methods. If it is really clear how to provide
these mappings you can leave it to others to implement them.

It would be pleasing to can tick all the boxes for BioRuby in



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