[Bioperl-l] Using Graph?

[Hilmar Lapp]

It is already a dependency, just a silent one :) The OntologyEngineI implementation by Chris Zmasek depends on it, I just haven't gotten around to document this. Yes, it is an excellent module and installs smoothly out of the box.

	-hilmar

> -----Original Message-----
> From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk]
> Sent: Thursday, November 07, 2002 1:46 AM
> To: Bioperl
> Subject: [Bioperl-l] Using Graph?
> 
> 
> 
> Background: 
> 
> I needed to find the shortest path of location mapping between
> coordinate systems and not finding anything useful from CPAN, wrote
> Bio::Coordinate::Graph that allowed me to do exactly what I wanted. 
> Nat pointed out the 'Graph' to me:
> 
> On Wed, 2002-11-06 at 00:03, Nathan (Nat) Goodman wrote:
> > 3)  Did you consider using an existing general purpose 
> graph package?  I've
> > used the one in CPAN which works reasonably well.  I 
> realize it's overkill
> > here, but graphs are such a basic modeling tool that there 
> may be some value
> > in adopting a standard graph package for BioPerl.  Then, 
> modules dealing
> > with taxonomies and phylogenies, etc., etc. could use the 
> standard graph
> > package instead of everyone coding their own special case.
> 
> I had a look at it and seems pretty good. (Written by a Finn, 
> so it has
> to be good. ;-)  ) Most importantly, it is really general purpose.
> 
> http://search.cpan.org/author/JHI/Graph-0.20101/
> it has a dependecy for
> http://search.cpan.org/author/JMM/Heap-0.50/
> 
> 
> Question:
> 
> Is anyone in a position to start using Graph now or in near future?
> I'd be much more confortable to add one more dependency into 
> bioperl if
> I knew that other modules will be using it, too.
> 
> Any opinions welcome,
> 
> 			-Heikki
>  
> -- 
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>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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