[Bioperl-l] Using Graph?

[Hilmar Lapp]

Heikki, I added this dependency to Makefile.PL now that 
OntologyEngine is committed.

	-hilmar

On Thursday, November 7, 2002, at 10:05 AM, Hilmar Lapp wrote:

> 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
>>
>> --
>> ______ _/      _/_____________________________________________________
>>       _/      _/                      http://www.ebi.ac.uk/mutations/
>>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
>> ___ _/_/_/_/_/________________________________________________________
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--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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