[Bioperl-l] RE: Integrating caBIOperl with BIOperl

Steve Chervitz sac at portal.open-bio.org
Thu Nov 4 17:17:23 EST 2004

Sorry for the cryptic message. Somehow it got sent prematurely (pesky

I definitely favor the bridge plan rather than direct assimilation into
Bioperl. My comments pertained to Peter's mention of MAGE-OM:

>>> In the next major caBIOperl release (~March 2005) we are going to include a
>>> full implementation of the MAGE-OM microarray data standard as part of the
>>> caBIOperl API

Sounds great. MAGE-OM/ML has been lacking a tie-in to Bioperl (and vice
versa) for some time. Looks like caBIOperl could provide this link. I'm
curious if the caBIO implementation will make use of any of the MAGEstk perl
work: http://mged.sourceforge.net/software/MAGEstk.php  (e.g., object
generators, parsers, writers).

There's a bioperl CVS repository called "bioperl-microarray" that would be a
good location for any MAGE-specific caBIOperl bridge modules. However, a
more generic bridge module should go into bioperl-live (where, perhaps


> From: Steve Chervitz Trutane <steve at trutane.net>
> Date: Wed, 03 Nov 2004 17:35:30 -0800
> To: Hilmar Lapp <hlapp at gmx.net>, "Covitz, Peter (NIH/NCI)"
> <covitzp at mail.nih.gov>
> Cc: "'bioperl-l at bioperl.org'" <bioperl-l at bioperl.org>, Lincoln Stein
> <lstein at cshl.edu>
> Subject: Re: [Bioperl-l] RE: Integrating caBIOperl with BIOperl
> Note: 
> * perl MAGEstk - any tie in?
> * Always thought it would be nice to have a bridge into bioperl from MAGEstk.
> Would caBIO perl act as this bridge?
> * Are the caBio perl MAGE objects autogenerated from MAGE-OM?
> Steve
>> From: Hilmar Lapp <hlapp at gmx.net>
>> Date: Wed, 3 Nov 2004 09:35:59 -0800
>> To: "Covitz, Peter (NIH/NCI)" <covitzp at mail.nih.gov>
>> Cc: "'bioperl-l at bioperl.org'" <bioperl-l at bioperl.org>, "'lstein at cshl.edu'"
>> <lstein at cshl.edu>
>> Subject: Re: [Bioperl-l] RE: Integrating caBIOperl with BIOperl
>> I very much agree with Lincoln's comment. One of the more frequent
>> comments we have gotten is that expecially to newbies the plethora of
>> modules in Bioperl and the apparent diversity of its APIs are already
>> confusing. A bridge that binds the caBIOperl API to the existing
>> Bioperl object model would be a great addition though.
>> -hilmar
>> On Wednesday, November 3, 2004, at 06:47  AM, Covitz, Peter (NIH/NCI)
>> wrote:
>>> Agreed, getting it into CPAN is the first order of business.
>>> caBIOperl is itself a wrapper around a lower-level SOAP-XML API.  That
>>> gives
>>> us some flexibility on how we present the visible API interfaces.
>>> Once we
>>> get it into CPAN, I'd be interested in continuing the discussion of
>>> what the
>>> appropriate bridging and interface strategy would be to make it more
>>> suitable for use with bioperl.
>>> Thanks for the feedback!
>>> Regards,
>>> Peter

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