Fields, Christopher J | 9 Feb 14:51 2013

Re: [Gmod-gbrowse] BioPerl future


The branch is where the old (v1.x) code would reside.  Master branch would be v2.


Sent via phone

-------- Original message --------
From: Sheldon McKay <sheldon.mckay <at>>
To: "Fields, Christopher J" <cjfields <at>>
Cc: BioPerl List <Bioperl-l <at>>,gmod-gbrowse <at>
Subject: Re: [Gmod-gbrowse] BioPerl future

Hi Chris,

This sounds like a good idea.  I think it will eventually allow bioperl to evolve into a leaner, meaner
package that would be more likely to be adopted by new or isolated bioinformaticians, who tend to be put off
by the size and complexity of bioperl as it now stands.

One question I have is whether the name of branch v1 might be perceived as a step backward.  How about v2?


On Saturday, February 9, 2013, Fields, Christopher J wrote:

(cross-posting to gmod-gbrowse)

I want to gauge the community's thoughts on a few things.  At the moment I think we can safely say that BioPerl
1.x is in maintenance mode.  By 'maintenance mode', I mean that we can only do so much with it w/o breaking
backwards compatibility with old scripts.  We need a way forward so that we can address fundamental
problems within the core codebase, namely speed.

I am thinking at the moment of pushing a 'v1' branch next week after I make an official announcement, with a
new 1.6 release coming out from that branch (as already announced, tentatively scheduled for March 1). 
That frees up master for any code development, removal of modules/cruft, etc.  This will open an initial
path forward and at least enable us to do more.  Make sense?  This of course means that any code reliant on v1
should pull from that branch instead of 'master'.


Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
Gmod-gbrowse mailing list
Gmod-gbrowse <at>

Sheldon McKay, PhD
Computational Biologist
DNA Learning Center
Cold Spring Harbor Laboratory
1 Bungtown Rd
Cold Spring Harbor, NY 11724
(516) 367-5185<>