[Bioperl-l] GSoC BioPerl Project Page

[Chris Fields]

Well, BioPerl was initially designed (with the various pluggable IO systems and interfaces) to accommodate this, so one could have focused packages (for instance, on RNA structural analysis, NGS, etc).  That has always been in place, but the standard practice has been to drop everything into the main repo, which isn't tenable long-term.  In fact, what has occurred in a number of cases is circular dependencies that will have to be teased apart, and some (possibly bad/unoptimized) code can become entrenched and hard to remove.  

I'm not sure why this never became a standard practice; I have a feeling it was just easier on the developers to have everything in one place. I'm just as guilty as everyone else though.

Anyway, I just conversed with Pjotr Prins re: BioRuby's plugin work, and judging on the BioRuby plugin design we're probably going to go even further, in that some previously core components (Map, Coordinate, Cluster) may be pulled into their own repos as they are pretty self-contained and mainly rely on simpler core components.  We'll see how Sheena approaches it :)

chris

On May 23, 2011, at 9:16 AM, Rutger Vos wrote:

> Great project, good luck Sheena. Perhaps the way BioRuby organizes
> this (with its plugin system) might be a source of inspiration?
> 
> Rutger
> 
> On Mon, May 23, 2011 at 12:31 AM, Sheena Scroggins
> <sheena.scroggins at gmail.com> wrote:
>> Hey everyone,
>> 
>> 
>> The BioPerl project can be followed at www.techomics.com.
>> 
>> The relevant github links will be posted there soon.
>> 
>> Sheena
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading, RG6 6BX, United Kingdom
> Tel: +44 (0) 118 378 7535
> http://rutgervos.blogspot.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l