[Bioperl-l] SearchIO speed up

Chris Fields cjfields at uiuc.edu
Thu Aug 17 22:27:09 EDT 2006


...
> I.e., if you talk about drastic architecture changes you are no
> longer talking about Bioperl as we know it ("1.x"). A few years ago
> several bright young people wanted to get together to build what at
> the time was dubbed Bioperl 2.0 ... Unfortunately, we all get older
> and we move on in our lives ... As a result those people are now
> scattered and I doubt will ever take this on. I.e., Bioperl 2.0 will
> need a new crop to pick up the challenge.

Yeah, I have thought of a few things I would like to change but  
can't.  I like D. Conway's inside-out classes/objects for  
encapsulation but I can't see using those in BioPerl w/o major  
architecture changes, as pretty much every class is hash-based  
(Bio::Root::Root).

With Perl6 not too far off now, we could start thinking about what  
works well and what doesn't.  Then when (if?) the eventual Perl5- 
 >Perl6 changeover begins in BioPerl, try implementing new ideas.

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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