[Bioperl-l] bioperl reorganization

Chris Fields cjfields at illinois.edu
Sat Jul 18 03:31:33 UTC 2009

On Jul 17, 2009, at 4:23 PM, Robert Buels wrote:

> I was going to write a longer post, but Jay wrote everything I was  
> going to write, plus more, and did a better job.

I think both of you made very good arguments.  Will have to nickname  
you guys the IRC Mob.

> ...
> If there were not so many person-years of development time already  
> in BioPerl, I would probably be pushing for ground-up rewrite to  
> simplify things.  But as chromatic frequently says (he's fantastic,  
> look him up), ground-up rewrites of large projects almost never  
> work.  You lose a year (or multiple years) of person time rewriting  
> instead of adding features, or if you also add features to the old  
> version in parallel, you have to also port those features to the new  
> version (over a really long time period).  It's theoretically  
> possible to do, but in practice it almost never works, he says.  I  
> don't know, I've never been involved in an attempt like that from  
> start to finish.

I agree.  The Bio::Moose stuff is an initial attempt to see if it's  
worth porting code to Moose (I think it will be, but we'll see).  If  
anything it'll be a port and will simplify the code.  bioperl6 is  
similar in scope, using some concepts we would learn first from  
Bio::Moose, but with the additional fun of grammar-based parsing.

>> Okay I rambled, hope that was helpful.
> Quite helpful!  Please keep it up if you can!
> Rob

Just don't waste too much time talkin' and not spend enough time codin'


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