[Biojava-dev] bjv2

[Thomas Down]

Hi John,

I don't think the two projects are competing with each other at the  
moment -- the BioJava 1.x code is still being actively maintained and  
developed (and is just coming up to a 1.4 release some time in the next  
few).  It offers a mature set of libraries for computational biology,  
with a bias towards the handling and analysis of sequence data  
(although an API for 3d structures has been added recently).  If you  
want to see what it can do, may I suggest the "BioJava in Anger"  
website:

        http://www.biojava.org/docs/bj_in_anger/index.htm

On the other hand, I'd somewhat disagree about re-writes: the bjv2  
project aims to build a rather different framework, with much more  
emphasis on integrating and querying arbitrary data sources, rather  
than providing specific object models for particular types of data.  I  
think re-writes are a good idea when developers want to try out some  
radically new ideas.  I like some of the ideas about "evolutions and  
revolutions" which have been circulating in the Apache project:

       http://incubator.apache.org/learn/rules-for-revolutionaries.html

BioJava 1.x won't be going away any time soon, though.

       Thomas.


On 28 Jul 2004, at 07:09, john morris wrote:

> A few days ago I read with a lot of interest the article about BioJava  
> on the Sun website  
> (http://java.sun.com/developer/technicalArticles/javaopensource/ 
> biojava/) and today I learn that we need to re-write it from the  
> ground so badly designed it is (http://bjv2.derkholm.net/)! I don’t  
> have the background to judge about the need for bjv2, but I clearly  
> feel uncomfortable with the fact that multiple projects are going to  
> compete to each other.
>
> Do we know what are the plans for bjv2 and how it is going to interact  
> with biojava? Rewriting a code from the ground is never a good  
> solution.  Is-there really no way to develop bjv2 from biojava by  
> branching the cvs tree and progressively adapt the API through  
> deprecations? I’ll be interested in reading other opinions.
>
> Thanks again to all Biojava developers for this great piece of work