[Biojava-dev] an outsider's take on Biojava 3

[Mike Smoot]

Hi Everyone,

I thought I'd respond to Andreas' request for participation in the BioJava 3
design discussions that he made last week on the normal BioJava list.  I'm
the lead developer on the Cytoscape project (http://cytoscape.org), so I
thought I'd provide some perspective on what a project using BioJava might
look for in BioJava 3.

Basically, I'd just like to voice my strong support for the "Basic
Principles" listed here: http://biojava.org/wiki/BioJava3_Design.  Finer
granularity of jars, acyclic dependencies, and the separation of API and
implementation are precisely the things we're doing in Cytoscape 3.  The
first two points will go a long way towards making it easier to use specific
parts of the library without needing everything at once.  The second point
will allow alternative implementations of certain interfaces, which is one
approach to dealing with issues like parallel vs. non-parallel versions of
algorithms.  Maven also sounds great.

If I could add one bullet to the list, it would be to add OSGi metadata to
the jars to allow easy integration with OSGi-based projects (such as
Cytoscape 3 and (as I'm told) the next version of Taverna). There are maven
plugins to make this dead simple and it wouldn't impact anyone not using
OSGi.

Please take that with a large grain of salt, I just thought you might
appreciate an outsider's perspective!

thanks,
Mike

-- 
____________________________________________________________
Michael Smoot, Ph.D.               Bioengineering Department
tel: 858-822-4756         University of California San Diego