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

[Mark Schreiber]

Thanks for the comments. The OSGi system sounds interesting. I think
we should consider it.

I have also added two more recommendations for the Design Principles:


On Fri, May 22, 2009 at 7:47 AM, Mike Smoot <msmoot at ucsd.edu> wrote:
> 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
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