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

[Mark Schreiber]

Sorry, sent before I said what the new principles were.

1. Extensive use of the Logging API
2. (At the risk of having a fatwa declared against me) Most biojava
exceptions should derive from RuntimeException and be unchecked

See the wiki page for more details.

- Mark

On Fri, May 22, 2009 at 10:59 AM, Mark Schreiber
<markjschreiber at gmail.com> wrote:
> 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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>> biojava-dev at lists.open-bio.org
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>>
>