[Biojava-dev] BioJava3 Use Cases

[Mark Fortner]

Along the lines of ease-of-use, I've been using BioJava for the past few
weeks in conjunction with the Groovy scripting language.  It's easy to
setup, and works wherever Java works.  It also makes it easy to leverage any
Java libraries.  You can use either Java syntax or Groovy syntax, and the
scripts can either be compiled to Java bytecode or interpreted.  You can
make the scripts either procedural or object-oriented to suit your needs.
You can find out more about Groovy here: http://groovy.codehaus.org

Regards,

Mark

On Mon, Jul 28, 2008 at 11:33 PM, Richard Holland <holland at eaglegenomics.com
> wrote:

> That's what I've thought too... ease of use (and ease of extension)
> seems to be people's highest priority. I'll give it till the 1st as
> promised then make a summary.
>
> cheers,
> Richard
>
> 2008/7/29 Michael Heuer <heuermh at acm.org>:
> > Richard Holland wrote:
> >
> >> Hi guys,
> >>
> >> I'd like to repeat an earlier request for use cases to guide the new
> >> BioJava 3 development work. We have a wiki page for this but it hasn't
> >> seen many updates:
> >>
> >> http://biojava.org/wiki/BioJava_3_Use_Cases
> >>
> >> Could anyone who has a task which BioJava cannot currently achieve, or
> >> does not achieve correctly, please add that task to this wiki page, so
> >> that we can try and implement it in the new code.
> >>
> >> A template for a use case has been provided on that same wiki page
> >> which you should follow when submitting your own suggestions.
> >> Basically the rule is that saying something like 'I want microarray
> >> support' isn't likely to get much of a response, but asking for a
> >> specific function, e.g. 'I want to be able to parse MAGE files' or 'I
> >> want to use XYZ technique to analyse my own chip designs', will get
> >> you a lot further.
> >>
> >> I'm setting a cut-off date for the initial list of use-cases at August
> >> 1st. Whatever's on the page at that point will be considered for
> >> implementation in the first phase of development over the next 6
> >> months, along with updates or transfers of functionality from the
> >> existing code base where appropriate. Anything that gets added to the
> >> list after that date will only get implemented in the second later
> >> phase, date indeterminate as yet, unless whoever submits the use case
> >> also chooses to submit their own code to solve it!
> >
> > Hello Richard,
> >
> > Very brief notes from the Biojava BOF session at BOSC 2008 are up at
> >
> > http://biojava.org/wiki/BOSC2008_Presentation
> >
> > Much of the conversation was about how to make Biojava more convenient to
> > use rather than about what features were missing.
> >
> >   michael
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
>
>
> --
> Richard Holland
> Bioinformatics Software Developer
> Eagle Genomics
> http://www.eaglegenomics.com/
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> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
Mark Fortner

blog: http://feeds.feedburner.com/jroller/ideafactory