[Biojava-l] bioclojure

[Daniel Quest]

Hey guys, before you get too far into this you may want to consider
Sun's JSR223.  In theory JSR223 would allow you to write some code in
Clojure, then write some code in plain old Java, then write some code
in python (Jython actually).  This would probably open up your
technology stack and allow others to play.  I successfully write code
in Groovy using BioJava and that is kind of fun.  One important thing
to consider:
As far as I know ScriptEngine implementations are is incorrect for
Clojure and jRuby. They are not using bindings correctly. You may want
to nag the authors about this.  Rhino, Groovy, AppleScript, and
Gremlin are all languages that are correctly implementing the
specification. Jython apparently recently updated its implementations
of JSR 223 to also be compliant.

Just thought I would pass this information along.
-Daniel

On Thu, Aug 4, 2011 at 7:53 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Jay;
> Awesome that you and Lee are working on this. I've been doing more
> in Clojure recently and am really enjoying it.
>
> There are a few people I'm aware of doing biology related
> programming in Clojure that you might want to get in touch with:
>
> - Jan Aerts -- he has some bioclojure code on GitHub
>  (https://github.com/jandot/bioclojure) and he's been leading some
>  discussions about having a more formal collection of biological
>  Clojure code. Definitely send him and e-mail and coordinate; it
>  would be excellent to have a centralized community for this.
>
> - Ray Miller -- Ray has a BioMart Clojure interface on GitHub
>  (https://github.com/ray1729)
>
> - Christopher Maier -- He's had a few recent blog posts talking about
>  Clojure in the context of biological work: http://christophermaier.name/
>
> Thanks again for taking this on,
> Brad
>
>>  Hi guys : We are working on extending biojava w/ a Clojure API for building
>> bioinformatics workflows.
>>
>> Anyone out there interested in doing some functional bioinformatics ?
>>
>> Right now, we are looking for contributors for various modules and planning
>> at a higher level.
>>
>> Lee Hinnman, has been helping me so far, and will be helping to drive the
>> low-level, highly clojure specific design issues... so you don't have to be
>> an "Expert" in clojure to contribute.
>>
>> --
>> Jay Vyas
>> MMSB/UCHC
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