[Biojava-l] BioGroovy

Mark Fortner phidias51 at gmail.com
Fri Aug 15 15:49:30 UTC 2008

Hi Andy,
The builders and closures definitely make it easier to use and cut
down on the verbosity of the language. You also have built-in support
for CLI, and can leverage libraries like ORO for regular expression
handling.   The XmlSlurper makes it easier to handle downloading and
parsing XML.

I created a roadmap for a series of blog articles on various common
bioinformatics-related tasks.  I started out with a couple of quick
entries on using NCBI's EUtils with Groovy.  If there's some interest,
I'll see about posting the roadmap on a wiki somewhere (along with
some of the "recipes" that I've written).  Anyone who's interested
could then contribute their own "recipes" to it.

I'm just getting started with Grails.  My initial thought was to
identify the BioSQL objects  (i.e. SimpleNamespace, SimpleNCBITaxon,
SimpleBioEntry, etc) as domain objects and have the grails ant script
handle generating the gui and persistence stacks for them (perhaps
using Derby).

This might be overly-simplistic, but I'm looking for ways to make
biojavax, and biosql more easily accessible.


On Fri, Aug 15, 2008 at 1:55 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> Hi Mark,
> There has been talk in the past about a groovier version of BioJava or at
> the very least showing where Groovy can help to reduce the verbosity of some
> parts of the biojava framework. I've done a tiny bit but my work has only
> been into prototyping Java code & quickly asserting some assumptions I had
> about BioJava (as in how the framework works).
> What would be a brilliant step in a Groovier BioJava is to start levering
> the builders (http://groovy.codehaus.org/Builders). I mean imagine being
> able to write something like:
> def myReferences = getReferences();
> new EmblBuilder().build {
>        id('U00096')
>        myReferences.each{ ref ->
>                reference {
>                        //
>                }
>        }
> }
> I admit it's not a fully formed idea at the moment but hopefully you can see
> where I'm going with this :)
> WRT Grails; our supported BioSQL API is written in Hibernate; just the same
> as GORM (Grails' ORM solution). So technically I cannot see a reason why it
> wouldn't be possible; my only wonder is how Grails controls transaction
> boundaries and translating this to our BioSQL.
> Andy
> Mark Fortner wrote:
>> I've been using the biojava library with groovy lately and I ran
>> across the BioGroovy.org site.  The site seems to be a placeholder and
>> doesn't really have much information on it.  I was wondering if it was
>> an official Bio* site?  Has anyone else been using Groovy (or any
>> other scripting languages) with BioJava?
>> Also has anyone looked at using Grails with BioSQL?  It would seem
>> like an easy way to get something started quickly.
>> Regards,

Mark Fortner

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

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