Tag Archives: BioGroovy

Fetching Data Files With BioGroovy

It’s often useful to fetch data from a web service and cache it in your local directory. This cuts down on the amount of traffic between your machine and the web service you’re invoking, and it makes unit testing your … Continue reading

Posted in Bioinformatics, Informatics | Tagged | 2 Comments

Fetching Data With BioGroovy

With BioGroovy 1.1 we’ve added support for fetching data from a variety of RESTful webservices, including: EntrezGene, PubMed, UniProt and many others. Fetching Data In this example, we’ll fetch gene information from EntrezGene for 3 genes, and output the result … Continue reading

Posted in Bioinformatics, Informatics | Tagged | Leave a comment

BioGroovy and Web Service Identity

With the recent release of BioGroovy 1.1, we added support for a number of web services. Web service providers like NCBI’s eUtils, EntrezAjax and JournalTOCs have requirements for tracking usage of their services.  In some cases, a token must be … Continue reading

Posted in Bioinformatics, Informatics | Tagged , , | Leave a comment

Tinkering With BioGroovy 1.1

Since the initial release of BioGroovy, a lot has changed, and the library has continued to grow substantially. With the recent BioGroovy 1.1 release, I thought I would review some of the changes, and update the information on how you … Continue reading

Posted in Bioinformatics | Tagged , , | Leave a comment

BioGroovy 1.0 Classes Released

It’s been a pretty busy weekend, and the recent work on BioGroovy 1.0 is part of the reason.  One of the goals of the BioGroovy project has been to leverage the Java libraries that are currently available, and the samples … Continue reading

Posted in Bioinformatics, Informatics | Tagged , , | Leave a comment

BioGroovy and the Semantic Web

Recently, I found myself putting together a presentation on BioGroovy.  One of the key features that I’ve been taking advantage of is the ability to use BioGroovy models as Grails domain objects.  This makes it possible to easily download and … Continue reading

Posted in Bioinformatics, Informatics, Semantic Web | Tagged , , , , | Leave a comment

BioGroovy and Grapes

As many Perl programmers know CPAN (the Comprehensive Perl Archive Network) is an invaluable repository for Perl modules.  You can easily download and install a module and add its functionality to your script.  In order for scripting languages like Groovy … Continue reading

Posted in Bioinformatics, Informatics | Tagged , , | 1 Comment