Monthly Archives: December 2010

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

BioGroovy: Fetching PubMed Data

As part of the series of blog entries on BioGroovy, I thought I’d start with some rather simple tasks using some of the functionality found in NCBI’s eUtils API. NCBI has both RESTful and SOAP APIs that you can use. … Continue reading

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

Fetching Gene Cartoon With BioGroovy

EntrezGene provides a gene cartoon which shows the coding regions and untranslated regions for a gene. This informative cartoon shows the mRNA and the resulting protein for a particular gene. In this BioGroovy example, I’ll show you how to fetch the … Continue reading

Posted in Uncategorized | Tagged , , , | Leave a comment

BioGroovy

Groovy is a powerful scripting language that allows you to leverage a large number of Java libraries. This series of articles describes how you can combine Groovy with bioinformatics-related libraries to solve a variety of problems. Traditionally, Perl has been … Continue reading

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