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The BioGroovy Project

BioGroovy is an open-source project dedicated to providing a Groovy framework for processing biological data. Like it's sister projects BioPerl and BioPython, BioGroovy can be used either in interpreted or compiled mode, or one can mix both compiled and interpreted code. The Groovy scripting language can be used with any Java-based library (such as the BioJava API) or with native code (such as the EMBOSS library) through the Java Native Access API, or through the Java Native Interface. Groovy syntax can be either Java-like or Groovy-fied to take advantage of constructs like Closures, which are not found in Java. Groovy is also the basis for Web Development frameworks like Grails (Groovy on Rails) which makes it possible to generate fully functional web applications within a few minutes. Thus Groovy is well-suited for a wide-variety of bioinformatics-related tasks.

BioGroovy is under LGPL 2.1.

Getting Started

• Installing Groovy
• Installing the BioJava Libraries
• Shell Scripting With BioGroovy

BioGroovy Cookbook

• Hello World
• Parsing FASTA Files
• Parsing BLAST Results
• Using NCBI's eUtils
  • Fetching Annotations From Entrez-Gene
    • BIND Interactions
    • GO Annotations
    • Gene Cartoons
  • Fetching Sequences
  • Fetching PubMed Entries
  • Searching PubMed