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Related Experiment Video

Updated: May 24, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

Raoul J P Bonnal¹, Jan Aerts, George Githinji

¹Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy. bonnal@ingm.org

Bioinformatics (Oxford, England)

|February 15, 2012

Summary

Biogem offers an open-source software development environment for Ruby, fostering community collaboration in bioinformatics. This approach simplifies development and promotes best practices for scalable, decentralized bioinformatics projects.

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Area of Science:

Bioinformatics
Software Engineering

Background:

Biogem is a free, open-source software (OSS) development environment.
It supports community-based software development in bioinformatics.
Biogem is compatible with Linux, Mac OS X, and Windows.

Purpose of the Study:

To provide a software development environment for the Ruby programming language.
To encourage community-based software development in bioinformatics.
To lower the barrier to entry and promote best practices in bioinformatics software development.

Main Methods:

Utilizes a targeted, modular, and decentralized approach.
Incorporates a software generator and various tools.
Features tight web integration.

Main Results:

Biogem facilitates collaborative open-source software development.
It offers an improved model for scaling bioinformatics projects.
Encourages adherence to best practices.

Conclusions:

Biogem enhances community-driven bioinformatics software development.
Its modular and decentralized model is effective for scaling open-source projects.
Biogem lowers entry barriers and promotes best practices in the field.