Motivation
Many bioinformatics workflows involve large datasets in which high performance computing is needed. Cloud computing provides researchers with the ability to perform computations using a practically unlimited pool of virtual machines, using platforms such as Amazon EC2, Eucalyptus or VirtualBox. CloudBioLinux utilizes these resources to enable instant access to biological software, programming libraries and data.
CloudBioLinux is a community project and we welcome contributors and feedback. Software and data are built using Fabric for fully automated installation and deployment. Packages are specified in simple configuration files for both Linux packages and programming language libraries. Please fork our code on GitHub and suggest improvements and additions.
These resources are designed for biologists as well as programmers. With the help of the NEBC Bio-Linux development team, images include the biological software and libraries available in local installations along with a FreeNX desktop environment designed to ease the transition to remote computational analysis.
Resources
- Amazon EC2: ami-fb00ca92 -- 64 bit image, Ubuntu 11.10 (12 December 2011)
Amazon EC2: ami-31bc7758 -- 64 bit image, Ubuntu 10.04 LTS (29 November 2011) - These images work with micro instances, a cost effective way to explore Amazon resources.
- Cloud BioLinux can be executed on a desktop computer without the need for a cloud:
- Cloud BioLinux 32-bit VirtualBox appliance Information for end-users for installing Virtualbox and importing Cloud BioLinux images for execution within Virtualbox.
- Cloud BioLinux images are available for execution on a private Eucalyptus cloud:
- Cloud BioLinux 32-bit Eucalyptus .img The .img file can be uploaded to your Eucalyptus cloud by simply running "uec-publish-image file.img" from the Ubuntu cloud-utils
- Vagrant .box images, for developers who want to work locally with Cloud BioLinux:
-
Ubuntu 11.04 64bit; Vagrant 0.8 (19 October 2011)
Ubuntu 11.04 32bit; Vagrant 0.7 (29 June 2011)
Debian squeeze 32bit; Vagrant 0.7 (27 April 2011) - Information on how to import Cloud BioLinux images in VirtualBox can be found here
- Indexed genome builds for aligners such as Bowtie, BWA and Novoalign in the biodata S3 bucket. An automated script pulls the requested genomes and aligner indexes to an Amazon machine or your local computer; integration with Galaxy is also provided.
Documentation
- Getting Started with CloudBioLinux -- a gentle guide for new users.
- Build framework -- a high level overview of the automated build environment.
- Developer build documentation -- details on using and contributing to the framework.