BioNode

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BioNode/CloudBiolinux is an open source software initiative to provide a scalable Linux virtual machine image for bioinformatics, based on Debian Linux and Bio Med packages. The image can be deployed on the desktop, using VirtualBox, on a number of networked PCs, and in the cloud (currently Amazon EC2 is supported; and OpenStack is planned for).

The BioNode/CloudBiolinux image is a prepared Debian Bio Med image, which can be run both in a VirtualBox on Windows and OS/X, or in the Amazon EC2 cloud.

The general idea is to have an up-to-date Debian image containing most available Bioinformatics packages, that can be downloaded, and deployed on a local cluster of desktops, or in the Cloud. BioNode and Bio Med are also discussed in a book on evolutionary computational biology (in press). The Bio Med paper is at Community-driven computational biology with Debian Linux. This way, VMs are similar enough for different targets. An investment is only made once. I.e. get BioNode on VirtualBox running, it should be straightforward to move to the Cloud.

Contents

News

  • The list of current BioLinux software packages can be found here (July 2012)
  • We are creating a BioLinux Phylogeny VM - downloads are here (October 2011)
  • BioNode is using the BioLinux bootstrap install for future versions, see the source (May 2011)
  • Released BioNode-0.90 for VirtualBox-i386 and Amazon EC2, see ChangeLog (April 2011)
  • New R+Bionconductor packages available in Debian and BioNode (by Tony, Steffen and others, March 2011)
  • Updated description of building a new BioNode image for Amazon EC2 from scratch at debian.org (by Dominique, Feb 2011)
  • The rq scheduler has been adopted by BioNode, see [1] (by Pjotr, Jan 2011)

Download a ready-made BioNode image

BioNode comes in two flavours. One for VirtualBox, the other for Amazon EC2 (a third is planned for Open Stack).

VirtualBox

The development version of VirtualBox 32-bit and 64-bit images can be downloaded from

(32-bits is available for Windows, OSX, Linux; a 64-bits update is coming soon).

After downloading you may need to set the uuid for the VDI on your machine:

 VBoxManage internalcommands setvdiuuid bionode-ver.vdi

thereafter it can be added to VirtualBox.Use guest as a password for guest, and bionode for getting root with 'su'. Continue reading Running BioNode.

Amazon AMI BioNode

The Amazon AMI image can be installed on a node from the EC2 image list. Search for images named bionode, or google bionode+ami.

 AMI ID: ami-027a896b
 Name: bionode-alpha5
 Description: BioNode Alpha 5
 Source: bionode/bionode-alpha5.img.manifest.xml

Use guest as a password for guest, and bionode for getting root with 'su'. Continue reading Running BioNode.

VirtualBox Bionode Image

Download a VirtualBox image

Either download from the URL mentioned higher up on this page.

Create a VirtualBox image

Create a BioNode image for VirtualBox here.

Install BioNode Packages

Install all BioNode software on the image for VirtualBox here.

Running BioNode

After all software is installed, check out run BioNode

Amazon EC2 BioNode Image

The BioNode image can be fired up from within Amazon EC2. Also, a description for creating the BioNode image from scratch can be found here.

Start and Login with the following commands as usual:

 ec2-run-instances ami-7eee1e17 -k <YOURKEY> -t m1.large
 ssh -i <YOURKEYFILE> root@...

FAQ

How do I get support for BioNode?

Mailing list

BioNode has a mailing list.

IRC

When online you may also try IRC: irc.freenode.net, channel #bionode

How does BioNode differ from BioLinux?

BioNode uses the same build system as CloudBioLinux. To facilitate multiple targets we have added support for Editions and Flavors into BioLinux. Essentially, both are different targets of the same build system.

Some at a first sight important differences are:

  1. BioLinux is based on Ubuntu, BioNode is based on Debian
  2. BioLinux is a full blown desktop, while BioNode(s) are minimalistic and target server mode computing
  3. BioLinux has a size over 8Gb, Bionode(s) are less bloated, normally <1Gb

Also

  1. Debian and Ubuntu are similar, when it comes to the user level biomedical packages; Ubuntu uses Debian packages
  2. Still, Debian does most of the packaging work

And, we work together:

A recent meeting (Travemunde, January 2011) brought many bioinformaticians working with Debian and Ubuntu together. It was co-funded by BioLinux and Debian, and it has helped to overcome hurdles for an active collaboration. The BioLinux developers can now commit to the Debian Med source repository to collaboratively update or otherwise improve packages. There should be one single repository for source packages.

How does BioNode differ from CloudBioLinux?

Good ideas come in pairs. CloudBioLinux is conceptually very similar to BioNode, though currently targeting Ubuntu, rather than Debian. We aim to pool resources. Active development is on github https://github.com/pjotrp/cloudbiolinux/tree/bionode

How does BioNode perform?

Dominique created some BioNode timings running MrBayes MPI on Amazon instances. See here

How do I add BioNode special packages to the image?

We have a special repository for packages that have not (yet) made it into Debian. Add the following lines to sources.list inside your image

 cat << EOLIST | sudo tee -a /etc/apt/sources.list
 deb http://master.dermacloud.uni-luebeck.de/debian ./
 # The regular source packages should be available from
 # Debian unstable, instead. The following should nonetheless work
 #deb-src http://master.dermacloud.uni-luebeck.de/debian ./
 EOLIST
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