Linuxlandia

Bio-Linux is designed for researchers within the NERC Environmental Genomics (EG) and NERC Post Genomics and Proteomics (PGP) community, but we also welcome applications from academics based within the wider scientific community.

To request Bio-Linux you will need to complete an application form and send it to admin@envgen.nox.ac.uk. After your application is processed, we will send you a Bio-Linux installation CD, floppy disk, and installation instructions.

Unlike a true 'distribution' of Linux, Bio-Linux is an 'image' (snapshot), of a system. This 'image' is downloaded to your computer via the Internet (5Gb) during installation, so for all practical purposes each Bio-Linux computer is a software 'clone'. When you receive the installation pack, please contact the NEBC helpdesk to arrange a time to download the Bio-Linux image from our server.

NERC EG and PGP Awardees may be eligible to receive a computer from the NEBC on which to install Bio-Linux. If you are not an EG or PGP Awardee, you will need to supply your own hardware.

NERC EG and PGP Awardees have full access to the support provided via our electronic helpdesk.

For all Bio-Linux administrators, we host a mailing list where you can post questions and provide help to others. All of our documentation is available freely online.

Hardware Requirements

Bio-Linux has been developed and optimised for use on hardware meeting the following specification:

• Dell Precision 490 N-Series Dual Xeon 5110 1.6GHz/1066MHz/4MB
• 1GB DDR2 533 ECC Dual Channel Memory (2 x 512MB)
• 3.5in 1.44MB Floppy Drive
• 2 x 80GB (7200rpm) SATA II Hard Drive
• 48X CDRW/DVD Drive
• 128MB PCIe x 16 NVIDIA Quadro NVS 285 VGA Video Card

Bio-Linux has been run successfully on a variety of different hardware and should be fine on any system that can support the Debian distribution. However, we cannot guarantee or support the running of Bio-Linux on alternative hardware.

Network Requirements

To download (install) the Bio-Linux image, your machine will need a static IP address registered in the DNS. Please talk with your local IT staff about this. In addition to the IP address, we need the following details to enable your Bio-Linux machine to be correctly configured. There is space in the application form to include this information:

1. Hostname of the new machine (e.g. darwin):
2. Domain name (e.g. evol.ac.uk):
3. Device (e.g. eth0):
4. IP of new machine:
5. Netmask of new machine:
6. Network IP for new machine:
7. Broadcast IP for new machine:
8. Gateway IP for new machine:
9. Primary DNS server IP:
10. Secondary DNS server IP:

Installing Bio-Linux

The Bio-Linux package is downloaded to your computer via the Internet (5Gb). The links below take you to documentation that describes what you will see on-screen during installation. You may find it useful to have this text available during installation of Bio-Linux.

• How to install Bio-Linux 4 on a new machine




• How to upgrade to Bio-Linux 4 from earlier versions

Bio-Linux provides both standard and cutting edge bioinformatics software tools on a Linux base. It is powerful, configurable and easy to maintain. Bio-Linux has been customised for ease of use and provides an ideal system for scientists handling and analysing biological data.
Bio-Linux has been developed for NERC researchers, but is also available to the wider research community on submission of a Bio-Linux application form.

Bio-Linux also comes with many development tools, providing a solid base for bioinformatics software development. It can also be easily deployed as a computer cluster.

• Request and Install Bio-Linux

• Bio-Linux Documentation

• Software Packages on Bio-Linux

• Bio-Linux Project History

• Bio-Linux Live DVD

As of version 4.0, Bio-Linux is based on the Debian GNU/Linux distribution. Bioinformatics-related customisations include a large number of bioinformatics programs and programming libraries, the addition of graphical menus for much of the bioinformatics software, and links from the desktop to key documentation and applications. The system also includes a comprehensive, categorised and searchable documentation system for bioinformatics software.

There are many other customisations, including the addition of the Condor package, the inclusion of a powerful and configurable firewall and the presence of web-based system administration software. For full details, please see the Bio-Linux development log.

A large amount of documentation is available for Bio-Linux, including course materials. Support for NERC funded researchers is available via our helpdesk as well as a variety of other mechanisms. For others, we provide a mailing list where Bio-Linux related issues can be discussed with other Bio-Linux system administrators.

As of November 2005, a DVD version of Bio-Linux is also available called Bio-Linux Live.
Bio-Linux Live is a great solution for working at home or anywhere you don't have access to bioinformatics applications like those on a Bio-Linux machine. It emulates the look and feel of working on a full Bio-Linux system without requiring installation.

Bio-Linux Live DVD

Now you can run Bio-Linux from a Live DVD... Version 1.4, released on 8 November 2006, includes updated packages and "Handlebar" demo.

Introduction

Bio-Linux Live is a great solution for working at home or from anywhere that you don't have access to bioinformatics applications like those on a Bio-Linux machine. It emulates the look and feel of working on a full Bio-Linux system without requiring installation.

As Live Linux systems run entirely in the memory of your machine, nothing is written to the hard disk, so results files should be saved to a memory stick or floppy disk before logging out.

• How does the Live DVD differ from a standard Bio-Linux installation?

• FAQ for the Bio-Linux Live DVD

• System Requirements

Download Bio-Linux Live

Right click and save the latest Bio-Linux Live ISO image (~1.9GB, md5sum), and then burn that image to a blank DVD (use "Record CD from CD Image" option within your copying software). You can then boot your system from the DVD to run Bio-Linux Live.

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