Bio-Linux is an ideal system for scientists handling and analysing biological data.

BioLinux is a term used in a variety of projects involved in making access to bioinformatics software on a Linux platform easier using one or more of the following methods:

* Provision of complete systems
* Provision of bioinformatics software repositories
* Addition of bioinformatics packages to standard distributions
* Live DVD/CDs with bioinformatics software added
* Community building and support systems

There are now various projects with similar aims, on both Linux systems and other Unices, and a selection of these are given below. There is also an overview in the Canadian Bioinformatics Helpdesk Newsletter that details some of the Linux-based projects.

Package repositories.

Package repositories are generally specific to the distribution of Linux the bioinformatician is using. A number of Linux variants are prevalent in bioinformatics work. Fedora is a freely-distributed version of the commercial Red Hat system. Red Hat is widely used in the corporate world as they offer commercial support and training packages. Fedora Core is a community supported derivative of Red Hat and is popular amongst those who like Red Hat's system but don't require commercial support. Many users of bioinformatics applications have produced RPMs (Red Hat's package format) designed to work with Fedora, which you can potentially also install on Red Hat Enterprise Linux systems. Other distributions such as Mandriva and SUSE use RPMs, so these packages may also work on these distributions.


* Biolinux (Fedora)
* BioRPMs (RedHat and Fedora)
* RPMfind.net (Various RPM-based distributions, indexed by category)

Updates:

Bio-Linux 6.0 is a 64-bit workstation system developed for biologists and bioinformaticians by the NERC Environmental Bioinformatics Centre. Bio-Linux 6.0 is based on the popular Ubuntu Linux system, giving you the benefits of a free, user-friendly, comprehensive computing environment, as well as the convenience of the bioinformatics tools you need. Bio-Linux 6.0 comes with over 500 bioinformatics programs pre-installed, including software for handling sequence data from Roche 454 and Illumina systems, and R libraries of interest to biologists, such as vegan, ShortReads, Rsamtools, and the the biocLite selection of packages from Bioconductor. It also includes a comprehensive documentation system providing information on all the bioinformatics software on the system, categorised according to functionality. To help you get started, a folder of sample data is linked to the desktop, so you can try out new programs easily.

Installation of the system is simple, or you can boot directly from USB stick or DVD to run the system without installing anything to your hard disk. Bio-Linux 6.0 also comes with the FreenNX server, making it easier than ever to log in remotely from other machines and run a full, graphical Bio-Linux session. Of course, Bio-Linux also includes other customisations to make getting started on the system easy, while ensuring you are working in a secure environment.

Bio-Linux 6.0 can be downloaded from the NEBC website, and used to create a bootable USB stick or DVD. You can then either run the system live from either of these, or install the system. Full details, including links to download the new system, can be found on our website: http://nebc.nerc.ac.uk/tools/bio-linux

Debian.

Debian is another very popular Linux distribution in use in many academic institutions, and some bioinformaticians have made their own software packages available for this distribution in the deb format.

* Debian Med (Debian contains a lot of medical software internally)
* NEBC Bio-Linux (Non-standard Debian)

Apple/Mac

Many Linux packages are compatible with Mac OS X and there are several projects which attempt to make it easy to install selected Linux packages (including bioinformatics software) on a computer running Mac OS X. These include:

* Fink scientific packages
* Homebrew

Similarly, eBioinformatics provides a Mac OS GUI for over 300 open source bioinformatics programs.

You can install Bio-Linux on your machine, either as the only operating system, or as part of a dual-boot setup which allows you to use your current system and Bio-Linux on the same hardware.

Bio-Linux also runs Live from the DVD. This runs in the memory of your machine and does not involve installing anything. This is a great, no-hassle way to try out Bio-Linux, demonstrate or teach with it, or to work with when you are on the move.

Bio-Linux is built on open source systems and software, and so is free to to install and use. Read the paper on Bio-Linux and open source systems for biologists.


Getting Bio-Linux.

Getting Bio-Linux is simple. Just download the image, burn it to a DVD, and boot the machine from that DVD. See this page for troubleshooting help regarding the DVD.

Bio-Linux can also be run from a USB memory stick. This is an ideal way to work with Bio-Linux Live, as files you create are saved to the stick. Of course, you can install the system from the memory stick also.

You can easily create bootable memory sticks yourself using the bio-linux-usb-maker package.

Until recently, you could request a Bio-Linux on a 4.0Gb memory stick if you were funded by the NERC or have a working relationship with the NEBC. This service will be offered again, after the release of Bio-Linux 6.0 in June 2010.

You can install our software packages onto a pre-existing Debian or Ubuntu system.

You can set up the system in various configurations depending on your needs.

You can submit feedback or ideas for Bio-Linux using our feedback form.

User Guide

Live Memory Stick

Software Packages

Accessing Bio-Linux

Other Bio-Linux Documentation

High throughput sequence data handling on Bio-Linux

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KDE, Latest Announcements and Latest Applications.

Latest Announcements.

KDE Ships November Updates
On 3rd November 2010, KDE has released 4.5.3, containing translation updates, performance and stability improvements and other bugfixes. KDE recommends everybody running 4.5.2 or earlier versions to update.

KDE Releases Development Platform, Applications and Plasma Workspaces 4.5.0
On 10th August, 2010, KDE released new versions of the Plasma Workspaces, the KDE Applications and the KDE Development Platform in version 4.5.0. While focus within this release cycle lay on stability, the overall polish and performance gain is well noticable. Features such as the reworked notification area, Marble's map routing and support for WebKit in Konqueror round up this release.

KDE Software Compilation 4.4.5 released
On 30th June 2010, KDE SC 4.4.5 was released. 4.4.5 provides bugfix and translation updates and is a recommended update for everybody running 4.4.4 or earlier versions.

View more announcements...

Latest Applications.

	LyX LyX is a document processor that encourages an approach to writing based on the structure of your documents, not their appearance. LyX is for people that write and want their writing to look great, right out of the box. No more endless tinkering with formatting details, 'finger painting' font attributes or fuzzing around with page boundaries. You just write. In the background, Prof. Knuth's legendary TeX typesetting engine makes you look good. On screen, LyX looks like any word processor; its printed output -- or richly cross-referenced PDF, just as readily produced -- looks like nothing else. Gone are the days of industrially bland .docs, all looking similarly not-quite-right, yet coming out unpredictably different on different printer drivers. Gone are the crashes 'eating' your dissertation the evening before going to press.
	Flacon Flacon extracts individual tracks from one big audio file containing the entire album of music and saves them as separate audio files. To do this, it uses information from the appropriate CUE file. Besides, Flacon makes it possible to conveniently revise or specify tags both for all tracks at once or for each tag separately. Features: * Supported input formats: WAV, FLAC, APE, WavPack, True Audio (TTA). * Supported out formats: FLAC, WAV, WavPack, OGG or MP3. * Replay Gain analysis (album-gain and track-gain modes). * Multi-threaded conversion process. Requires: * python * PyQt * shntool * flac (optional, for decoding and encoding FLAC files) * mac (optional, for decoding APE files) * wavpack (optional, for decoding WV files) * ttaenc (optional, for decoding TTA files) * oggenc (optional, for encoding OGG files) * lame (optional, for encoding MP3 files) * metaflac (optional, for FLAC replay gain) * vorbisgain (optional, for OGG replay gain) * mp3gain (optional, for MP3 replay gain) Now Flacon is a pure Qt application.
	Xt7-Player Yet another gui for mplayer. It aims to be a complete interface to its tons of options, while trying to keep usability in mind. Please, double check your distribution ships latest gambas libraries, any version < 2.15 will cause problems, expecially with metacity under gnome. Hint for mandriva users Maybe you'll find a better package on MIB repositories: http://mib.pianetalinux.org/mib/component/search/xt7-player Screenshots and features: http://xt7player.homelinux.org/xt7forum/viewtopic.php?f=7&t=2 Please, submit bugs to xt7player@gmail.com If you care to help me by writing translations, documentation, ask for a new feature or else, feel free to write a line here: http://xt7-player.sourceforge.net/xt7forum/viewforum.php?f=4
	Random Album An amarok script that monitors the playlist, and, when it's finished, repopulates it with a random album from the collection. Differently from amarok's built-in "random album" mode, you don't need to keep the whole collection in the playlist; so when you add new stuff to the collection the script will automatically pick it up, and it's easy to manually enqueue songs into the current playlist without the "random mode" triggering whenever the current album finishes playing. This script is inspired and very loosely based on the randomalbum.py script for amarok 1.4, available at the following URL: http://www.kde-apps.org/content/show.php?content=42764
	KGraphViewer and KGraphEditor KGraphViewer is a Graphviz dot graph file viewer for KDE. It is part of the KDE extragear graphics package. Release of version 2.1.1. This is a bugfix only release that makes the kgraphviewer library cleaner: all necessary headers are installed and no more and with a proper d-pointer in its sole exported class. There is also a little bugfix in the background color setting dialog. Previous version (2.1) included one new visible feature (option to set the default background color) and a bunch of bug regression corrections (thanks to new contributors) and, more importantly, new integration possibilities as the viewer can now be integrated in an application either as a plugin (KPart) or as a real widget. Note that from now on, the kgraphviewer code is hosted on the KDE git repository instead of svn. Last but not least, Milian Wolf has setup kgraphviewer to be built on OpenSuse build service, thus giving a bunch of new binary packages for various distributions (see links below). The editor works but is still very young. It demonstrates the use of the KGraphViewer part (KDE plugins) as a changeable view of a graph. KGraphViewer is now included in several GNU/Linux distributions ! The tool works very well for most dot graphs. Here are some of its currently implemented features: - zooming - threaded loading of several graphs in tabs; - saving of the recent files list; - manual reload of files; - display of a bird-eye view of the graph; - moving of the graph by dragging; - full featured printing; - perfect drawing of all graphviz example graphs; - automaticaly choose dot for directed graphs and neato for undirected - possibility to use an arbitrary layout algo as soon as it produces xdot format - automatic reloading with user confirmation of (externaly) modified files (configurable) ; - open new instances as new tabs in the existing window (configurable) - help system - internationalization - background color selection

More Applications

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ConnochaetOS will be a free operating system for the desktop with old computers in mind but with modern software.

ConnochaetOS (formerly DeLi Linux) is an Arch-based Linux distribution for old computers, from i486 to Pentium MMX 166. It's focused on desktop usage.

It includes email clients, a graphical web browser, an office package with word processor and spreadsheet. A full install, including X window system and development tools, needs no more than 300 MB of hard disk space.

Updates (via Distrowatch):

Henry Jensen has announced the release of ConnochaetOS 0.9.0, a lightweight desktop distribution, formerly known as DeLi Linux, designed for old and low-resource computers (Pentium I, 64 MB of RAM): "I am pleased to announce the release of ConnochaetOS 0.9.0. After one year of development and after three years after the last release of its predecessor, DeLi Linux, this is the first stable release of ConnochaetOS. In the last weeks since RC1 we simplified the installer once again, fixed some more bugs and updated the kernel, the web browser XXXTerm and other packages, and produced some documentation. ConnochaetOS 0.9.0 provides: kernel Linux-Libre 2.6.32.43, the IceWM desktop 1.3.7, a lightweight WebKit-based web browser - XXXTerm, GOffice...."

See the release announcement for more information.

Download the installation CD image: connos-0.9.0.iso (391MB, MD5)..

Recent releases:

 • 2011-08-11: Distribution Release: ConnochaetOS 0.9.0
 • 2010-11-13: Development Release: ConnochaetOS 0.8.9 Beta 1
 • 2008-05-29: Distribution Release: DeLi Linux 0.8.0
 • 2007-05-18: Distribution Release: DeLi Linux 0.7.2
 • 2006-10-17: Distribution Release: DeLi Linux 0.7.1
 • 2006-09-16: Distribution Release: DeLi Linux 0.7


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Rocks is a complete "cluster on a CD" solution for x86 and x86_64 Red Hat Linux clusters.

Rocks is a complete "cluster on a CD" solution for x86 and x86_64 Red Hat Linux clusters.

Building a Rocks cluster does not require any experience in clustering, yet a cluster architect will find a flexible and programmatic way to redesign the entire software stack just below the surface (appropriately hidden from the majority of users).

Although Rocks includes the tools expected from any clustering software stack (PBS, Maui, GM support, Ganglia, etc), it is unique in its simplicity of installation.

Updates (via Distrowatch):

Greg Bruno has announced the release of Rocks Cluster Distribution 5.4, a CentOS-based Linux operating system for computer clusters: "Rocks Cluster Distribution 5.4 (Maverick) is released for Linux on the i386 and x86_64 CPU architectures. New features: redesign of the Avalanche installer; channel bonding for nodes is now controlled by the Rocks command line; all nodes' firewall rules are controlled by the Rocks command line; introduction of 'Air Traffic Control'; 'greceptor' replaced with 'channeld'; DNS resolution for multiple domains; login appliance support; set the name of a host based on the name of a specific network interface; easily swap two interfaces with one Rocks command; created a GIT repository for Rocks-related source code...."

See the release announcement and release notes to learn more about the enhancements in this version of Rocks Cluster Distribution.

Download (MD5): area51+...+xen-5.4.i386.disk1.iso (2,480MB), area51+...+xen-5.4.x86_64.disk1.iso (2,552MB)

The first thing to manage is the physical deployment of a cluster. Much research exists on the topic of how to physically construct a cluster. A majority of the O'Reilly Book Building Linux Clusters is devoted to the physical setup of a cluster, how to choose a motherboard, etc. Finally, the book How to Build a Beowulf also has some good tips on physical construction.

We favor rack-mounted equipment because of its relative reliability and density. There are Rocks clusters, however, that are built from mini-towers. Choose what makes sense for you.

The following diagram shows how the frontend and compute nodes must be connected:

On the compute nodes, the Ethernet interface that Linux maps to eth0 should be connected to the cluster's Ethernet switch. This network is considered private, that is, all traffic on this network is physically separated from the external public network (e.g., the internet).

On the frontend, at least two ethernet interfaces are required. The interface that Linux maps to eth0 should be connected to the same ethernet network as the compute nodes. The interface that Linux maps to eth1 should be connected to the external network (e.g., the internet or your organization's intranet).

Install and Configure Your Frontend.

This section describes how to install your Rocks cluster frontend.

The minimum requirement to bring up a frontend is to have the following rolls: Kernel/Boot Roll CD Base Roll CD Web Server Roll CD OS Roll CD - Disk 1 OS Roll CD - Disk 2 The Core Meta Roll CD can be substituted for the individual Base and Web-Server Rolls. Additionally, the official Red Hat Enterprise Linux 5 update 4 CDs can be substituted for the OS Rolls. Also, any true rebuild of RHEL 5 update 4 can be used -- distributions known to work are: CentOS 5 update 4 and Scientific Linux 5 update 4. If you substitute the OS Rolls with one of the above distributions, you must supply all the CDs from the distribution (which usually is 6 or 7 CDs).

1. Insert the Kernel/Boot Roll CD into your frontend machine and reset the frontend machine.

   For the remainder of this section, we'll use the example of installing a bare-bones frontend, that is, we'll be using the Kernel/Boot Roll, Core Roll, OS - Disk 1 Roll and the OS - Disk 2 Roll.

2. After the frontend boots off the CD, you will see:

   

   When you see the screen above, type:

   build

   The "boot:" prompt arrives and departs the screen quickly. It is easy to miss. If you do miss it, the node will assume it is a compute appliance, and the frontend installation will fail and you will have to restart the installation (by rebooting the node).

   If the installation fails, very often you will see a screen that complains of a missing /tmp/ks.cfg kickstart file. To get more information about the failure, access the kickstart and system log by pressing Ctrl-Alt-F3 and Ctrl-Alt-F4 respectively.

   After you type build, the installer will start running.

3. All screens in this step may not appear during your installation. You will only see these screens if there is not a DHCP server on your public network that answers the frontend's DHCP request.

   If you see the screen below:

   

   You'll want to: 1) enable IPv4 support, 2) select manual configuration for the IPv4 support (no DHCP) and, 3) disable IPv6 support. The screen should look like:

   

   After your screen looks like the above, hit "OK". Then you'll see the "Manual TCP/IP Configuration" screen:

   

   In this screen, enter the public IP configuration. Here's an example of the public IP info we entered for one our frontends:

   

   After you fill in the public IP info, hit "OK".

4. Soon, you'll see a screen that looks like:

   

   From this screen, you'll select your rolls.

   In this procedure, we'll only be using CD media, so we'll only be clicking on the 'CD/DVD-based Roll' button.

   Click the 'CD/DVD-based Roll' button.

5. The CD will eject and you will see this screen:

   

   Put your first roll in the CD tray (for the first roll, since the Kernel/Boot Roll is already in the tray, simply push the tray back in).

   Click the 'Continue' button.

6. The Kernel/Boot Roll will be discovered and display the screen:

   

   Select the Kernel/Boot Roll by checking the 'Selected' box and clicking the 'Submit' button.

7. This screen shows you have properly selected the Kernel/Boot Roll.

   

   Repeat steps 3-5 for the Base Roll, Web Server Roll and the OS rolls.

8. When you have selected all the rolls associated with a bare-bones frontend, the screen should look like:

   

   When you are done with roll selection, click the 'Next' button.

9. Then you'll see the Cluster Information screen:

   

   The one important field in this screen is the Fully-Qualified Host Name (all other fields are optional). Choose your hostname carefully. The hostname is written to dozens of files on both the frontend and compute nodes. If the hostname is changed after the frontend is installed, several cluster services will no longer be able to find the frontend machine. Some of these services include: SGE, NFS, AutoFS, and Apache.

   Fill out the form, then click the 'Next' button.

10. The private cluster network configuration screen allows you to set up the networking parameters for the ethernet network that connects the frontend to the compute nodes.

    

    It is recommended that you accept the defaults (by clicking the 'Next' button). But for those who have unique circumstances that requires different values for the internal ethernet connection, we have exposed the network configuration parameters.

11. The public cluster network configuration screen allows you to set up the networking parameters for the ethernet network that connects the frontend to the outside network (e.g., the internet).

    

    The above window is an example of how we configured the external network on one of our frontend machines.

12. Configure the the Gateway and DNS entries:

    

13. Input the root password:

    

14. Configure the time:

    

15. The disk partitioning screen allows you to select automatic or manual partitioning.

    

    To select automatic partitioning, click the Auto Partitioning radio button. This will repartition and reformat the first discovered hard drive that is connected to the frontend. All other drives connected to the frontend will be left untouched.

    The first discovered drive will be partitioned like:

    Table 2-1. Frontend -- Default Root Disk Partition

    Partition Name	Size
    /	16 GB
    /var	4 GB
    swap	1 GB
    /export (symbolically linked to /state/partition1)	remainder of root disk

    When you use automatic partitioning, the installer will repartition and reformat the first hard drive that the installer discovers. All previous data on this drive will be erased. All other drives will be left untouched. The drive discovery process uses the output of cat /proc/partitions to get the list of drives. For example, if the node has an IDE drive (e.g., "hda") and a SCSI drive (e.g., "sda"), generally the IDE drive is the first drive discovered. But, there are instances when a drive you don't expect is the first discovered drive (we've seen this with certain fibre channel connected drives). If you are unsure on how the drives will be discovered in a multi-disk frontend, then use manual partitioning.

16. If you selected manual partitioning, then you will now see Red Hat's manual partitioning screen:

    

    Above is an example of creating a '/', '/var', swap and '/export' partitions.

    If you select manual partitioning, you must specify at least 16 GBs for the root partition and you must create a separate /export partition.

    LVM is not supported by Rocks.

    When you finish describing your partitions, click the 'Next' button.

17. The frontend will format its file systems, then it will ask for each of the roll CDs you added at the beginning of the frontend installation.

    

    In the example screen above, insert the Kernel/Boot Roll into the CD tray and click 'OK'.

    The contents of the CD will now be copied to the frontend's hard disk.

    Repeat this step for each roll you supplied in steps 3-5.

    After all the Rolls are copied, no more user interaction is required.

18. After the last roll CD is copied, the packages will be installed:

    

19. Finally, the boot loader will be installed and post configuration scripts will be run in the background. When they complete, the frontend will reboot.

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