BioSlax – Live Media Operating System
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BioSlax – Live Media Operating System
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Copyright 2010. National University of Singapore. All rights reserved.ⓒ
What is BioSlax?
• Slackware Linux on a CD/DVD/USB + bioinformatics modules included
• Created and released by Bioinformatics Centre (BIC) Resource Unit, NUS – Mark De Silva, Lim Kuan Siong and Tan Tin Wee
• Uses alternative Unification File System (aufs)/squashfs that allows read-only file system to have writable access by saving all changes in memory
• Uses LZMA compression to make images small
• Slax - created by Tomas Matejicek. Website is at: http://www.slax.org/
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Copyright 2010. National University of Singapore. All rights reserved.ⓒ
BioSlax in the public eye
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Copyright 2010. National University of Singapore. All rights reserved.ⓒ
Why use BioSlax/Slax?
• Complete OS by itself running off a CD/DVD/USB
• On machines with sufficient RAM, it can be loaded completely into memory
• Isolated from and independent of OS already installed on hard disk (eg. Windows XP, Windows Vista, etc)
• Need not format hard disk for installation. Existing data stays intact
• Modular
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Copyright 2010. National University of Singapore. All rights reserved.ⓒ
Modularity of BioSlax
• There are 2 parts to the BioSlax build – Part 1: core system (Linux OS + basic tools)– Part 2: modules
• Modules– individual utilities user wants– easily added or removed prior to CD/DVD creation– easily upgraded when new version’s available– modules are single images (lzm files), proability of tampering is low
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Copyright 2010. National University of Singapore. All rights reserved.ⓒ
Modularity of BioSlax
Applications can be made into modules
Modules inserted either dynamically or via a special folder in the media
Easy to customize the live system to your needs – especially when running from USB
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Copyright 2009. National University of Singapore. All rights reserved.ⓒ
Modules in BioSlax …
Bioinformatics Modules:Artemis Glimmerhmm Primer3 BioGrep
Hmmer PyMOL BioPERL JalView
JMOL BLAST (CLI, WI) JAligner R with BioConductor
Modeller ReadSEQ ClustalW (CLI, WI, XGUI) NJPlot
Sequence Manipulation Suite (SMS2)
PamL TCoffee (CLI, WI) Patscan
EMBOSS (CLI, WI, JI) Phylip (CLI, WI) TreeView Weka
Genesplicer Ploticus
Many other application/utility modules, eg: agrep, tomcat, java, etc
* CLI – Command Line Interface WI – Web Interface XGUI – X Windows Graphical User Interface JI – Java Interface
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BioSlax in action
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Booting Up BioSlax
1. CD (without Open Office) – not being produced any longer, unless by special request
2. DVD (with Open Office)
3. USB drive (with Open Office - writable)
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Screenshot – BioSlax Booting Up
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Screenshot – BioSlax Booting Up
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The X-Window Desktop
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Copyright 2010. National University of Singapore. All rights reserved.ⓒ
Networking
•Comes with network drivers – fixed line and wireless
•Additional drivers for lesser known fixed line and wireless network cards compiled and added
•Supports all Intel based wireless cards, Atheros and both legacy and current Broadcom based wireless cards
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BioSLAX – A Portable Blast Server
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Web BLAST demo
• Insert your USB drive into the PC• Make sure your USB drive is detected
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Copyright 2009. National University of Singapore. All rights reserved.ⓒ
Web BLAST demo
• If you don’t see the db directory, open Konsole & type:
cd /mnt/sda1_removable/
wget ftp://sf01.bic.nus.edu.sg/incoming/blast-db-demo.tar.gz
tar –zxf blast-db-demo.tar.gz
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Web BLAST demo
• To setup BLAST database, go to K-Menu -> BioSLAX -> Desktop Apps -> BLAST DB Setup
• Fill in the location of the BLAST formatted database files
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Web BLAST demo
• Start web BLAST & select the list of BLAST programs:
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Web BLAST demo
•Regular BLAST page
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Web BLAST demo
•BLAST result
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BioSLAX on Virtual Machines
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Copyright 2009. National University of Singapore. All rights reserved.ⓒ
Running BioSlax on Virtual Machines
• BioSLAX can be run on virtual machines
• Different virtual machines available– VMWare (Linux/Mac/Windows)– Microsoft Virtual PC/Hyper V (Windows)– QEMu (Linux)– Virtualbox (Linux)– XEN Citrix Server
• Can boot from physical CD/DVD media or from ISO image
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Screenshot – VMWare Version
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Copyright 2009. National University of Singapore. All rights reserved.ⓒ
The Power of BioSlax - Modularity
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Copyright 2009. National University of Singapore. All rights reserved.ⓒ
BioSlax application modules
• Slax is versatile because of modules
• Modules available for almost anything– http://www.slax.org/modules.php
• Very few available modules for Bioinformatics – http://www.bioslax.org/modules.shtml
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BioSlax module manager
• Modules can be inserted or removed dynamically (no shutdown required) using the GUI based BioSlax module manager
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Copyright 2010. National University of Singapore. All rights reserved.ⓒ
How to use a Slax module
• Automatically inserted on boot up: – save modules in /modules directory of the CD
• To activate a module, use:
activate </path/module.lzm>e.g. activate /tmp/blast.lzm
• To deactivate a module, use:deactivate </path/module.lzm>e.g. deactivate /tmp/blast.lzm
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Retaining modifications (changes)
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How to save/restore modifications
• To save and restore your settings, hit the ‘TAB’ key at the BioSLAX boot menu selection. Use:
changes=/mnt/sda1_removable/mychanges
where /mnt/sda1_removable is a mounted USB drive
and /.../mychanges is a directory created in the USB drive to store settings
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How to save/restore modifications
• If no changes directory is specified on boot up changes or the directory specified is not writable or doesn’t exist, all changes are saved to /mnt/live/memory/changes
• /mnt/live/memory/changes is deleted when system shuts down
• Can create a module from the directory /mnt/live/memory/changes
– dir2lzm /mnt/live/memory/changes /tmp/mychanges-07092009.lzm– insert the module dynamically using “activate”– copy the module to the modules folder
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Creating your own live media OS
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Creating your own live media
• BioSLAX has tools for almost every area of study
• Advantage – anyone in any bioinformatics field of study can use it
• Disadvantage – large size (890MB) for a live OS
• Age old question : “Give a man a fish or show him how to fish?”
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• Download the linux base
• Customized base with all necessary libraries and dependancies available
- ftp://sf01.bic.nus.edu.sg/incoming/bioslax/distro/v7.5/bioslax_v75_base.iso
• Select your modules from •http://www.slax.org/modules.php •http://www.bioslax.org/modules.shtml
• USB Media : -format USB device to FAT32
-extract contents of ISO to the ROOT of the USB device
-“bioslax” and “boot” directories now on USB device
-cd to “boot” directory and run “bootinst” program
-USB device is now bootable and will boot base BioSlax
• Copy modules to bioslax/modules folder and reboot – ALL DONE!
Creating your own live media
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Copyright 2010. National University of Singapore. All rights reserved.ⓒ
Creating your own live media
• CD/DVD: – mount the ISO with ISO Tool (eg: WinISO, Magic ISO)– put modules in the bioslax/modules folder– re-burn the image to CD/DVD
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BioSLAX on the GRID and in Clusters
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BioSLAX on the GRID
• Various GRID agents available
• Easy to create modules for any of these GRID agents
• With the GRID agents running on BioSLAX, possible to rapidly setup a large cluster of slave nodes
• BioSLAX as nodes on NUS Tera Campus GRID (TCG)
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Rapid Deployment of Clusters
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BioSLAX Clusters
• BioSLAX can be easily replicated on any number of mahines
• Ideal for creating clusters
• Cluster software easily made into modules
• Single configuration will work for all nodes
• ROCKS, LSF, Beowulf
• Don’t need to wipe out current OS – boot from CD/DVD/USB
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Installing BioSLAX as a full Linux server
• Possible to install BioSLAX to a PC in an uncompressed format, ie: FULL Linux installation (takes up 3.5GB of disk space)
• Makes rapid deployment (eg: class room/lab environment) simple
• GUI based tool for full installation comes with BioSLAX
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Summary
• BioSLAX is :– a versatile live operating system– easy to customize– modules can be added or removed as necessary– an ideal tool for learning
• All software is covered under GNU public license and are free
• A lot of work is put into the modularization of the various software, especially bioinformatics tools and applications
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Recommended reading/viewing
1. http://www.slax.org/
2. http://www.bioslax.com/
3. http://www.slax.org/documentation.php
4. http://en.wikipedia.org/wiki/BioSLAX
5. http://www.youtube.com/watch?v=MfNCUGj2AUg
6. http://bioinfotutlets.blogspot.com/2009/05/17-installing-bioslax-as-full-linux.html