bioslax – live media operating system · – a versatile live operating system – easy to...

BioSlax – Live Media Operating System

Copyright ⓒ 2009. National University of Singapore. All rights reserved.

What is BioSlax?

• Slackware Linux on a CD/DVD/USB + bioinformatics modules included

• Released by Bioinformatics Centre (BIC) Resource Unit, NUS

• Uses alternative Unification File System (aufs)/squashfsthat 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/


BioSlax in the public eye


Why use BioSlax/Slax?

• Complete OS by itself running off a CD/DVD/USB

• Uses computer’s memory to load itself

• 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


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), proabilityof tampering is low


Modularity of BioSlax

Applications can be made into modules

Modules inserted either dynamically or via a special folder in the USB/CD

Easy to customize the live system to your needs


Modules in BioSlax …

Bioinformatics Modules:

-BLAST -PatScan -Primer3 -PyMOL-ClustalW -T-Coffee -Artemis ACT -RasMOL

-ClustalX -PHYLIP -Artemis ART -ReadSeq-EMBOSS -GeneSplicer -jAlign -TreeView

-Modeller -GlimmerHMM -Jalview

-PamL -HMMER -NjPlot

-SequenceManipulationSuite v2


BioSlax in action


Booting Up BioSlax

1. CD (without Open Office)

2. DVD (with Open Office)

3. USB drive (with Open Office - writable)


Screenshot – BioSlax Booting Up


The X-Window Desktop


Network setup

Open Konsole and type iwconfig to list all possible wireless devices on the system

Wireless Asst Select your wireless device (can be referred to as wlanX, wifiX, athX, brX, ethX)

If you don't have a built in wireless device, plug in your external wireless card before running Wireless Asst.

Select DHCP and a pop up message will appear at the bottom right if the card successfully obtains an IP address. Run Mozilla, the web browser


BioSLAX on Virtual Machines


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)etc..

• Can boot from physical CD/DVD media or from ISO image


Running BioSlax on Windows Using VMware player

• Download and install VMware Player

– http://www.vmware.com/download/player/– ftp://sf01.bic.nus.edu.sg/incoming/bioslax/VMware-player-2.0.2-59824.exe

• Download BioSlax Version Customized For VMPlayer

– ftp://sf01.bic.nus.edu.sg/incoming/bioslax/distro/v7.5/BSVM75-LSM.zip– Unzip to C drive (e.g. C:\BS71VMCD)– Run VMPlayer and open C:\ BS71VMCD \Other Linux 2.6.x kernel.vmx

• Portable VMWare Player – Moka5 (http://www.moka5.com)


Setting up your internet connection in VMware version of BioSlax

• If there is no network, change the network setting (on the top menu) from “Bridged” to “NAT”

• Open Konsole

• Type “dhcpcd” and press “Enter”


Screenshot – VMWare Version


BioSLAX – A Portal Blast Server


Web BLAST demo

• Insert your USB drive into the PC• Make sure your USB drive is detected


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


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


Web BLAST demo

• Start web BLAST & select the list of BLAST programs:


Web BLAST demo

•Regular BLAST page


Web BLAST demo

•BLAST result


The Power of BioSlax - Modularity


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


BioSlax module manager

• Modules can be inserted or removed dynamically (no shutdown required) using the GUI based BioSlax module manager


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


Retaining modifications (changes)


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 driveand /.../mychanges is a directory created in the USB drive to store settings


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


Creating your own live media OS


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?”


• Download the linux base

• Customized base with all necessary libraries and dependanciesavailable- 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!




• 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


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


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


Recommended reading/viewing

1. http://www.slax.org/2. http://www.bioslax.com/3. http://www.slax.org/documentation.php4. http://en.wikipedia.org/wiki/BioSLAX5. http://www.youtube.com/watch?v=MfNCUGj2AUg6. http://bioinfotutlets.blogspot.com/2009/05/17-installing-

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