BioSlax – Live Media Operating System

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)/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/
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
BioSlax in the public eye

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

 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

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 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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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

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 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 -Sequence
-PamL -HMMER -NjPlot Manipulation
Suite v2

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

BioSlax in action

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 Booting Up BioSlax

1. CD (without Open Office)

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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 Network setup

Open Konsole and type iwconfig to list all

possible wireless devices on the system

Wireless Asst Æ 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

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

BioSLAX on Virtual Machines

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 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

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

 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)

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

 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”

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Screenshot – VMWare Version

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BioSLAX – A Portal 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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 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

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

 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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The Power of BioSlax - Modularity

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 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

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

 BioSlax module manager

• Modules can be inserted or removed

dynamically (no shutdown required) using the
GUI based BioSlax module manager

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 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

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

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

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

 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

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

Creating your own live media OS

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

 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?”

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

 Creating your own live media

• 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!

Copyright ⓒ 2009. 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

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

 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

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

 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

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

 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

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