Bioslax – Live Media Operating System What Is Bioslax?

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/

• 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

• 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

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

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

1. CD (without Open Office)

2. DVD (with Open Office)

3. USB drive (with Open Office - writable)

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

• 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

• 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)

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

• Open Konsole

• Type “dhcpcd” and press “Enter”

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

• 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

• To setup BLAST database, go to K-Menu -> BioSLAX -> Desktop Apps -> BLAST DB Setup • Fill in the location of the BLAST formatted database files

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

•Regular BLAST page

•BLAST result

• 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

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

• Automatically inserted on boot up: – save modules in /modules directory of the CD

• To activate a module, use: activate e.g. activate /tmp/blast.lzm

• To deactivate a module, use: deactivate e.g. deactivate /tmp/blast.lzm

• 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

• 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

• 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 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!

• 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

• 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

• 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

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