BioSlax – Live Media Operating System

Copyright ⓒ 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:

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

Copyright ⓒ 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

Copyright ⓒ 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

Copyright ⓒ 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

Copyright ⓒ National University of Singapore. All rights reserved. Modules in BioSlax … Bioinformatics Modules: ArtemisGlimmerhmmPrimer3BioGrep HmmerPyMOLBioPERLJalView JMOLBLAST (CLI, WI)JAlignerR with BioConductor ModellerReadSEQClustalW (CLI, WI, XGUI)NJPlot Sequence Manipulation Suite (SMS2) PamLTCoffee (CLI, WI)Patscan EMBOSS (CLI, WI, JI)Phylip (CLI, WI)TreeViewWeka GenesplicerPloticus 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

Copyright ⓒ National University of Singapore. All rights reserved. BioSlax in action

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

Copyright ⓒ National University of Singapore. All rights reserved. Screenshot – BioSlax Booting Up

Copyright ⓒ National University of Singapore. All rights reserved. Screenshot – BioSlax Booting Up

Copyright ⓒ National University of Singapore. All rights reserved. The X-Window Desktop

Copyright ⓒ 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

Copyright ⓒ National University of Singapore. All rights reserved. BioSLAX – A Portable Blast Server

Copyright ⓒ National University of Singapore. All rights reserved. Web BLAST demo Insert your USB drive into the PC Make sure your USB drive is detected

Copyright ⓒ 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.gzftp://sf01.bic.nus.edu.sg/incoming/blast-db-demo.tar.gz tar –zxf blast-db-demo.tar.gz

Copyright ⓒ 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

Copyright ⓒ National University of Singapore. All rights reserved. Web BLAST demo Start web BLAST & select the list of BLAST programs:

Copyright ⓒ National University of Singapore. All rights reserved. Web BLAST demo Regular BLAST page

Copyright ⓒ National University of Singapore. All rights reserved. Web BLAST demo BLAST result

Copyright ⓒ National University of Singapore. All rights reserved. BioSLAX on Virtual Machines

Copyright ⓒ 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

Copyright ⓒ National University of Singapore. All rights reserved. Screenshot – VMWare Version

Copyright ⓒ National University of Singapore. All rights reserved. The Power of BioSlax - Modularity

Copyright ⓒ National University of Singapore. All rights reserved. BioSlax application modules Slax is versatile because of modules Modules available for almost anything – Very few available modules for Bioinformatics –

Copyright ⓒ 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

Copyright ⓒ 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 e.g. activate /tmp/blast.lzm To deactivate a module, use: deactivate e.g. deactivate /tmp/blast.lzm

Copyright ⓒ National University of Singapore. All rights reserved. Retaining modifications (changes)

Copyright ⓒ National University of Singapore. All rights reserved. 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 ⓒ 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 lzm – insert the module dynamically using “activate” – copy the module to the modules folder

Copyright ⓒ National University of Singapore. All rights reserved. Creating your own live media OS

Copyright ⓒ 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 ⓒ National University of Singapore. All rights reserved. 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 ftp://sf01.bic.nus.edu.sg/incoming/bioslax/distro/v7.5/bioslax_v75_base.iso Select your modules from 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

Copyright ⓒ 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 ⓒ National University of Singapore. All rights reserved. BioSLAX on the GRID and in Clusters

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

Copyright ⓒ National University of Singapore. All rights reserved. Rapid Deployment of Clusters

Copyright ⓒ National University of Singapore. All rights reserved. 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

Copyright ⓒ 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 ⓒ 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 ⓒ National University of Singapore. All rights reserved. Recommended reading/viewing bioslax-as-full-linux.htmlhttp://bioinfotutlets.blogspot.com/2009/05/17-installing- bioslax-as-full-linux.html