BioSlax – Live Media Operating System

1. BioSlax – Live Media Operating System

2. 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/

3. BioSlax in the public eye

4. 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

5. 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

6. 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

7. Modules in BioSlax … • Bioinformatics Modules:

8. BioSlax in action

9. Booting Up BioSlax • CD (without Open Office) • DVD (with Open Office) • USB drive (with Open Office - writable)

10. Screenshot – BioSlax Booting Up

11. Screenshot – BioSlax Booting Up

12. The X-Window Desktop

13. 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

14. BioSLAX on Virtual Machines

15. 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

16. 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)

17. 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”

18. Screenshot – VMWare Version

19. BioSLAX – A Portal Blast Server

20. Web BLAST demo • Insert your USB drive into the PC • Make sure your USB drive is detected

21. Web BLAST demo • If you don’t see the db directory, open Konsole & type: • cd /mnt/sda1_removable/ • wgetftp://sf01.bic.nus.edu.sg/incoming/blast-db-demo.tar.gz • tar –zxf blast-db-demo.tar.gz

22. 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

23. Web BLAST demo • Start web BLAST & select the list of BLAST programs:

24. Web BLAST demo • Regular BLAST page

25. Web BLAST demo • BLAST result

26. The Power of BioSlax - Modularity

27. 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

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

29. 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

30. Retaining modifications (changes)

31. 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

32. 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

33. Creating your own live media OS

34. 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?”

35. 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

36. 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

37. 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

38. 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

39. Recommended reading/viewing http://www.slax.org/ http://www.bioslax.com/ http://www.slax.org/documentation.php http://en.wikipedia.org/wiki/BioSLAX http://www.youtube.com/watch?v=MfNCUGj2AUg http://bioinfotutlets.blogspot.com/2009/05/17-installing-bioslax-as-full-linux.html