1. Using BioSlax and the BioSlax Server Tin Wee Tan National University of Singapore

2. Copyright ⓒ 2009. National University of Singapore. All rights reserved. What is BioSlax? Slackware Linux on a CD + bioinformatics modules included Released by Bioinformatics Centre (BIC), NUS Uses Unification File System (aufs) that allows read- only file system to have writable access by saving all changes in memory Slax - created by Tomas Matejicek. Website is at: http://www.slax.org/ http://www.slax.org/

3. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Why use BioSlax/Slax? Complete OS by itself running off a CD 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

4. Copyright ⓒ 2009. 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 creation – easily upgraded when new version’s available

5. Copyright ⓒ 2009. National University of Singapore. All rights reserved. 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 Manipulation Suite v2 -PamL-HMMER-NjPlot

6. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Booting Up Bioslax 1.CD (without Open Office) 2.DVD (with Open Office) 3.USB drive (with Open Office)

7. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Configuring your Boot Device Priority of the BIOS of your PC When you boot up your computer. Press F2 (or F1/ESC/DELETE etc) to enter the BIOS Configuration mode (Setup) Select the BOOT tab, and the BOOT device priority list Select CD-Rom to be the first boot device by using the arrow/F5/Pg Up key. If you are booting from USB drive – Select “USB Key” to be the second boot device Save and Exit

8. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Screenshot – Bioslax Booting Up

9. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Screenshot – Bioslax Booting Up

10. 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/http://www.vmware.com/download/player/ Download BioSlax Version Customized For VMPlayer – Unzip to C drive (e.g. C:\BS71VMCD) – Run VMPlayer and open C:\ BS71VMCD \Other Linux 2.6.x kernel.vmx

11. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Setting up your internet connection in VMware version of Bioslax Change the network setting (on the top menu) from “Bridged” to “NAT” Open Konsole Type “dhcpcd” and press “Enter”

12. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Screenshot – VMWare Version

13. Copyright ⓒ 2009. National University of Singapore. All rights reserved. The X-Window Desktop

14. Copyright ⓒ 2009. National University of Singapore. All rights reserved. How to create a Slax module To convert tgz package to Slax module: tgz2lzm e.g. tgz2lzm blast.tgz blast.lzm To install an application to a separate directory: dir2lzm module.lzm e.g. dir2lzm /usr/local/blast blast.lzm

15. Copyright ⓒ 2009. National University of Singapore. All rights reserved. How to use a Slax module To create own LiveCD: – 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

16. Copyright ⓒ 2009. National University of Singapore. All rights reserved. How to save/restore settings 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

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

18. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Web BLAST demo Insert your USB drive into the PC Make sure your USB drive is detected

19. Copyright ⓒ 2009. 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

20. 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

21. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Web BLAST demo Start web BLAST & select the list of BLAST programs:

22. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Web BLAST demo Regular BLAST page

23. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Web BLAST demo BLAST result

24. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Recommended reading 1.http://www.slax.org/http://www.slax.org/ 2.http://www.bioslax.com/http://www.bioslax.com/ 3.http://www.slax.org/documentation.phphttp://www.slax.org/documentation.php

25. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Hands-On Practice 1.htdocs and cgi-bin folders 2.Modules

26. Copyright ⓒ 2009. National University of Singapore. All rights reserved. Bioslax as server 1.Host BLAST database 2. Hosting web server