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Using BioSlax and the BioSlax Server. Tin Wee Tan National University of Singapore. Bioinformatic and Comparative Genome Analysis Course HKU-Pasteur Research Centre - Hong Kong, China August 17 - August 29, 2009. What is BioSlax?. Slackware Linux on a CD + bioinformatics modules included - PowerPoint PPT Presentation
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Using BioSlax and the BioSlax Server
Bioinformatic and Comparative Genome Analysis CourseHKU-Pasteur Research Centre - Hong Kong, China
August 17 - August 29, 2009
Bioinformatic and Comparative Genome Analysis CourseHKU-Pasteur Research Centre - Hong Kong, China
August 17 - August 29, 2009
Tin Wee Tan
National University of Singapore
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/
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
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
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
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)
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
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Screenshot – Bioslax Booting Up
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Screenshot – Bioslax Booting Up
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/
• 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
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”
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Screenshot – VMWare Version
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
The X-Window Desktop
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
How to create a Slax module
• To convert tgz package to Slax module:tgz2lzm <application.tgz> <application.lzm>
e.g. tgz2lzm blast.tgz blast.lzm
• To install an application to a separate directory:dir2lzm <directory> module.lzm
e.g. dir2lzm /usr/local/blast blast.lzm
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 </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.
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
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
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
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.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
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
• Start web BLAST & select the list of BLAST programs:
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
•Regular BLAST page
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Web BLAST demo
•BLAST result
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Recommended reading
1. http://www.slax.org/
2. http://www.bioslax.com/
3. http://www.slax.org/documentation.php
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Hands-On Practice
1. htdocs and cgi-bin folders
2. Modules
Copyright ⓒ 2009. National University of Singapore. All rights reserved.
Bioslax as server
1. Host BLAST database
2. Hosting web server
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