using bioslax and the bioslax server

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/


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


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


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


Booting Up Bioslax

1. CD (without Open Office)

2. DVD (with Open Office)

3. USB drive (with Open Office)


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


Screenshot – Bioslax Booting Up


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


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”


Screenshot – VMWare Version


The X-Window Desktop


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


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


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


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


Web BLAST demo

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


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


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


Web BLAST demo

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


Web BLAST demo

•Regular BLAST page


Web BLAST demo

•BLAST result


Recommended reading

1. http://www.slax.org/

2. http://www.bioslax.com/

3. http://www.slax.org/documentation.php


Hands-On Practice

1. htdocs and cgi-bin folders

2. Modules


Bioslax as server

1. Host BLAST database

2. Hosting web server

using bioslax and the bioslax server

Documents

bioslax bioinformatics

bioslax serverbioinformatic

modularity of bioslax

vmware version of bioslax

download bioslax version

open c

cd bioinformatics modules

boot tab