Distribution of the Live CD/DVD systems as bootable CDs or their images (~700MB), is free to educational institutions and so far has been done via http, ftp, bittorrent, p2p and physical CD. With portable and scalable systems like BioSLAX, it is now easy to set-up bioinformatics labs, fully equipped with LAMP (Linux-Apache-MySQL-PHP/PERL), Mediawiki and more than 200 freely available bioinformatics software, see below. New software packages can always be made available by remastering the live CD/DVD systems.
Software preinstalled in BioSLAX
° Mozilla Firefox (web browser)
° Open Office
° BLAST
° ClustalW
° ClustalX
° EMBOSS
° Modeller
° PamL
° PatScan
° T-Coffee
° PHYLIP
° GeneSplicer
° GlimmerHMM
° HMMER
° Primer3
° Artemis ACT
° Artemis ART
° jAlign
° Jalview
° NjPlot
° PyMOL
° RasMOL
° ReadSeq
° TreeView
° Sequence Manipulation Suite v2
1. Getting a copy of BioSLAX
There are several ways of booting BioSLAX, but all of them will involve the initial step of obtaining the BioSLAX iso image (a kind of special file) and burning it into a bootable DVD/CD or thumbdrive. You can download the latest BioSLAX iso from either one of the following URLs:
ftp://sf01.bic.nus.edu.sg/incoming/bioslax/distro/v7.1/
http://www.bioslax.com/download/bslax71-dvd-incob.iso
Note that when downloading using a Web browser, you have to turn off your cache, or set the cache to zero to prevent a cache copy from being created. In this way, the iso file will immediately be written to your hard disk. Save it conveniently as C:\slax\bslax71-dvd-incob.iso or something easier to type, e.g. C:\slax\bslax.iso.
2. Creating a bootable DVD/CD or USB thumbdrive
Once you get the iso copy of the BioSLAX, you need to save it into a DVD/CD or a USB thumdrive, favorably, please make a backup copy as well.
*Note that using any software that allows burning of DVDs/CDs from iso files (eg, Nero, EZ media creator, Magic ISO, or CDBurnerXP) enable you to burn the downloaded iso file into a bootable DVD/CD, this is NOT the same as copying the iso file into the DVD. Burning the image means transferring the entire image of the iso file including the file system and all its constituent files into the DVD/CD, instead of copying the iso file into the DVD/CD’s file system.
Please refer to the “How to burn the ISO into a bootable Live CD/DVD”, “How to create a bootable USB thumbdrive” and “How to make a backup of the Live CD/DVD” sections if you have no idea on how to do these.
3. Starting BioSLAX by booting from the Live DVD/CD or USB thumbdrive
Method 1: Booting directly from the CD/DVD/USB thumbdrive
There are two ways of doing this:
a. Selecting CD/DVDROM or USB device as the boot device when starting the computer.
When you switch on the computer, you will see a line of instructions asking you to press F12 (or some other key depending on the PC) for you to select Boot Menu. Press it, then select to boot from the CD/DVD Drive or the USB device.
Typically, the options may look like as follows:
Boot Menu
Floppy Disk
USB Device
Hard Disk
CD/DVD Rom
Network
When you see this screen, use the arrow keys to move up and select the CD/DVDROM option (if you are booting from DVD) or the USB DEVICE option (if you are booting from a USB thumbdrive), and press ENTER. The boot sequence will then read from the CD/DVD Rom or USB thumbdrive, where BioSLAX is located.
If this doesn’t work, try option b. If it works, skip the next step (b).
b. Configuring your Boot Device Priority of the BIOS of your PC.
When you boot up your computer, press F2 (or ESC, or DELETE, etc, depending on your PC) to enter into the BIOS Configuration mode. Select the BOOT tab, and the BOOT device priority list. Select CD/DVDROM or USB Device to be the first boot device by using the arrow key or PgUp depending on your PC. Save and Exit (typically pressing F10).
When this is configured properly, the PC knows to boot from the CD/DVDROM or USB DEVICE first (instead of the usual Hard Disk). BioSLAX will then start to load as the operating system.
Figure 1. BioSLAX booting up
When it does boot up from BioSLAX, you will see the BioSLAX splash screen as in the first diagram in Figure 1.
BioSLAX has several booting modes to cater for different experiences and hardware. For most of the new PCs and laptops, the first option should be fine. If you are having trouble with your display, choose the 2nd option which is the Safe option. If any of your hardware fails to work, try to boot with the other (No ACPI or No PCMCIA) options.
Method 2: Booting from the BioSLAX files on a hard disk
Generally, a Pentium 4 machine with 512 Mbyte RAM is the minimum configuration that should just work. However, you might find that the overall experience of booting from the CD is too slow.
If so, you can make it boot faster, by having the system access the BioSLAX files from your hard disk. Reading data from the hard disk is generally faster than reading data from a Bioslax CD/DVD in the CD/DVDRom Drive.
There are 2 ways to boot from the hard disk,
a. from files of BioSLAX copied into the hard disk
b. from a single BioSLAX.iso file containing the BioSLAX image, copied into the hard disk.
Copying the contents of the CD/DVD/USB thumbdrive onto your hard drive
Boot up as usual into your Microsoft Windows environment. Create a subdirectory on your Windows hard drive (eg; C:\SLAX) then copy the contents of the BioSLAX CD/DVD or the USB thumbdrive to that directory. Just drag and drop the contents into the C:\SLAX directory in your file explorer.
IMPORTANT NOTE:
In the Microsoft Windows (XP or Vista) environment, disk drives are typically labeled C: or D: for hard disks, A: for Floppy and E: for CDROM drives.
Now, in the Linux OS, the different drives are not represented by letters (eg, A, C, D, etc). They are represented by devices. Again these are represented differently for IDE, SATA and SCSI hard disk drives. The following is a table showing the different representation of the different drives:
Therefore C:\SLAX in the Microsoft Windows OS would be represented as /dev/sda1/slax to the Linux OS (if it is a SCSI or SATA drive). Note that Linux is CASE SENSITIVE, so the case of the directory name matters.
Once you have copied the contents of the DVD onto your hard drive or have copied the BioSLAX ISO to your hard drive (eg C:\bslax.iso), you have to use the BioSLAX CD/DVD or USB thumbdrive to boot up, and at the initial BioSLAX menu selection screen, press the TAB KEY while over any of the boot up selections of your choice.
In the following example, we will assume you are on option 2 (Safe option).
i. Press the TAB KEY while the selection bar is over option 2.
ii. You will see a line of text at the bottom.
Figure 2. Select your option and press the TAB KEY
Figure 3. Command text appears at the bottom after pressing the TAB KEY
iii. Press the space bar and then :
A) If you want to boot from the BioSLAX files extracted to your hard drive (files in C:\SLAX), type from=/dev/sda1/SLAX
Figure 4. Booting from BioSLAX files extracted to the hard drive
B) If you want to boot from the ISO file (C:\bslax.iso), type from=/dev/sda1/bslax.iso
Figure 5. Booting from a single BioSLAX ISO file on the hard drive
The system will start to boot up and will read the BioSLAX data from either the directory where the extracted BioSLAX files are or from the BioSLAX ISO file directly.
When the system boots up, you will see the device initialization screen and finally the X-Windows desktop.
Figure 6. BioSLAX device initialization screen and X-Windows desktop
NOTE: When booting from the iso or files from the hard disk, you need a BioSLAX DVD/USB thumbdrive to initiate the boot up, after which it will start to read the files from the hard drive. Since you won't know exactly when it starts to read from the hard drive, it’s best to leave the DVD/USB thumbdrive plugged in throughout the entire BioSLAX session.
TIP: name your iso to something easier to type, like b.iso. All you have to type now isfrom=b.iso
4. How to connect to the Internet
a. Wired connection
Plug your network cable to your PC and BioSLAX will auto detect it immediately and set up your network connections.
Consult your TAs if you are connecting from your home LAN.
b. Wireless connection
Wireless Asst à Insert wireless card à Select eth1.
If wireless network card is built-in, select eth0.
Select DHCP and an error message appears, at the same time as a pop-up at the lower bottom right corner. Run your Mozilla and login to NUSNET WINZONE EZXCESS login page and select NUSSTU, your login id and associated password.
5. Wireless Networking Support
If the above Wireless network connection doesn’t work, please note that BioSLAX has support for a variety of wireless cards and onboard wireless devices running the following chipsets:
° Intel 2100/2200/3945/4965
° Athereos
° TI ACX11x
° Broadcom
… and many more
Most laptops today run on the Intel wireless 3945 or 4956 which is fully supported by BioSLAX.
Note:
WPA/WPA2 secured access points cannot be accessed using the wireless manager. This requires more command line configuration which will not be covered in this document.
6. Saving Changes
After doing your work on BioSLAX you may have made changes to the configuration. Every time you reboot your machine, ANY CHANGES YOU HAVE MADE WILL BE LOST. To prevent this, you need to save changes regularly.
For portable data (eg, documents, results files, etc) you can plug in your USB thumbdrive and save the data to the USB thumbdrive and then access it later even after rebooting, but how do you save system changes?
Firstly, determine what device your thumbdrive is identified as in linux. It may be identified as /mnt/sdb. It could also be sdc or sdd instead of sdb, depending on how many other sata/scsi devices you have on the computer. For this example, we will assume that it is /mnt/sdb.
Make a directory on the thumb drive called mychanges.
When booting up, again hit the TAB KEY when you are at the BioSLAX menu selection. The command text will appear at the bottom. Press the space key and enter the following:
changes=/mnt/sdb/mychanges
Figure 7. Setting up persistent changes
If you are booting from the extracted BioSLAX files or the BioSLAX iso, proceed as instructed in section 3, method 2, and type the changes= command after the from= command.
With this command, any changes or modifications you make will be saved AND restored from the mychanges directory on your thumbdrive.
Note:
When you are saving changes with your BioSLAX booted up from a particular source (USB thumb drive, hard drive etc.), you must reboot BioSLAX from the same source to restore your changes. If you reboot BioSLAX from another source, you won’t be able to restore the changes that you’ve made.
For the more intuitive students, you will realize that you can create different directories on your thumbdrive to save different sessions of your BioSLAX runs. You may set up BioSLAX in different ways or run a sequence search using different programs and store the results individually, so that you may later do a comparison.
Content by: Mark De Silva, Lim Kuan Siong, Tan Tin Wee
Posted by: Sye Bee
Edited by: Sye Bee & Asif M. Khan
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