Asia Pacific BioGrid Project

Asia Pacific BioGRID Initiative

[ Home | APBioBox | APBioKnoppix | APBioKnoppix2 | BioWorldWideWorkflow | MDS Browser | Documentation | Download | Contact ]
APBioKnoppix2
APBioKnoppix2
Bioinformatics software in a LiveCD!

Download | Latest Update | Getting Started | Using APBioKnoppix

1. The original APBioBox project was an APBioNet project supported through a grant from the International Development Research Centre (IDRC) of Canada from 2002-2003 and hosted in the Dept of Biochemistry, National University of Singapore (NUS). For more details, please view APBioKnoppix page.

2. APBioKnoppix2 is a remaster of the popular Knoppix (specifically version 4.02) and it has since been deployed in the use of teaching and training in :

The 18th Pre-FAOBMB Symposium and workshop at CEMB of The University of Punjab, Lahore, Pakistan

University of Songkhla, Thailand

S* Alliance 1st International Bioinformatics Workshop

practical course of LSM2104 Essential Biocomputing module of the Dept of Biochemistry, National University of Singapore (NUS).

practical course of LSM5101 Advanced Cell Biology, NUS

APBioKnoppix2 - Open source bioinformatics packages in a CD
Download APBioKnoppix2 Before you do so, you must agree to the GNU Open Source licence and attribute the reference to this project.
"APBioKnoppix releases originate from the APBioNet-National University of Singapore collaborative project and the predecessor project, APBioBox, which was funded by IDRC, 2002/2003."

Latest version of APBioKnoppix2 is version 1.02
The complete CD in one ISO file (Warning: 684 Mbytes huge!)

If you feel that you can contribute in whatever way (systems development, help support APBioKnoppix, test the software, write some of the documentation, etc), please let us know. Having a sizable APBioKnoppix team will help progress APBioKNoppix.

APBioKnoppix is currently maintained by :

Justin Choo (justin@bic.nus.edu.sg)
Tan Tin Wee (tinwee@bic.nus.edu.sg)
Ong Guan Sin (gsong@scs.com.sg)

Getting Started with APBioKnoppix

Method 1: Just boot from the CD
If your computer boots straight from the harddisk, you have to reset your BIOS for its boot-up sequence to boot from a CD first and then the harddisk. To do this, you usually press [DELETE] key or F2 or whatever your PC tells you at the bottom (usually) of the screen as you are booting up.
Once it boots from the CD, there will be a "splash" screen with a prompt.
boot:
If you have enough RAM on your PC, ie more than 128Mbyte RAM, you shouldn't have any problems with just hitting the [RETURN] key. If you have 128Mbyte RAM or less, it will take a long time to boot up and it appears to hang. You can get more RAM for your PC, or else, there are several ways to get around this low-RAM problem.
(Under Construction: we will put up the low-RAM solution soon)
Once it boots up, be patient when use this boot-from-CD method as programs need to be read from the CD when you invoke them. The speed of reading CDs depends on your CD drive, and may take some time when you are launching programs.

Method 2: Copy APBioKnoppix into hard disk (as a file)
This method will speed up the execution of APBioKnoppix by accessing the CD content as a file on the hard disk. First copy the CD's ISO image file into the hard disk, call it say
C:\TEMP\APBIOKNOPPIX.ISO
if you are copying it into the C: drive. This ISO file in the harddrive is to be used during APBioKnoppix boot-up.
The advantage of this method (compared to Method 3 below) is that it does not require a separate partition, i.e. it can work with your existing hard disk partition and filesystem, be it a Linux ext2 filesystem or a Windows XT NTFS. (Note that currently ext3 filesystem found on Fedora Core and some Red Hat 9 is not supported.)
Not having to touch your hard disk partitions or run fdisk is a BIG plus, eliminating the potential (and very likely) risk of totally destroying the contents of your hard disk.

Step 1: Obtain the ISO image file: either download it from APBioKnoppix website (http://www.apbionet.org/apbioknoppix) or use your favourite CD-ROM software to save the CD into a ISO image file. Don't forget to burn a few backup copies of the ISO image as a LiveCD if you are downloading from the website.

Step 2: Copy the ISO image file (which is about 650MB in size) to the filesystem. for example, C:\TEMP\APBIOKNOPPIX.ISO

Step 3 Insert APBioKnoppix CD and boot from there. Once booted, find the C: drive on the APBioKnoppix desktop as an icon. Identify the name of the disk drive e.g. /mnt/hda2 or /mnt/hda5 etc, depending on how your computer detects this disk. Duble check to see if the TEMP\APBIOKNOPPIX.ISO is there. If your PC doesn't boot from the CD drive, you will need to setup the BIOS (press DEL or F2 or whatever key which the bootup procedure tells you, and edit the BIOS configuration to boot up from the CD drive first, and then the Hard Disk).

Step 4 Once the name of the disk drive is identified, logout and restart the computer, again booting up from the APBioKnoppix CD.
At Knoppix boot prompt (which looks like: boot:), enter the words (in blue below), for example,
boot:
knoppix bootfrom=/dev/hda2/TEMP/APBIOKNOPPIX.ISO

where /dev/hda2/TEMP/APBIOKNOPPIX.ISO is the partition_number_and_path_to_ISO_file, depending on what is the name of your disk drive (hda2 or hda5 as in the example above) as determined from Step 3 and the name of the ISO file as copied in Step 2. So if you have determined the drive you copied the ISO from the Step 3 above as hda5, then you key in /dev/hda5/TEMP/APBIOKNOPPIX.ISO instead of hda2 for example.
If you copied the ISO file to your NTFS file system which happens to be the second partition on your first hard disk, it's likely to work with "knoppix bootfrom=/dev/hda2/TEMP/APBIOKNOPPIX.ISO". If you saved the ISO file in the subdirectory "C:\MyDir\APBioKnoppix.iso", then boot with
knoppix bootfrom=/dev/hda2/MyDir/APBioKnoppix.iso
Once you have done this, you can boot up with APBioKnoppix CD, but your computer will read the operating system data from the harddisk at a much faster speed.

(Useful Tip: And to cut down your typing time, always name your iso file as tersely as possible, e.g. C:\ap.iso so that you only get to type "knoppix bootfrom=/dev/hda2/ap.iso" each time you boot up.)

Method 3: Copy APBioKnoppix into a Linux partition
This will speed up execution of APBioKnoppix by accessing the CD content from the hard disk. You copy the CD content into a supported filesystem on your hard disk. You will need to create a dedicated partition for this purpose. The following steps assume that you have free space on the hard disk where a new partition to be created for this purpose.

Step 1 Boot from the APBioKnoppix CD and press Enter at boot prompt to go ahead (Method 1).

Step 2 Click K-Start -> KNOPPIX -> Root Shell to launch a root shell terminal

Step 3 Execute the Unix format harddisk command: "fdisk /dev/hda" to create a partition on the hard disk (assuming your hard disk is on "hda"). Note that within the fdisk command, do "n" to create, "p" for primary partition, select the cyclinders and size, and "w" to write changes. (WARNING! Only do this if you have experience, or grab hold of a experienced person while you are doing this, or experiment with a totally useless computer that you can afford to destroy the harddisk!)

Step 4 Execute "mkfs.ext3 /dev/hda2" to make a filesystem on the new partition (assuming it is created on "hda2"). BE VERY CAREFUL!

Step 5 Restart the system. At the boot prompt, enter "knoppix tohd=/dev/hda2" to tell APBioKnoppix to copy its CD content to the new filesystem. Be patient. It takes a while to completely transfer 650Mbytes of operating system and bioinformatics and other goodies into your harddisk.

Step 6 Once this is completed, you can boot up with the APBioKnoppix CD, and start using the command "knoppix fromhd=/dev/hda2" at the boot prompt from now on. This will tell APBioKnoppix to use the contents on the hard disk rather than read from the CD. You will have a much faster response time reading from the harddisk than from the CD drive.

Using APBioKnoppix

All APBioKnoppix instructions are available on the webpage which will auto-popup when you boot up.

You have two options, of using APBioKnoppix in a non-configurable mode, or in a configurable mode.

Non-Configurable Mode: use the CD as it is (or using Method 2 or 3 as mentioned above to speed up your computer's response). You will not be able to save your desktop configurations. Any files you have created in your home directory will be lost when you logout, unless you have deliberately saved them into your hard disks. Hard disks are auto-detected by Knoppix and auto-mounted and displayed as Hard disk icons on your desktop. Save all files into the hard drives ALWAYS.

If you wish to save your configurations (and this is the mode most people would find most convenient), boot up the APBioKnoppix with a USB Flash Memory stick inserted into the computer's USB port (also popularly known as Thumbdrives). APBioKnoppix will auto-detect this USB drive and mount the configurations and home directories into the USB drive and save it there. Each time you boot up from your APBioKnoppix CD with your USB drive, you will autoload the configuration.

After you have saved your configuration, the home page may not load up. Power up your Konqueror web browser and go to http://localhost/ to see the instruction homepage on how to use APBioKnoppix.

Handling Memory Limitations

APBioKnoppix depends on a sufficiently large RAM memory for the operating system to work efficiently. Use at least a machine with 128 Mbyte RAM, if not > 256 Mbyte for tolerable performance, or for professional work, at least 512 Mbytes and if you are doing remastering and software development work, at least one 1 Gbyte memory in RAM.

If you have insufficient memory, you should specify the amount of RAM in a swapfile knoppix is asked to create using the cheatcode
boot: knoppix mem=100M

Some folks with NTFS hard disk partitions will be afraid that Knoppix might automatically create a swapfile in the NTFS disk, and this may cause corruption to the NTFS partition. To ensure, there is a cheatcode noswap to tell Knoppix to boot up without using any swap files.

If you do not specify anything, or which partition or Hard Disk to use as swap, Knoppix will by default, search for for 83-coded partitions and use them for swap.

If there are no 83-coded partitions found, and if the free mem is less than 80Mbytes during boot up (see /etc/init.d/knoppix-autoconfig), Knoppix will search for DOS (*FAT*) partitions with enough space and dynamically create swap file(s) through a user dialog (/usr/sbin/mkdosswapfile) before the boot up procedure can be be completed.

Note that any NTFS disk partitions are skipped to prevent any corruption of NTFS partitions which are not compatible with Unixes.

At boot up time for machines with insufficient memory detected, this dialog gives the user control where to create the swap file (knoppix.swp) and at what size to create the file. Suppose the user specifies (accidentally) an NTFS partition for the swapfile to be created. Will that cause file corruption?

In some cases, some PC boards don't pass on the proper memory size to the linux kernel, and cause a "Panic" message, and the system may hang. Reboot and use the "knoppix mem=128M" to bypass this problem through explicitly stating that your machine has 128Mbyte RAM (or whatever size you have). (Caution, use capital uppercase M for the memory!).

If you want to remaster your own APBioKnoppix, please see the step-by-step guide :
APBioKnoppix Remastering Recipe

Updated Oct; July; Apr 2004; 4 Dec 2003 (ttw); 16 Sep 2003 - ogs

APBioKnoppix2 Bioinformatics software in a LiveCD!

APBioKnoppix2
Bioinformatics software in a LiveCD!