Asia Pacific BioGRID Initiative

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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).

2. Through collaboration with the Asia Pacific Science and Technology Center (APSTC), Sun Microsystems, this project was expanded to include a BioBox for the Solaris platform, now called Bio-Cluster Grid. Since then, we are looking at expanding the portfolio of platforms supported, as well as to integrate other software and databases from the APAN-APBioNet collaboration, BioMirrors project in the new APBioBox II initiative

3. In Jul 2004, Dr Derek Kiong introduced Knoppix as a stable, powerful and small-footprint Unix (Debian-based) platform to Dr Tan Tin Wee in a workshop organised by the Institute of Systems Science (ISS), NUS. By September 2004, through Mr Ong Guan Sin, we were able to create a Knoppix remaster template by building software in APBioBox plus other goodies into a prototype APBioKnoppix, as a project for the practical course of LSM2104 module of the Dept of Biochemistry, NUS.

4. This was expanded into the APBioKnoppix v0.1 beta released for testing at the ASEAN-China Bioinformatics Workshop 17-23 October 2004, Center for Bioinformatics (CBI), Peking University, Beijing, PR China.

APBioKnoppix - Bioinformatics in a CD

Download APBioKnoppix 0.2 Before you do so, you must agree to the GNU Open Source licence and attribute the reference to this project.

  • "APBioKnoppix beta releases originate from the APBioNet-National University of Singapore collaborative project and the predecessor project, APBioBox, which was funded by IDRC, 2002/2003."
  • Alternatively, download the following files and do something like
    cat APBioKnoppix-0.2.iso.part? > APBioKnoppix-0.2.iso to reconstruct the ISO file:

    For Windows users, you can download the following files into a folder and then double-click the first file (EXE) to reconstruct the ISO file:

  • LATEST UPDATE - 25 Oct 2004: In the latest version 0.2, we have got Jemboss (and the required Java) working. Booting up using the APBioKnoppix CD, you will see the Jemboss icon on the Desktop. Click on it to launch Jemboss locally.

    We wish to turn APBioKnoppix into something useful to the life sciences community. Please test it and give us feedback to make it work better. Comments and suggestions for improvement are most welcome. If you feel that some useful packages are missing, let us know and we will consider include them.

    Better still, if you feel that you can contribute in whatever way (systems development, help support APBioKnoppix, test the software, write some of the documentation, etc), let me know. Having a sizable APBioKnoppix team will help progress the product.

    Getting Started with APBioKnoppix

    Using 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!).

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