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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."


  • 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


  • 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!).


    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