BioSlax 2-in-1

Setting up as a Bioinformatics Resource Server

1. Download BioSlax from NUS BIC customised for this workshop
2. Burn iso into a CD.
3. Insert BioSlax LiveCD into CDROM drive.
4. Boot up Intel PC with the LiveCD connected to a network, preferably a high-RAM PC, with VFAT-formatted harddisks (NTFS may cause some problems) (Press F12 or Esc to set it to boot from the CDROM Drive first priority).
5. After a few minutes, your PC will become a full-fledged Linux bioinformatics server providing bioinformatics web services at port 80, ssh login at port 22, mysql server with Webmin access at port 10000, etc.

To make your Bioinformatics Resource Server run faster

1. Detect which drive is conveniently available and what is its device (e.g. hda1, sda1, etc) on the BioSlax Desktop.
2. Reboot the computer into the PC's original Windows.
3. Copy the whole CDROM Drive directory into the C: or D: drive etc. in a separte folder.

   To replicate your CDROM

   1. To replicate your Live CDROM, you can make an extra copy yourself, by using a CDROM Drive which is a CDROM burner.
   2. Boot up into Windows.
   3. Download from the Internet the software "CD2ISO".
   4. Install this software by unzip'ing and doubleclicking on the cd2iso.exe
   5. Run cd2iso.exe to rip the Live CDROM as an iso file. Call the file bioslax.iso
   6. Save the file into a directory, say C:/bioslax.iso.
   7. You can use this iso file to burn new Live CDROMs.
   8. Tip: next time you boot up your BioSlax, you can actually trigger it to read from the iso CDROM.
   9. You can use this iso file to burn new Live CDROMs.
   10. Tip: next time you boot up your BioSlax, you can actually trigger it to read from the iso CDROM Boot up into Windows.
   11. Tip: Thus installed above, next time you boot up your BioSlax, you can get your computer to read from the iso, say C:/bioslax.iso by using the command line during boot up session, and enter the following cheat-code.

        linux from=bioslax2.iso
       

       Thus stated, the PC will hunt down the root directories containing bioslax2.iso, for example, C:/bioslax2.iso and start reading from the harddisk far quicker than it runs on Laptop folders.
       It will read as fast as if you did the previous procedure.

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   Name for server
   
   • Goto http://www.no-ip.com
   • Register yourself as a user. Go to email, click and confirm registration
   • Add the domain name desired with the IP address available e.g. biowww.no-ip.com
   • Boot up the server (databases drives already switched on)
   • "Set Internet IP Address" to the IP address available on your network.
   • edit /etc/hosts and append
     
   • apachectl restart
   • check hdd nd hdd2 whether they are working, find out which drive /mnt/sdb1 or whatever
   • If so, proceed to go to http://biowww.no-ip.com/blast
   • Configure to be sdb1 / blastdb oncee and only once. If not, go to /usr/local/wwwblast and delete the db softlink. Go back to http://biowww.no-ip.com/blast/index.cgi

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   Troubleshooting

   Remote access to server

   • 1. /etc/hosts.deny should only contain comments i.e. # Comments
   • 2. /etc/hosts.allow should only contain comments too
   • 3. ps -ef | grep sshd should show "/usr/sbin/sshd" running
   • 4. netstat -a | grep ssh should show a line with "*:ssh"
   If ps -ef or netstat -a doesn't show sshd running, try doing "/etc/rc.d/rc.sshd start" to start the server.

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   What doesn't work
   • Does NOT work on a Mac.
   • Works on Intel PCs.
   • Sun Solaris on Intels will work, but the Sun video may give problems as Slax may not detect it.