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Using BioSlax
and the BioSlax Server

An APBioNet-InCoB-NUS Tutorial


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National Yang Ming University

Biochemistry NUS


Using BioSlax and the BioSlax Server

You are cordially invited to participate in a hands-on workshop on BioSlax

DATE: Thu 23 Oct 2008
TIME: 9am - 12.30pm
National Yang Ming University
Taipei, Taiwan

Please bring your laptop and power cable. Minimum requirements 1 Gbyte RAM INTEL PC with DVD reader. LiveCD will be issued. Alternatively, you can install on your Windows operating system VMPlayer and download a vmk file which will we customise for you.

Training material:
They will be placed online in advance. If you need hardcopy, please inform us.

Basic understanding of Unix operating system


Many teachers and trainers of bioinformatics and computational biology face a recurrent problem of keeping their software tools and databases up to date. In addition, they have to set up entire clusters of PCs installed with up-to-date software applications which they intend to teach. This is very troublesome and as a consequence takes up a lot of time and effort, and distracts from the teaching/learning process.

Our solution is to package a whole list of commonly used software into a single LiveCD/DVD that includes an entire operating system (Slax). This system called BioSlax has been in use for several years at the National University of Singapore. A server version and a VMWare version are also available.

With the BioSlax Server version, one can set up an entire server with a terabyte harddisk to act as a classroom bioinformatics server within minutes which can work in conjunction with the BioSlax LiveCDs.

This tutorial will cover the basics of getting up to speed with using BioSlax and the BioSlax Server.

The BioSlax Tutorial
Tentative Schedule

   a. What is BioSlax
   b. Getting Started with BioSlax User
      1. Visualising molecules with Rasmol
      2. Using Pymol
      3. BLAST
      4. Creating your private blast database
      5. Setting up a MySQL database
      6. Setting up a BioWeb server
      7. Learning Perl and CGI
      8. HMM for bioinformatics
      9. Sequence analysis with EMBOSS and Jemboss and Wemboss
      10. Sequence analysis with SMS3
      11. Multiple sequence alignment with CLUSTAL, CLUSTALX and T-Coffee
      12. More advanced Unix shell scripting
   c. BioSlax Server for your bioinformatics classroom
      1. Setting up the biomirror hard disk 1 min
      2. Plugging in the bioslax server 1min
      3. Running the bioslax server 1min
      4. Accessing a biowiki site on the server for group learning and sharing



  1. Justin Choo, Institute for InfoComm Research, A*STAR, Singapore
  2. Tan Tin Wee, Biochemistry Dept, NUS, Singapore
  3. Mark De Silva, Bioinformatics Centre, NUS, Singapore
  4. Lim Kuan Siong, Bioinformatics Centre, NUS, Singapore


  1. Justin Choo, Institute for InfoComm Research, A*STAR, Singapore
  2. Angela Jean, Nanyang Polytechnic, Singapore


Ms Angela Jean
Bioinformatics Group
School of Chemical and Life Sciences
Nanyang Polytechnic
Tel: (65) 65500440
angelajean --at--

Last Updated: 27 August 2008
First Created: 26 Aug 2008 Tan Tin Wee