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Project title : Building a Mac OS X Biocluster                Last Updated : 11 March 2003
Trainee Name and Contacts:          Foo Chuen Shien, Derrick
Supervisor(s) Name and Contacts: Lai Loong Fong
                                                          Kenny Hoi

 

My mini-tutorial page

Description :

The application of a cluster in the field of Bioinformatics is not a new thing. In this project, you are supposed to build a Mac OS X Biocluster, ie. A turnkey cluster solution that is specially tune for Bioinformatics. Firstly, you will setup a generic Beowulf cluster. Then, install a suite of Bioinformatics software. Next, install a Distributed Resource Management (DRM) Software. After this, you are supposed to install other relevant software and download relevant bioinformatics databases to your cluster. Finally, we will run some bioinformatics analysis on this cluster. If time permits, you will connect your Biocluster to the Grid.

Equipment:
A mini cluster consisting of 4 Apple’s Xserve server connected to each other using Fast Ethernet.

 


Status

Project completed on 10/03/2003

 

             
  Introduction
  This project mainly consists of clustering(networking), bioinformatics and databases. I will be doing the bioinformatics(the bio-tools) aspect of the project. The aim is to test the capability of Apple's Xserve servers, which are configured as clusters,on the performances of running the bio-tool applications on them.
             
Here is a list of the bio-informatics tools installed on the Biocluster

 

Database searching

NCBI-Blast2 - search against nucleotide and protein databases using the Blast-All program.

FASTA - search against nucleotide and protein databases using the FASTA program.

HMMER - do sensitive database searching using statistical descriptions of a sequence family's consensus.

 

Evolution

Phylip - a package of programs for inferring phylogenies (evolutionary trees).

ClustalW - a fully automatic program for global multiple aligment of DNA & protein sequences.

 

Informatics Analysis Software

Wise2/Dynamite - Wise2 is a package focused on comparisons of bio polymers, commonly DNA                                           sequence and protein sequence. Dynamite is a code generating language whose main                              purpose is to produce efficient code for dynamic programming. Wise2 makes                                           heavy use of the Dynamite code generating language.

 

 

Primer3 - picks primers for PCR reactions.

Emboss - The European Molecular Biology Open Software Suite. EMBOSS is a package of high-quality                 FREE Open Source software for sequence analysis.

Phrap & Pred

 

 

Inital Preparation/ Background studies
 

ClustalW

NCBI-Blast2

FASTA

HMMER

Phylip

Primer

Wise2/Dynamite

Emboss

Phrap & Pred

 

done

done

done

done

done

done

done

done

done

  
Reference(s)/Tutorial(s):

Biology:
Genome Glossary
DNA from the beginning - An animated primer on the basics of DNA, genes and heredity

BioInformatics:
What is bioinformatics? An introduction and overview

BioTools:
HMMER - HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
BLAST Program Selection Guide - This BLAST Program Selection Guide uses tables to help you decide which BLAST program to use. This site also links to the BLAST tutorial by NCBI.
ClustalW - README for Clustal W
FASTA - A very basic tutorial on FASTA.
PHYLIP - A PHYLIP introduction.
WISE2/DYNAMITE - A brief introduction on WISE2/DYNAMITE.
EMBOSS - EMBOSS's organisation web site. Contains lots of information.

BioTools: Documentation
BLAST - A documentation on the NCBI-BLAST package.
FASTA - A documentation on the FASTA package.
PHYLIP - A very complete detailed documentation on the PHYLIP package.
HMMER - A documentation on the HMMER package.
PRIMER3 - A very detailed documentation on the PRIMER3 package.
WISE2 - A very detailed documentation on the WISE2 package.
DYNAMITE - A very detailed documentation on the DYNAMITE package.
EMBOSS - The EMBOSS Administrators Guide.


Other:
Bioinformatics Tools - Tips, Tutorials, and Terminology for Using Selected Resources in Genome Database Guides
Toolbox at the EBI - The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics.
BioInformatics Practical - Protein sequence analysis. A practical guide from University of Manchester Bioinformatics Education and Research .

Books:
Introduction to bioinformatics by T K Attwood & D J Parry-Smith


   
Sources/Manpages  

 

BLAST DATABASES : Contains the databases for BLAST in FASTA format.

Manpage of BLAST : UNIX-like manpage for BLAST.

 		  
           
MAC OS Links:

Mac OS X:
Mac OS X Hints: A community-built site of hints and tips on using Apple's new Mac OS X operating system.
Mac OS X Apps: A Community of Mac OS X users and developers discussing developing new application softwares for Apple's newest operating system.
SecureMac: A site devoted to Apple Macintosh security and Mac OS X Security.
Developer.apple.com This page contains a collection of links to valuable resources for developers writing software that runs on the Macintosh..

Fink:
fink.sourceforge.net: The Fink project bring the full world of Unix Open Source software to Darwin and Mac OS X.

 

 

           
 
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