Hamilton Bioinformatics Portal

* Overview

Bioinformatics is one of the hottest items in biology research today. Bioinformatics techniques can be applied to a wide variety of fields such as molecular medicine, gene therapy, drug development and evolutionary studies.

The Hamilton College Bioinformatics Portal is a server to run bioinformatics applications through a web-based interface called iNquiry. This interface integrates over 200 commonly used programs and allows the user to submit jobs to the server from anywhere, then retrieve the results at a later time. Having this resource on campus opens up new and exciting research possibilities for the entire Hamilton community.

 

* Access and Usage - Students and Faculty may use the Hamilton Bioinformatics Portal for research and projects.

 

* Cluster Hardware - The Hamilton Bioinformatics Portal consists of 8 dual processor (2 Ghz) Xserve G5 servers. Each server has 2 GB of RAM. Storage space totaling 750 GB is used for blast databases and research results. The cluster is connected via gigabit ethernet, both between the cluster nodes and to the Hamilton Network, to allow for the speedy transfer of the often large input and output files used in bioinformatics research activities.

 

* Hamilton Bioinformatics Portal Software List

Btblastall A parallel version of NCBI blastall The Bioteam	ClustalW A general purpose multiple sequence alignment program European Bioinformatics Institute
ClustalW-MPI Parallel version of clustalW Singapore Bioinformatics Institute	Emboss 2.8.0 Over 100 programs for sequence alignment, display, manipulation, and phylogeny. EMBOSS Home
Glimmer A system for finding genes in microbial DNA The Institute for Genomic Research	HMMer A package of programs for biological sequence analysis using profile hidden Markov models HMMer Home
MrBayes MrBayes is a program for the Bayesian estimation of phylogeny. MrBayes Home	NCBI Tools Blast tools from NCBI (Blastall, bl2seq, psiblast, phiblast, blast2cours) NCBI
PAML A program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood PAML Home	Phylip PHYLIP is a free package of programs for inferring phylogenies University of Washington
R An integrated suite of software facilities for data manipulation, calculation and graphical display. R Documentation	Wise2 A package focused on comparisons of bio polymers, commonly DNA sequence and protein sequence European Bioinformatics Institute