Home arrow Software & Tools
Software & Tools PDF Print E-mail

The  Visual Genomics Centre maintains a comprehensive set of program libraries and software packages to support Bioinformatics research across Canada. We provide access to dozens of locally mirrored databanks, and compute power dedicated to Bioinformatics including TimeLogic Decypher database search engines, as well as the world’s first Java 3D TM-enabled CAVE automated virtual reality environment

Software Packages

 Note: If you need something that is not currently provided please contact us with a request.
 

Editors
  • OpenOffice.org, scribus, bluefish
  • gedit, vi, vim, xemacs, nedit
Development
  • Sun Studio, Eclipse, Netbeans
  • Bioperl, R, BioConductor
  • Apache, PHP, MySQL, Perl, Python etc
Homology & Similarity Search
  • BLAST, ParacelBLAST
  • FASTA
  • HMMER
  • Smith-Waterman, etc

Sequence Analysis /  Conversion      
  • ClustalW
  • MEME
  • T-Coffee
  • Readseq
Phylogeny
  • FastDNAml
  • PHYLIP
  • PAUP, etc
Visualization
  • Rasmol
  • ImageJ
  • Graphviz etc
Application Suites
  • EMBOSS
Model Organism Dbs
  • Wormbase, Xenbase searches
Remote Access
  • Sun Secure Global Desktop
  • VNC
  • SSH
     

TimeLogic DeCypher - Web Interface

An accelerator platform for high-throughput bioinformatics database searches. Using field-programmable gate arrays (FPGA), it performs highly sensitive sequence similarity searches such as the various types of Hidden Markov Model (HMM) or Smith-Waterman analyses that would otherwise be too large for public resources and too time-consuming for local computer clusters.

BioView Workbench - Web Interface

A high-throughput accelerator for biological sequence similarity searches and genomic sequence annotations. The Workbench allows users to deploy highly sensitive algorithms for sequence comparison such as the Smith-Waterman algorithms, with speedups of hundreds or even thousands of times compared to regular computer installations. The Workbench has a web-based interface for submitting searches, performing genomic sequence annotation, and displaying results graphically.

Secure Remote Access 

The Sun Center of Excellence for Visual Genomics provides support for SSH or Sun Secure Global Desktop access. With SSH you can access coe01.ucalgary.ca and login with your username / password provided. Alternatively, you may login with Secure Global Desktop which will provide you with a full remote desktop. 

 
< Prev   Next >
Login Form





Lost Password?