Useful Links

General Bioinformatics Links and Resources

Bioinformatics Links Directory
A searchable directory of links maintained by the Bioinformatics Graduate Program at the University of British Columbia

The Database for Annotation, Visualization and Integrated Discovery (DAVID)
A web-accessible set of functional annotation tools to aid in deriving biological meaning from large lists of genes

European Bioinformatics Institute (EBI) Toolbox
A comprehensive range of web-accessible bioinformatics tools

Systems Biology
A portal for useful information relevant to systems biology

BioCarta
Vendor provides interactive cellular and molecular pathway maps

AAAS Signal Transduction Knowledge Environment
Resources for signal transduction research

Cytoscape
Free, open source software for visualizing networks (e.g. Pathways analysis, systems biology)

KEGG - Kyoto Encyclopedia of Genes and Genomes
Pathway maps and genome resources

Ggobi
Free, open source software for visualizing high dimensional data

Bioinformatics Organization
Map of free bioinformatics software useful to biomedical research

CellDesigner
Purpose: Biologists can use this free software to build diagrams of pathway for simulation, it can be modified by java plug-ins

Open Clinica
Free, open source clinical trial software

University of Maryland Center for Bioinformatics and Computational Biology (CBCB)
A collection of open-source bioinformatics tools for the assembly and analysis of whole genomes

NCBI

Phylogenetics

Phylogeny Applications
A comprehensive list of Phylogeny Programs complied by Dr. Joseph Felsenstein?s group in the Department of Genome Sciences at the University of Washington

ExPASy (Expert Protein Analysis System)
Resources for analyzing protein sequence data

University of California, Santa Cruz Genome Bioinformatics Site
For performing genomic analysis, especially alignments of complete chromosomes/genomes

Structural Biology

PyMOL
PyMOL is a widely used , open source software for structure biology modeling and analysis

Visual Molecular Dynamics (VMD)
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting

UCSF Chimera
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles

Statistics

GraphPad CurveFit
A complete guide to curve-fitting for dose response and ELISA experiments using the statistics software Prism

Engineering Statistics Handbook from the National Institute of Standards and Technology (NIST)
This is a great resource for Design of Experiments (DOE, Ch. 5) and survival tests (Ch. 8), among other statistics concepts

SAS
The online documentation for SAS 9.1.3 provides lots of great info about statistical tests of all kinds. The information here ranges from specific SAS procedures to general statistics concepts, mostly written for advanced statisticians but some material is provided for nonexperts

R Statistics Language
Home page for the R statistics language / software environment. R is a free, open source statistics software.

Bioconductor
Resources for bioinformatics research in using the R statistics language

Weka 3 Data Mining Software
Free, open source WEKA software for data mining (e.g. Machine learning)

The BUGS (Bayesian inference Using Gibbs Sampling) Project
Free Windows PC software for Bayesian, Markov Chain Monte Carlo (MCMC) methods

OpenBUGS
Free, open source software for Bayesian MCMC methods

Interactive Statistical Pages Project
Provides an extensive list of statistics web tools for many purposes

Bioinformatics Application Development

MacResearch
MacResearch is an open and independent community for scientists using Mac OS X and related hardware in their research.

Google Web Toolkit
Google Web Toolkit (GWT) allows developers to quickly build and maintain complex, high performance JavaScript front-end applications in the Java programming language.

BioPerl
Open source Perl packages specific for Bioinformatics applications. The site includes an FAQ and also HOWTOs and Tutorials for most popular algortihms.

BioJava
Open source Java Framework for processing biological data and developing Bioinformatics applications.