Phenotype Database

Site: http://rgd.mcw.edu/rgdweb

Developed by: RGD

RGD is developing a database to house detailed phenotype data derived from both large-scale and small-scale phenotyping projects. The data currently includes a subset of the results from the PhysGen Programs for Genomic Applications at MCW and Japan’s NBRP.

Apropos

Site: http://apropos.mcw.edu/

Developed by: Simon Twigger

Apropos is an open source project. Addictional information including screenshots, screencasts and other details are available from the project's development site:

http://apropos.rubyforge.org/

Biomart

Site: http://biomart.mcw.edu:9999/

Developed by: Simon Twigger / Andrew Vallejos

As part of our work at the NHLBI proteomics center at the Medical College of Wisconsin, (http://proteomics.mcw.edu) we have been developing a new data annotation tool and it is ready for a more public release. The tool is called Apropos and it combines a comprehensive list of rat, mouse and human protein data with Gene Ontology, pathway and phenotype annotations along with mapping data to provide a three-species annotation database. This enables you to see orthology relationships between species and functional annotations from all three species. For example, you can easily view annotations from mouse and human when studying rat genes/proteins, or to pull in information about rat and mouse when studying human genes/ proteins.

The tool has two main uses: 1) as a personal data annotation tool where you can create personal account and then upload your lists of rat, mouse or human genes or proteins from your 'omic experiment and create an annotation dataset, and 2) as a 3 species annotation database that you can use to find out information about individual genes or pathways in Rat, Mouse and Human.

PhpLiteFramework

Site: http://phplitefw.wiki.sourceforge.net/

Developed by: Wes Rood

A lightweight framework developed in PHP for creating dynamic websites and web apps. Provides clean form handling, and uses ADODB db abstraction layer for database operations. Includes template system and error logging. Runs on PHP 4 or PHP 5.

Snplotyper

Site: http://snplotyper.mcw.edu/

Developed by: Simon Twigger

SNPlotyper is built upon a database of SNPs and their genotypes in a variety of rat strains. To create a haplotype view of a region of the rat genome, select the chromosome and start/stop coordinates for the region and then select the strains you wish to include in the analysis.