The GUS Platform
for functional genomics
Introduction

With the availability of high-throughput sequence and expression data, project-focused sequence databases are envisioned for a wide range of model organisms, pathogens and system-specific communities. The Genomics Unified Schema (GUS) platform offers these efforts a sophisticated database system and user interface without requiring them to commit the substantial overhead and expertise required to build from scratch. Individual sites are responsible for developing site-specific details. Depending upon their needs and resources this will range from web page programming and data loading to large scale schema extensions, providing for templated to highly distinctive installations. An open source CVS repository is used to incorporate modifications and extensions introduced by the external developer community.

GUS is based on an extensive strongly-typed relational schema and includes the GUS Application Framework to assist in development of data acquisition and analysis programs and the GUS Web Development Kit to assist in query-based website development. The GUS platform maximizes the utility of stored data by warehousing it in a schema that integrates the genome, transcriptome, and proteome of one or more organisms, gene regulation and networks, ontologies and controlled vocabularies, gene expression and inter-organism comparisons. The GUS relational database provides scaleable high-performance access to large amounts of data spread over hundreds of tables, and facilitates complex queries not available in many other systems. It provides programmatic access via SQL and the GUS Application Framework.


Access
Downloading and Installing GUS

With the upcoming GUS 3.1 release we plan on offering GUS in a ready-to-use package. Until then, the 3.0 version of the system must be downloaded and installed from the public CVS repository. Please note that we are still in the process of debugging and streamlining the installation procedure; check the gusdev-gusdev e-mail archive for known problems and workarounds. Roughly, the steps to install GUS are as follows:

  1. Download and install the GUS Build System
  2. Install the GUS schema (currently requires Oracle 8i/9i)
  3. Install the rest of the GUS system (generating the Perl and Java objects requires the schema to be installed first)
  4. Load data into the system using the GUS plugins
Additional Documentation

Our documentation effort is underway.

Schema Browsing

Use our schema browser to browse the tables and views in:

(*)Please note: this is the latest development version of the schema currently in use at CBIL. There may be slight differences between this version of the schema and the 3.0-tagged release in CVS.
Projects powered by GUS

These sites use the GUS platform:

  • AllGenes - A human and mouse gene index derived from assembled ESTs and mRNAs.
  • PlasmoDB - A genomic database for the malaria-causing parasite Plasmodium falciparum.
  • EPConDB - The Endocrine Pancreas Consortium web site
  • RAD - A gene expression database of array-based (microarrays, high-density oligo arrays, macroarrays) and non-array-based (e.g., SAGE) experiments
  • GeneDB - A curated database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei
Mailing List

We have a mailing list focused on GUS development hosted by SourceForge. You must subscribe in order to get and post mail. Or you can read the archive.

Bug and Feature Trackers
Source Code Repository
  • The GUS source code is available through a CVS repository hosted by the Sanger Institute
  • Some additional files are available from the CBIL download site (see the installation instructions above)

Collaborators

The GUS project is a collaboration between:

  • CBIL - The Computational Biology and Informatics Laboratory at The University of Pennsylvania's Center for Bioinformatics
  • PSU - The Pathogen Sequencing Unit of the Wellcome Trust Sanger Institute
  • The Kissinger Lab, CTEGD and the Department of Genetics, University of Georgia

Links

Here are additional related links.

  • www.gmod.org - The Generic Model Organism Database Construction Set



$Revision: 1.4 $ $Date: 2003/06/10 05:41:18 $ $Author: crabtree $Contact: webmaster@gusdb.org