Genes4all

Overview

Genes4all is a visualization module for the Drupal CMS. It is species and data-type neutral and unlike most Drupal modules, it relies on dynamically generated content and does not store much information on the Drupal database (i.e. does not create nodes).It currently drives the InsectaCentral database, an insect transcriptome database with 1,578,321 gene models from 12,800,018 ESTs.

It is not yet fit for public consumption but Drupal developers can get a taste from http://drupal.org/project/gmod_dbsf and http://gmod-dbsf.googlecode.com.

Dependencies

Genes4all is written for Drupal 6 and it depends on the Drupal gmod_dbsf module (http://drupal.org/project/gmod_dbsf). It requires BioPerl.

Features

Genes4all is built with the notion that Chado is a read-only data warehouse where only administrators can edit it but web-users can retrieve data. The Drupal database offers a bidirectional interface with the users.

• Currently these two are publicly available:
  • genes4all_experiment - RNAi experiment databasing module is an ontology-driven system which was built for the Lepidoptera RNAi Working Group and can be adapted for other types of experiments.
  • genes4all_download - Download est2assembly data which have been stored in Chado.

• Other modules deployed in InsectaCentral but not available to developers yet:
  • genes4all_explore - Create gene pages for sequence features directly from Chado
  • genes4all_curation - Provide a community curation system where web users write to the Drupal database and curators can visualy 'save' accepted annotations to Chado.

• • These modules are currently being developed.
  • genes4all_upload - upload your est2assembly transcriptome assembly for integration into a genes4all database.
  • Integration with the Geneious software and provide other web services

For the 2011-2012 season we are planning to go beyond transcriptome data and support genomes as well as ecological and geographical characters.

Demos and Screenshots

• A | screencast on how to use the RNAi experiment module.

License

This software is GPLv2+ licensed as part of the Drupal package. It is currently supported by Alexie Papanicolaou while at CSIRO, the Australian Commonwealth Scientific and Research Organization (http://www.csiro.au).