The genes4all and Drupal Bioinformatics Server Framework (DBSF) are a set of routines for building bioinformatic tools for the Drupal Content Management System (http://drupal.org). This project is tightly integrated with GMOD (http://www.gmod.org) and utilized the Chado database schema. It is freely available as GPLv3

Gesnes4all is an API for Drupal bioinformatic tools.

DBSF is the module for deploying command line software. Out of the box, a BLAST, IprScan, annot8r and SSAHA2 servers are available and developers can quickly build their own tools. The GMOD-DBSF developers are adding new functionalities, such as the genes4all software which drives the GMOD transcriptome database InsectaCentral.org.

The DBSF has the following attractive features:

For the system administrator:

• Secure & fast to deploy: the demonstration required 30' to setup from scratch, 10' of which was the BLAST server. The administrator has to merely click on a checkbox to activate the software and then choose which databases will be available to the plugins.

• Secure with private data: We know that laboratories often have two types of data: those they wish to make public and the unpublished ones they wish to utilize only in-house. The solution is often the creation of two separate servers, one password protected. The DBFS takes care of user management and allows you to choose which datasets are available to which users. An unlimited number of user groups can be created included the anonymous/guest visitor who has not logged in.

• Plugin format: It comes with NCBI's BLASTALL but DBFS is an API framework and easy to extend, our publication will have a manual as supplementary material to guide bioinformaticians in writing their plugins with 1-2 days.

• High Performance Computing (HPC) support: Optionally (the demonstration server does), it can utilise the Condor job management system so jobs run on a PC-farm instead of the often meek BLAST server. A perl daemon manages the submissions automatically.

• Database API is Chado-compatible: The DBSF is GMOD compatible and uses the robust, normalized Chado database. As Chado is sequence feature-driven we created sequence-less table set which follows Chado-convention. The future aim is to be able to integrate multiple website deploying this software.

For the end-user:

• Build for wet-lab researchers. They can upload a multi-FASTA file to be used as the query or even the reference database: there is no need to restrict the user to the administrator's datasets. The file size limit is customizable (for demo it's set at 1 Mb). Users can bookmark their search and re-retrieve it within 7 days. Further, they can simultaneously run multiple BLAST algorithm searches.

• Driven by open-source software and adheres to community standards: The output is driven by BioPerl (XML, HTML, TXT and a graph using Bio::Graphics). The database infrastructure is GMOD-compatible and the visualization is securely managed by Drupal.

Tutorials

with figures can be found at http://insectacentral.org