Articlehybrid2010

The GMOD Drupal Bioinformatic Server Framework

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Scientific Computing and Data Management Genomics and Phylogenetic Studies Genetics, Bioinformatics, and Biomedical Research

Abstract

MOTIVATION: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). RESULTS: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. CONCLUSION: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. AVAILABILITY AND IMPLEMENTATION: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.

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2005Galaxy: A platform for interactive large-scale genome analysis 2004Taverna: a tool for the composition and enactment of bioinformatics workflows 2003The Human Genome Project: Lessons from Large-Scale Biology

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