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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

The GMOD Drupal bioinformatic server framework.

Alexie Papanicolaou¹, David G Heckel

¹Centre for Conservation and Ecology, University of Exeter in Cornwall, Penryn, UK. alexie@butterflybase.org

Bioinformatics (Oxford, England)

|October 26, 2010

Summary

This summary is machine-generated.

A new bioinformatic framework for Drupal CMS addresses the data and software deployment bottleneck. This system enhances data mining and archiving capabilities for researchers, streamlining omics applications.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Next-generation sequencing has increased omics data, creating a bioinformatic bottleneck.
Existing General Model Organism Database (GMOD) tools lack a robust online solution for deploying heterogeneous data and software within a Web Content Management System (CMS).

Purpose of the Study:

To present a novel bioinformatic framework integrated with the Drupal CMS.
To provide solutions for the bioinformatic bottleneck by enabling efficient data and software deployment.

Main Methods:

Development of a Drupal CMS bioinformatic framework comprising three modules: GMOD-DBSF (API), biosoftware_bench (software deployment), and genes4all_experiment (research community support).
Implementation in PHP and Perl, utilizing a graphical user interface for administration and data provision.

Main Results:

The GMOD-DBSF module simplifies the development of bioinformatics Drupal modules, serving as an expandable community resource.
The biosoftware_bench module enables rapid, secure deployment of bioinformatics software and pre-publication datasets.
The genes4all_experiment module has archived over 150 unpublished RNAi studies from Lepidoptera.

Conclusions:

The presented Drupal CMS infrastructure offers a powerful new toolkit for bioinformaticians.
The framework reduces development time for bioinformatics Drupal modules and enhances biologists' data mining capabilities.
The system facilitates the archiving of valuable, previously unpublished research data.