RegaDB : A Viral Data and Analysis Management Environment
Introduction
RegaDB is a database with software tools, which may be installed and managed locally, to store clinical data related to HIV and HCV treatment. It aims to support both clinicians and researchers in their work by delivering a free and open source software solution.
For researchers our objective is to offer several tools for HIV 1/2 and HCV sequence analysis, to support their research, and to enable collaborations between researchers of different hospitals and institutions.
Motivation
Although needed to improve our knowledge on issues such as drug resistance and the influence of natural variation, currently there is an inhibition to these collaborations on three levels;
- the data is sensitive and as such, privacy and ethical concerns complicate its sharing
- clinicians and virologists are reluctant to share data fearing to loose control over who performs which research
- at a technical level, different database formats provide a natural inhibition to share this highly relational data
Rationale
RegaDB attempts to address these issues by offering;
- a database that is installed locally, and in which each research center can organize its own data, in a format that facilitates sharing with other researchers that use RegaDB
- a mechanism to anonymize sensitive data when exporting data, so this information is invisible for collaborators in other institutions
- when set-up in a collaborative mode, a fine-grained permission system, leaving the sharing party with full control over his own data
RegaDB provides clinicians with bioinformatics tools that integrate with their own patient data.
A set of standard services is automatically configured when installing RegaDB;
- Codon-correct nucleotide sequence alignement with frame-shift detection and correction
- Drug Resistance interpretation, based on several algorithms (with support for the ASI XML format)
- Rega HIV-1/2 and Oxford HCV subtyping tools
- Patient history graph
- Mutation visualisation module
These tools may be extended with other (third-party) bioinformatics services.
The development of RegaDB is a joint collaboration between the Rega Institute, Katholieke Universiteit Leuven and MyBioData Biomedical IT Solutions.
