RegaDB: Community-driven data management and analysis for infectious diseases. Bioinformatics, 29 (11): 1477-1480, doi: 10.1093/bioinformatics/btst162 (2013).

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Title: RegaDB: Community-driven data management and analysis for infectious diseases
Authors: Libin P, Beheydt G, Deforche K, Imbrechts S, Ferreira F, Van Laethem K, Theys K, Carvalho AP, Cavaco Silva J, Lapadula G, Torti P, Assel M, Wesner S, Snoeck J, Ruelle J, De Bel A, Lacor P, De Munter P, Van Wijngaerden E, Zazzi M, Kaiser R, Ayouba A, Peeters M, de Oliveira T, Alcantara L, Grossman Z, Sloot P, Otelea D, Paraschiv S, Boucher C, Camacho R, and Vandamme AM.
Journal: Bioinformatics,29 (11):1477-1480, doi: 10.1093/bioinformatics/btst162 (2013)

Journal Impact Factor (I.F.): 5.468
Number of citations (Google Scholar): 14

Abstract

Summary: RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyze patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.

Availability and implementation: Source code, binaries and documentation are available on http://regaweb.med.kuleuven.be/software/regadb/ RegaDB is written in the Java programming language, using a web-service oriented architecture.

Opportunities for researchers: Another example of the utility of RegaDB is the collaborative database used within the Southern African Treatment and Resistance Network (SATuRN). This network has 24 member institutions working in Southern Africa, the region at the epicenter of the HIV epidemic. Currently there are more than ten institutions using the SATuRN RegaDB for patient data management, data curation and research. Under SATuRN, more than 7,000 genotypes with treatment and monitoring data has been collected. Using the built-in customized report and query functionality, data of specific attributes is selected, analyzed and used to answer specific clinical and research questions (Manasa et al. 2012, de Oliveira et al. 2010). In addition, members of the SATuRN project recently published a book (Rossouw, Lessells & de Oliveira 2013) containing a series of case studies used for training. More than 1,450 physicians and nurses have been trained through conferences, workshops and online web-tutorials RegaDB: Community-driven data management and analysis for infectious diseases.

Download: Full text paper

Citation: Libin P, Beheydt G, Deforche K, Imbrechts S, Ferreira F, Van Laethem K, Theys K, Carvalho AP, Cavaco Silva J, Lapadula G, Torti P, Assel M, Wesner S, Snoeck J, Ruelle J, De Bel A, Lacor P, De Munter P, Van Wijngaerden E, Zazzi M, Kaiser R, Ayouba A, Peeters M, de Oliveira T, Alcantara L, Grossman Z, Sloot P, Otelea D, Paraschiv S, Boucher C, Camacho R, and Vandamme AM. RegaDB: Community-driven data management and analysis for infectious diseases Bioinformatics,29 (11):1477-1480, doi: 10.1093/bioinformatics/btst162 (2013).


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KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), K-RITH Tower Building, Nelson R Mandela School of Medicine, UKZN

Contact: Prof. Tulio de Oliveira, Tel: +27 31 260 4898, Email: tuliodna@gmail.com & deoliveira@ukzn.ac.za

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