RegaDB: Community-driven data management and analysis for infectious diseases

Summary: RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB pr

Databases and Ontologies RegaDB: Community-driven data management and analysis for infectious diseases

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

A collaborative environment allowing clinical investigations on integrated biomedical databases

In order to perform clinical investigations on integrated biomedical data sets and to predict virological and epidemiological outcome, medical experts require an IT-based collaborative environment that provides them a user-friendly space for building and executing their complex studies and workflows on largely available and high-quality data repositories. In this paper, the authors introduce such a novel collaborative working environment a so-called virtual laboratory for clinicians and medical researchers, which allows users to interactively access and browse several biomedical research databases and re-use relevant data sets within own designed experiments. Firstly, technical details on the integration of relevant data resources into the virtual laboratory infrastructure and specifically developed user interfaces are briefly explained. The second part describes research possibilities for medical scientists including potential application fields and benefits as using the virtual laboratory functionalities for a particular exemplary study.</p

The Epidemiology of HIV-1 Transmitted Drug Resistance

The human immunodeficiency virus (HIV) was first discovered in 1983. In 2009, it was estimated that 33.3 (31.4 -35.3) million individuals are infected with HIV worldwide. In that year 1.8 (1.6-2.1) million people died from HIV. Although the virus continues to spread, the number of new infections has fallen from an estimated 3.2 (3.0 -3.5) million in 1997 to 2.6 (2.3 – 2.8) million in 2009. There are several explanations for this decrease. First, the use of antiretrovirals has slowed down the epidemic by suppressing viral replication and thereby the HIV RNA load [2]. This RNA load is a key factor in determining transmissibility of HIV. Second, sexual risk behaviour has decreased in most countries. Third, HIV prevalence follows an ‘S’ curve, like any infectious disease where it start slowly and gradually. In the final phase of the epidemic, people are either no longer infectious (due to effective treatment) or deaths outnumber new cases, so that the total number alive and infected passes its peak and begin to decline or reach a plateau. The majority of new HIV infections continue to occur in sub-Saharan Africa. Here, an estimated 1.8 (1.6 -2.0) million people were newly infected in 2009 and 22.5 million (20.9 -24.2) people were living with HIV in this region (figure 1). In Europe, the HIV-1 epidemic is much smaller, with an estimated 130,000 (110,000-160,000) newly infected in Western and Central Europe in 2009. This results in 820,000 (720,000-910,000) individuals living with HIV-1 and a prevalence of 0.2% in this region