The UK Department of Trade and Industry (DTI) funded BRIDGES project (Biomedical Research Informatics Delivered by Grid Enabled Services) has developed a Grid infrastructure to support cardiovascular research. This includes the provision of a compute Grid and a data Grid infrastructure with security at its heart. In this paper we focus on the BRIDGES data Grid. A primary aim of the BRIDGES data...

Reverse engineering of genetic regulatory networks from time series microarray data are investigated. We propose a dynamic Bayesian networks (DBNs) modeling and a full Bayesian learning scheme. The proposed DBN directly models the continuous expression levels and also is associated with parameters that indicate the degree as well as the type of regulations. To learn the network from data, we pr...

We investigate in this paper reverse engineering of gene regulatory networks from time-series microarray data. We apply dynamic Bayesian networks (DBNs) for modeling cell cycle regulations. In developing a network inference algorithm, we focus on soft solutions that can provide a posteriori probability (APP) of network topology. In particular, we propose a variational Bayesian structural expect...

Galahad (https://galahad.esat.kuleuven.be) is a web-based application for analysis of drug effects. It provides an intuitive interface to be used by anybody interested in leveraging microarray data to gain insights into the pharmacological effects of a drug, mainly identification of candidate targets, elucidation of mode of action and understanding of off-target effects. The core of Galahad is ...

The increasing availability and maturity of DNA microarray technology has led to an explosion of cancer profiling studies for identifying cancer biomarkers, and predicting treatment response. Uncovering complex relationships, however, remains the most challenging task as it requires compiling and efficiently querying data from various sources. Here, we describe the Stress Response Array Profile...

The majority of microarray studies evaluate gene expression differences between various specimens or conditions. However, the causes of this variability often remain unknown. Our aim is to identify underlying causes of these patterns, a process that would eventually enable a mechanistic understanding of the deregulation of gene expression in cancer. The procedure consists of three phases: pre-p...

Description SCAN is a microarray normalization method to facilitate personalized-medicine work-flows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by model-ing and removing probe-and array-specific background noise using only data from within each array. SCAN can be applied to one-chan...

SUMMARY BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ub...

BACKGROUND Public data integration may help overcome challenges in clinical implementation of microarray profiles. We integrated several ovarian cancer datasets to identify a reproducible predictor of survival. METHODOLOGY/PRINCIPAL FINDINGS Four microarray datasets from different institutions comprising 265 advanced stage tumors were uniformly reprocessed into a single training dataset, also...

1) Description of the current situation According to the last census data of the Estonian Statistical Office, there are around one hundred nationalities of different ethnic origin in Estonia. There are an estimated 600 to 1,000 Roma living in Estonia and their largest communities are located in Southern Estonia (185 Roma), North-Eastern Estonia (92 Roma), and Western Estonia (69 Roma). Proporti...