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Prlic A.,University of California at San Diego | Yates A.,European Bioinformatics Institute | Bliven S.E.,University of California at San Diego | Rose P.W.,University of California at San Diego | And 12 more authors.
Bioinformatics | Year: 2012

Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model. © The Author 2012. Published by Oxford University Press. All rights reserved. Source

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.2.4.2-1 | Award Amount: 8.33M | Year: 2014

Asymptomatic vascular damage accumulates for years before patients are identified and subjected to therapeutic measures. The limited knowledge on early vascular disease pathophysiology is reflected in the lack of therapeutic options. SysVasc aims to overcome this limitation by mounting a comprehensive systems medicine approach to elucidate pathological mechanisms, which will yield molecular targets for therapeutic intervention. The consortium is based on established multidisciplinary European research networks, including specialists in pre-clinical and clinical research, omics technologies, and systems biology from research intensive SMEs and academia; partners synergistically provide access to an extensive number of selected population-based cohorts and associated datasets, cutting edge modeling and simulation methods, and established cardiovascular disease (CVD) animal models and patient cohorts. The coordinated application of these tools and know-how will identify pathophysiological mechanisms and key molecules responsible for onset and progression of CVD and validate their potential to serve as molecular targets for therapeutic intervention. To this end, the consortium will also use unique resources to evaluate molecular homology between the available model systems and human disease, which will yield reliable essential preclinical research tools to explore proof of concepts for therapeutic intervention studies and ultimately translate relevant results into novel therapeutic approaches. Collectively, SysVasc will identify and validate novel biology-driven key molecular targets for CVD treatment. Major scientific, societal and economic impact is expected including, but not limited to, providing a valuable resource to further CVD research, and enhance competitiveness of participating SMEs and European health industry in general by translating knowledge into innovative services in therapeutic target and drug research.

Chen C.,Cornell University | DeClerck G.,Cornell University | Tian F.,China Agricultural University | Spooner W.,Eagle Genomics | And 3 more authors.
PLoS ONE | Year: 2012

PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize - a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information. Source

McLaren D.,Stem Cell science UK Ltd | McLaren D.,Biologics | Gorba T.,StemCells | Marguerie De Rotrou A.,Stem Cell science UK Ltd | And 17 more authors.
Journal of Biomolecular Screening | Year: 2013

The aim of this study was to demonstrate proof-of-concept feasibility for the use of human neural stem cells (NSCs) for high-throughput screening (HTS) applications. For this study, an adherent human induced pluripotent stem (iPS) cell-derived long-term, self-renewing, neuroepithelial-like stem (lt-NES) cell line was selected as a representative NSC. Here, we describe the automated large-scale serum-free culture ("scale-up") of human lt-NES cells on the CompacT SelecT cell culture robotic platform, followed by their subsequent automated "scale-out" into a microwell plate format. We also report a medium-throughput screen of 1000 compounds to identify modulators of neural stem cell proliferation and/or survival. The screen was performed on two independent occasions using a cell viability assay with end-point reading resulting in the identification of 24 potential hit compounds, 5 of which were found to increase the proliferation and/or survival of human lt-NES on both occasions. Follow-up studies confirmed a dose-dependent effect of one of the hit compounds, which was a Cdk-2 modulator. This approach could be further developed as part of a strategy to screen compounds to either improve the procedures for the in vitro expansion of neural stem cells or to potentially modulate endogenous neural stem cell behavior in the diseased nervous system. © 2012 Society for Laboratory Automation and Screening. Source

Moller S.,University of Lubeck | Krabbenhoft H.N.,Debian Linux | Tille A.,Debian Linux | Paleino D.,Debian Linux | And 9 more authors.
BMC Bioinformatics | Year: 2010

Background: The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments.Results: The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software.Conclusions: Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. © 2010 Möller et al; licensee BioMed Central Ltd. Source

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