Cloud Bioinformatics in a private cloud deployment

This chapter describes service portability for a private cloud deployment, including a detailed case study about Cloud Bioinformatics services developed as part of the Cloud Computing Adoption Framework (CCAF). The Cloud Bioinformatics design and deployment is based on Storage Area Network (SAN) technologies, details of which include functionalities, technical implementation, architecture, and user support. Bioinformatics applications are written on the SAN-based private cloud, which can simulate complex biological sciences and present them in a way that anyone without prior knowledge can understand. Several bioinformatics results are discussed, particularly brain segmentation, which demonstrates different parts of the brain simulated by the private cloud. In addition, benefits of CCAF are illustrated using several bioinformatics examples such as tumour modelling, brain imaging, insulin molecules, and simulations for medical training. The Cloud Bioinformatics solution offers cost reduction, time-saving, and user friendliness. </jats:p

GenomeVIP: A cloud platform for genomic variant discovery and interpretation

Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional “download and analyze” paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets.</jats:p

CERN openlab Whitepaper on Future IT Challenges in Scientific Research

This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates