BioMed Research International

High-Performance Computing and Big Data in Omics-based Medicine


Publishing date
25 Jul 2014
Status
Published
Submission deadline
07 Mar 2014

Lead Editor

1Institute for Biomedical Technologies, National Research Council of Italy, Segrate, Italy

2Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy

3Computer Science Department, Catholic University of Murcia (UCAM), Murica, Spain

4Center for Research Computing, University of Notre Dame, Indiana, USA


High-Performance Computing and Big Data in Omics-based Medicine

Description

Omics sciences are able to produce, with the modern high-throughput techniques of analytic chemistry and molecular biology, a huge quantity of data. Next Generation Sequencing analysis of diseased somatic cells, genome wide annotations of biomarkers, systems pathology studies, discovering of novel compounds are examples of the great advantages that high-performance computing can provide to omics science, providing a fast translation of biomolecular results to the clinical practice. Medicine in the near future will be predictive, preventive, and personalized thanks to big data-driven analysis.

Massive parallel clusters, distributed technologies such as grid and cloud computing, on-Chip supercomputing such as GPGPU and Xeon Phi implementations represent well-established solutions in research laboratories, but their capabilities should be widespread from clinical and healthcare experts to reach their full potential. On the other hand, although not seen intensive from a computational perspective, big data presents huge concerns while scaled to healthcare problems. Managing terabytes of data requires specific technologies, redundant facilities, shared and distributed file systems, clustered databases, indexing and searching process, and dedicated network configuration.

The aim of this special issue is to present the latest advances in treating omics data with high-performance computing solutions and big data analysis paradigms, showing the potential repercussions of these technologies in translational medicine. We are especially interested in parallel implementations of systems and algorithms, use of case descriptions of on-Chip and distributed platforms for the biomedical community, or successful experiences of large-scale analysis and simulations in the field of high-performance computational biology. Potential topics include, but are not limited to:

  • Biological databases for big data management
  • HPC, grid, and cloud computing for omics sciences
  • Next generation sequencing data analysis
  • Genomics variants analysis and classification
  • Knowledge management for genomics and proteomics
  • Machine learning for big data analysis
  • Parallel algorithms for omics sciences
  • Genome wide identification of regulation patterns
  • Co-expression and coregulation gene expression analysis
  • Systems biology simulations and pathway analysis
  • Infrastructures for big data integration in omics sciences
  • Novel approaches for biomarkers identification
  • Large-scale computations for discovering novel drugs
  • Structural biology applications for modeling and simulations

Before submission, authors should carefully read over the journal's Author Guidelines, which are located at http://www.hindawi.com/journals/bmri/siguidelines/. Prospective authors should submit an electronic copy of their complete manuscript through the journal Manuscript Tracking System at http://mts.hindawi.com/submit/journals/bmri/computational.biology/bigdata/ according to the following timetable:


Articles

  • Special Issue
  • - Volume 2014
  • - Article ID 825649
  • - Editorial

High-Performance Computing and Big Data in Omics-Based Medicine

Ivan Merelli | Horacio Pérez-Sánchez | ... | Daniele D’Agostino
  • Special Issue
  • - Volume 2014
  • - Article ID 134023
  • - Review Article

Managing, Analysing, and Integrating Big Data in Medical Bioinformatics: Open Problems and Future Perspectives

Ivan Merelli | Horacio Pérez-Sánchez | ... | Daniele D’Agostino
  • Special Issue
  • - Volume 2014
  • - Article ID 539410
  • - Research Article

Sequence Alignment Tools: One Parallel Pattern to Rule Them All?

Claudia Misale | Giulio Ferrero | ... | Marco Aldinucci
  • Special Issue
  • - Volume 2014
  • - Article ID 207041
  • - Research Article

On Designing Multicore-Aware Simulators for Systems Biology Endowed with OnLine Statistics

Marco Aldinucci | Cristina Calcagno | ... | Angelo Troina
  • Special Issue
  • - Volume 2014
  • - Article ID 192646
  • - Research Article

Rank-Based miRNA Signatures for Early Cancer Detection

Mario Lauria
  • Special Issue
  • - Volume 2014
  • - Article ID 624024
  • - Research Article

Performance Studies on Distributed Virtual Screening

Jens Krüger | Richard Grunzke | ... | Sandra Gesing
  • Special Issue
  • - Volume 2014
  • - Article ID 863298
  • - Research Article

Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization

Paolo Cazzaniga | Marco S. Nobile | ... | Giancarlo Mauri
  • Special Issue
  • - Volume 2014
  • - Article ID 474219
  • - Research Article

A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing

Ginés D. Guerrero | Baldomero Imbernón | ... | José M. Cecilia
  • Special Issue
  • - Volume 2014
  • - Article ID 959645
  • - Research Article

Heart Health Risk Assessment System: A Nonintrusive Proposal Using Ontologies and Expert Rules

Teresa Garcia-Valverde | Andrés Muñoz | ... | Alberto Caballero
  • Special Issue
  • - Volume 2014
  • - Article ID 980501
  • - Research Article

Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems

Daniele D’Agostino | Giulia Pasquale | ... | Ivan Merelli
BioMed Research International
 Journal metrics
Acceptance rate31%
Submission to final decision67 days
Acceptance to publication30 days
CiteScore3.600
Impact Factor2.276
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