[hpc-announce] BIO-HPC IJHPCA Journal Special Issue

José María Cecilia Canales jmcecilia at ucam.edu
Sat Sep 8 08:36:07 CDT 2018

                         CALL FOR PAPERS
Journal Special Issue of the International Journal of High Performance Computing Applications (IJHPCA) on Novel High Performance Computing algorithms and platforms in Bioinformatics (BIO-HPC)


This special issue of the International Journal of High Performance Computing Applications (IJHPCA) calls for submissions on novel high performance computing algorithms and platforms in Bioinformatics. While this special issue is thematically connected to the workshops series on Bioinformatics and High Performance Computing (BIO-HPC), this call is open for all contributions.

The integration of the latest breakthroughs in biochemistry and biotechnology from one side and high performance computing and computational modelling from the other, enables remarkable advances in the fields of healthcare, drug discovery, genome research, systems biology and so on. By integrating all these developments together, scientists are creating new exciting personal therapeutic strategies for living longer and having healthier lifestyles that were unfeasible not that long ago. Those efforts have created new research fields such as Bioinformatics, Computational Biology or Computational Chemistry that work into many different research areas, such as life sciences, where there are many examples of scientific applications for discovering biological and medical unknown factors that could greatly benefit from increased computational resources.

However, we are witnessing a steady transition to heterogeneous architectures, where traditional CPUs and accelerators like Graphics Processing Units (GPUs), Intel MIC/Xeon Phi or FPGAs, are combined together to maintain the traditional increment in performance over the years. The underlying computational model of such architectures relies on massive vectorization to reduce the Energy per Instruction (EPI). Traditional algorithms are often tailored to sequential or modestly parallel based architectures that may not fit within this landscape of computation. However, novel algorithms that are inspired by nature procedures such as metaheuristics, artificial neural networks, just to mention a few, are gaining special interest in the community as they are massively parallel by its definition.

This special issue proposal is looking for original research works to explore the intersection between both algorithm design and hardware platforms to deal with the emergent challenges of the next century in the field of Bioinformatics, Computational Biology and Computational Chemistry. In this regard, one of the main objectives of this special issue proposal is discussing about the main trends in parallel processing, algorithm definition and problem-domain requirements altogether, which may anticipate future solutions to be translated into real benefits to the society.    

This is an open call for contributions, but also invites (extended) selected papers from the BIO-HPC’18, collocated with the ICPP conference. Extended versions of conference papers must contain at least 50% of new content.


The aim of the proposed Special Issue of IJHPCA is to promote research for disruptive proposals presented from a holistic perspective that really make a step forward in the fields of Bioinformatics, Computational Biology and Computational Chemistry.  In particular, contributions are solicited on, but are not limited to, the following topics:

- Programming Models and Systems for Multicore, Manycore, and Clusters of Multicore/Manycore.
- Parallel Stochastic Simulation.
- Biological and Numerical Parallel Computing.
- Parallel and Distributed Architectures.
- Emerging Processing Architectures (e.g. GPUs, Intel Xeon Phi, FPGAs, mixed CPU-GPU or CPU-FPGA, etc).
- Parallel Model Checking Techniques.
- Parallel Algorithms for Biological Analysis.
- Cluster and Grid Deployment for System Biology.
- Soft Computing Algorithms in Bioinformatics, Computational Biology and Computational Chemistry.
- Application of HPC Developments in Structural Bioinformatics, Computational Biology and Computational Chemistry.
- Biological and Chemical databases for Big Data Management.
- Automated Verification in Computational Biology.
- System Infrastructure for High Throughput Analysis.
- Biomolecular Structure Prediction and Large Molecular Systems.
- Molecular Visualization of Biological Big Data.
- Large Scale Proteomics.


Submission Due November 30, 2018

1st Round Notification February 1, 2019

Final Notification April 1, 2019

Publication Fall 2019


If you have any question, please don’t hesitate to contact

- José M. Cecilia, Universidad Católica de Murcia (UCAM), Jmcecilia {at} ucam.edu


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