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The 3rd IEEE International Workshop on Parallelism in Bioinformatics
held in conjunction with IEEE ISPA-15

August 20-22, 2015, Helsinki, Finland

In Bioinformatics, we can find a variety of problems which are affected by huge processing times and memory/storage consumption, due to the large size of biological data sets and the inherent complexity of biological problems. In fact, Bioinformatics is one of the most exciting research areas in which Parallelism finds application. Successful examples are mpiBLAST, RAxML-HPC or ClustalW-MPI, among many others. In conclusion, Bioinformatics allows and encourages the application of many different parallelism-based technologies. The focus of this workshop is on parallel and distributed processing in bioinformatics, and consequently, we welcome any technique based on: multicore computing, cluster computing, supercomputing, cloud computing, grid computing, green computing, hardware accelerators as GPUs, FPGAs, etc.

The goal of PBio is therefore to bring together researchers in the fields of Parallelism and Bioinformatics, hence establishing a forum for discussing challenges, new ideas, results, applications, and future directions. In conclusion, we seek original, high-quality research papers, clearly focused on the application of Parallelism to any possible Bioinformatics problem.

Scope and Interests

Topics of interest include, but are not limited to:

  • Parallel and distributed algorithms in Bioinformatics
  • Workload partitioning strategies in Bioinformatics
  • Memory-efficient algorithms in Bioinformatics
  • Parallel tools and applications in Bioinformatics
  • Data-intensive Bioinformatics (including Big Data storage and processing)
  • Multicore computing in Bioinformatics
  • Multithreaded computing in Bioinformatics
  • Cluster computing in Bioinformatics
  • Supercomputing in Bioinformatics
  • Cloud/Grid/P2P computing in Bioinformatics
  • Volunteer computing in Bioinformatics
  • Hardware accelerators (GPUs, FPGAs, etc.) in Bioinformatics
  • Heterogeneous computing in Bioinformatics
  • Green computing in Bioinformatics
  • Mobile computing in Bioinformatics
  • Emerging parallel programming models in Bioinformatics
  • Parallel performance evaluation, analysis, and optimization in Bioinformatics
  • Parallel visualization, modelling, simulation, and exploration in Bioinformatics

With regard to the Bioinformatics problems, many different alternatives exist: bioinformatics applied to biomedicine and drug design; biological sequence analysis, comparison and alignment; motif, gene and signal recognition/discovery; molecular evolution; phylogenetics and phylogenomics; determination or prediction of the structure of RNA and protein; DNA twisting and folding; gene expression and gene regulatory networks; deduction of metabolic pathways; microarray design and analysis; proteomics; functional genomics; molecular docking; design of DNA sequences for molecular computing; etc.

Submission Instructions

Papers submitted to the workshop should be written in English conforming to the IEEE Conference Proceedings Format (8.5" x 11", Two-Column). The paper should be submitted through the workshop submission system at the workshop website. The length of the papers should not exceed 6 pages + 2 pages for over length charges.

Accepted and presented papers will be included into the IEEE Conference Proceedings published by IEEE CS CPS and submitted to IEEE Xplore and CSDL. Authors of accepted papers, or at least one of them, are requested to register and present their work at the conference, otherwise their papers will be removed from the digital libraries of IEEE CS after the conference. Distinguished papers presented at the conference, after further revision, will be recommended to special issues of reputable SCI/EI-indexed journals.

Submitting a paper to the workshop means that, if the paper is accepted, at least one author should attend the workshop and present the paper.

Journal Publication

The authors of the best workshop papers, accepted and presented in PBio 2015, will be invited to submit properly extended and improved versions of their papers to a special issue in the International Journal of High Performance Computing Applications (ISSN: 1094-3420, Impact Factor 2013: 1.625, Quartile Q1).

Important Dates

Submission deadline: April 15th May 1st, 2015
Authors notification: May 31st, 2015
Camera-ready due: July 1st, 2015
Registration: July 1st, 2015

Program Chairs

Miguel A. Vega-Rodríguez, University of Extremadura, Spain
Alvaro Rubio-Largo, University of Extremadura, Spain
David L. González-Álvarez, University of Extremadura, Spain
Sergio Santander-Jiménez, University of Extremadura, Spain

PC Members (in alphabetical order)

Antonio Gómez-Iglesias, Texas Advanced Computing Center, USA
Fa Zhang, Institute of Computing Technology, Chinese Academy of Sciences, China
Francisco Prieto-Castrillo, NECSI (New England Complex Systems Institute), USA
José M. Granado-Criado, University of Extremadura, Spain
José M. Lanza-Gutiérrez, University of Extremadura, Spain
María Arsuaga-Ríos, CERN, Switzerland
María Botón-Fernández, CETA-CIEMAT, Spain
Marisa da Silva Maximiano, Polytechnic Institute of Leiria, Portugal
Miguel Cárdenas-Montes, CIEMAT, Spain
Sónia M. Almeida-Luz, Polytechnic Institute of Leiria, Portugal
Víctor Berrocal-Plaza, University of Extremadura, Spain


Please email inquiries concerning the workshop to Miguel A. Vega-Rodríguez.

Aalto ELEC