PBio 2015

PBio 2015

Third International Workshop on Parallelism in Bioinformatics

August 20-22, 2015 - Helsinki, Finland
to be held as part of
IEEE ISPA-15 (proceedings published by IEEE)



This is the third edition of this international workshop, the previous editions were organized as part of IEEE Cluster 2014 (see PBio 2014 and the special issue in the journal Concurrency and Computation: Practice and Experience) and ACM EuroMPI 2013 (see PBio 2013 and the special issue in the journal Parallel Computing). This year we organize the third edition of this international workshop as part of the prestigious conference IEEE ISPA 2015 (proceedings published by IEEE).

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 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 journal International Journal of High Performance Computing Applications. This special issue can be found here.


International Journal of High Performance Computing Applications

Impact Factor: 1.625, Quartile Q1

ISSN: 1094-3420



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. In particular, contributions are solicited on, but are not limited to, the following topics:

  • 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.


PBio 2015 welcomes original submissions that have not been published and that are not under review by another conference or journal. Contributors are invited to submit a full paper as a PDF document. Papers submitted to PBio 2015 should be written in English conforming to the IEEE Conference Proceedings Format (8.5" x 11", Two-Column). All submissions will be evaluated on their originality, technical soundness, significance, presentation, and interest to the workshop attendees. The papers should be submitted electronically through EasyChair, see https://easychair.org/conferences/?conf=pbio2015. The length of the papers should not exceed 6 pages + 2 pages for over length charges.

All submitted papers will be reviewed by PBio's technical program committee. 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 a special issue of a reputable SCI/EI-indexed journal.

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


Paper Submission Deadline: April 15th, 2015 May 1st, 2015 (extended)
Acceptation Notification: May 31st, 2015
Camera-Ready Submission: June 30th, 2015
Workshop at IEEE ISPA 2015: August 20th, 2015


The PBio program can be found below, as part of the IEEE ISPA 2015 program.

Thursday, August 20th 2015
10:45-12:30 SESSION 1: Cluster computing in Bioinformatics
Session Chair: Álvaro Rubio-Largo
10:45-11:10 Parallel Computation of Voxelized Macromolecular Surfaces by Spatial Slicing. Sebastian Daberdaku and Carlo Ferrari
11:10-11:35 Scalable RNA Sequencing on Clusters of Multicore Processors. Héctor Martínez, Sergio Barrachina, Maribel Castillo, Joaquín Tárraga, Ignacio Medina, Joaquín Dopazo and Enrique S. Quintana-Ortí
11:35-12:00 A Parallel Algorithm for Compression of Big Next-Generation Sequencing (NGS) Datasets. Sandino Vargas Pérez and Fahad Saeed
12:00-12:25 Assessment of a Black-box Approach for a Parallel Finite Elements Solver in Computational Hemodynamics. Ferdinando Auricchio, Marco Ferretti, Adrien Lefieux, Mirto Musci, Alessandro Reali, Santi Trimarchi and Alessandro Veneziani
12:30-13:50 Lunch
13:50-15:35 SESSION 2: Hardware accelerators in Bioinformatics
Session Chair: Álvaro Rubio-Largo
13:50-14:15 Smith-Waterman Protein Search with OpenCL on FPGA. Enzo Rucci, Armando de Giusti, Marcelo Naiouf, Guillermo Botella, Carlos García and Manuel Prieto-Matias
14:15-14:40 Accelerating Phylogenetic Inference on Heterogeneous OpenCL Platforms. Lídia Kuan, Leonel Sousa and Pedro Tomás
14:40-15:05 Accelerating DNA Sequencing Using Intel Xeon Phi. Suejb Memeti and Sabri Pllana
15:05-15:30 Fast Epistasis Detection in Large-Scale GWAS for Intel Xeon Phi Clusters. Glenn R. Luecke, Nathan T. Weeks, Brandon M. Groth, Marina Kraeva, Li Ma, Luke M. Kramer, James E. Koltes and James M. Reecy
15:35-16:05 Afternoon Coffee
16:05-17:50 SESSION 3: Many-core, multi-core and distributed computing in Bioinformatics
Session Chair: Álvaro Rubio-Largo
16:05-16:30 On the Performance of BWA on NUMA Architectures. Josefina Lenis and Miquel Angel Senar
16:30-16:55 Parallel H4MSA for Multiple Sequence Alignment. Álvaro Rubio-Largo, Miguel A. Vega-Rodríguez and David L. González-Álvarez
16:55-17:20 Discovering Candidates for Gene Network Expansion by Distributed Volunteer Computing. Francesco Asnicar, Luca Erculiani, Francesca Galante, Caterina Gallo, Luca Masera, Paolo Morettin, Nadir Sella, Stanislau Semeniuta, Thomas Tolio, Giulia Malacarne, Kristof Engelen, Andrea Argentini, Valter Cavecchia, Claudio Moser and Enrico Blanzieri


Miguel A. Vega-Rodríguez, University of Extremadura, Spain (mavega@unex.es)
Alvaro Rubio-Largo, University of Extremadura, Spain (arl@unex.es)
David L. González-Álvarez, University of Extremadura, Spain (dlga@unex.es)
Sergio Santander-Jiménez, University of Extremadura, Spain (sesaji@unex.es)

PROGRAM COMMITTEE (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