PBio 2018

6th International Workshop on Parallelism in Bioinformatics
(proceedings published by ACM Digital Library within its ICPS)

23 September 2018 - Barcelona, Spain
to be held as part of
EuroMPI 2018

IN-COOPERATION


ACM In-cooperation

SIGHPC In-cooperation


GENERAL SCOPE


This is the 6th edition of this international workshop, the previous editions were organized as part of:


This year we organize the sixth edition of this international workshop as part of the prestigious conference EuroMPI 2018.

The PBio 2018 proceedings will be published by ACM Digital Library within its International Conference Proceedings Series (ICPS).

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 computing 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.



JOURNAL SPECIAL ISSUE


The authors of the best workshop papers, accepted and presented in PBio 2018, will be invited to submit properly extended and improved versions of their papers to a special issue in the Journal of Supercomputing (Springer).


SUPE




Journal of Supercomputing (Springer)

Impact Factor: 1.326, Quartile Q2

ISSN: 0920-8542

 







TOPICS


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.



PAPER SUBMISSION, REGISTRATION, AND PUBLICATION


Submitted papers must not substantially overlap with papers that have been published or that are simultaneously submitted to a journal or a conference with proceedings. Papers must be clearly presented in English and must be formatted according to the "sigconf" style in the ACM 2017 Template. Papers must not exceed 10 pages. This page limit includes figures, tables, and appendices, but does not include references, for which there is no page limit. Margins and font sizes should not be modified.

All papers need to be submitted electronically (in PDF format) through the EasyChair website: https://easychair.org/conferences/?conf=pbio2018.

All submitted papers will be peer-reviewed by PBio's technical program committee. Papers will be selected based on their originality, technical soundness, timeliness, significance, relevance, presentation, and interest to the workshop attendees. Submission of a paper should be regarded as a commitment that, should the paper be accepted, at least one of the authors will register and attend the workshop to present the work. Complete sources must be provided for accepted papers. All accepted papers of registered authors will be included in the PBio 2018 proceedings published by ACM Digital Library within its International Conference Proceedings Series (ICPS). Authors of accepted papers will be required to submit an online ACM Copyright Form. Authors will be contacted by ACM requesting this information. The ISBN number assigned to PBio 2018 proceedings is 978-1-4503-6531-4.


ACM ICPS published



IMPORTANT DATES


Paper Submission Deadline: 1 June 2018 15 June 2018 (extended)
Acceptation Notification: 26 June 2018
Camera-Ready and Registration: 23 July 2018
Workshop at EuroMPI 2018: 23 September 2018



PBIO PROGRAM


The PBio program can be found below, as part of the EuroMPI 2018 program.


Sunday, September 23rd 2018
09:00-10:30 SESSION 1: Multicore and Parallel Optimization in Bioinformatics
Session Chair: Sergio Santander-Jiménez
09:00-09:30 Analysis of Scheduling Policies in Metaheuristics for Evolutionary Biology. Sergio Santander-Jiménez, Miguel A. Vega-Rodríguez and Leonel Sousa
09:30-10:00 Multimethod Optimization for Reverse Engineering of Complex Biological Networks. Patricia González, David R. Penas, Xoan C. Pardo, Julio R. Banga and Ramón Doallo
10:00-10:30 Parallel Computation of Voxelised Protein Surfaces with OpenMP. Sebastian Daberdaku
10:30-11:00 Coffee Break
11:00-13:00 SESSION 2: Hardware Accelerators and Cloud Computing in Bioinformatics
Session Chair: Sergio Santander-Jiménez
11:00-11:30 Speedup and Energy Analysis of EEG Classification for BCI Tasks on CPU-GPU Clusters. Juan José Escobar, Julio Ortega, Antonio Francisco Díaz, Jesús González and Miguel Damas
11:30-12:00 Accelerating a Geometric Approach to Molecular Docking with OpenACC. Emanuele Vitali, Davide Gadioli, Gianluca Palermo, Andrea Beccari and Cristina Silvano
12:00-12:30 FPGA-based OpenCL Accelerator for Discovering Temporal Patterns in Gene Expression Data Using Biclustering. Rui P. Duarte, Álvaro Simões, Rui Henriques and Horácio C. Neto
12:30-13:00 Protein Secondary Structure Analysis in the Cloud. Marco Ferretti and Luigi Santangelo


WORKSHOP ORGANIZERS


Miguel A. Vega-Rodríguez, University of Extremadura, Spain (mavega@unex.es)
Sergio Santander-Jiménez, INESC-ID, IST, University of Lisbon, Portugal (sergio.jimenez@tecnico.ulisboa.pt)
José M. Granado-Criado, University of Extremadura, Spain (granado@unex.es)
Alvaro Rubio-Largo, University Nova of Lisbon, Portugal (alvarorubiolargo@gmail.com)
Rosa M. Badia, Barcelona Supercomputing Center, Spain (rosa.m.badia@bsc.es)



PROGRAM COMMITTEE (in Alphabetical Order)


Antonio Gómez-Iglesias, ORNL (Oak Ridge National Laboratory), USA
Beatriz Paniagua, Kitware, USA
César Gómez-Martín, University of Extremadura, Spain
Francisco Prieto-Castrillo, MIT (Massachusetts Institute of Technology), USA
María Arsuaga-Ríos, CERN, Switzerland
María Botón-Fernández, Institute "Suarez de Figueroa", 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, Galgus, Spain
Wen Zhang, Icahn School of Medicine at Mount Sinai, USA



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