PBio 2017

5th International Workshop on Parallelism in Bioinformatics

22 August 2017 - Helsinki, Finland
to be held as part of
ICA3PP 2017 (proceedings published by Springer LNCS)

GENERAL SCOPE


This is the 5th edition of this international workshop, the previous editions were organized as part of:


This year we organize the fifth edition of this international workshop as part of the prestigious conference ICA3PP 2017 (proceedings published by Springer LNCS).

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 ISSUES


The authors of the best workshop papers, accepted and presented in PBio 2017, will be invited to submit properly extended and improved versions of their papers to special issues in the Journal of Computational Biology and the International Journal of Parallel Programming.


JCB



Journal of Computational Biology

Impact Factor: 1.537, Quartile Q1

ISSN: 1066-5277







IJPP



International Journal of Parallel Programming

Impact Factor: 0.680, Quartile Q3

ISSN: 0885-7458

 








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, must not exceed 10 pages (extra pages will be charged), including tables, figures, references and appendixes, in Springer LNCS Format with Portable Document Format (.pdf).

All papers need to be submitted electronically through the EasyChair website: https://easychair.org/conferences/?conf=pbio2017.

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. The workshop paper will be involved into the ICA3PP 2017 proceedings published by Springer Lecture Notes in Computer Science (LNCS, EI indexed). Complete sources must be provided for accepted papers. Papers should be typeset using the single column format. Authors of accepted papers will have to sign a Springer copyright form.



IMPORTANT DATES


Paper Submission Deadline: 26 April 2017 10 May 2017 (extended)
Acceptation Notification: 1 June 2017
Camera-Ready and Registration: 15 June 2017
Workshop at ICA3PP 2017: 22 August 2017



PBIO PROGRAM


The PBio program can be found below, as part of the ICA3PP 2017 program.


Tuesday, August 22nd 2017
10:05-11:50 SESSION 1: Multicore and cluster computing in Bioinformatics
Session Chair: José M. Granado-Criado
10:05-10:30 A Resource Manager for Maximizing the Performance of Bioinformatics Workflows in Shared Clusters. Ferran Badosa, Cesar Acevedo, Antonio Espinosa, Gonzalo Vera and Ana Ripoll
10:30-10:55 Massively Parallel Sequence Alignment with BLAST through Work Distribution Implemented using PCJ Library. Marek Nowicki, Davit Bzhalava and Piotr Bala
10:55-11:20 On the Use of Binary Trees for DNA Hydroxymethylation Analysis. César González, Mariano Pérez, Juan M. Orduña, Javier Chaves and Ana-Bárbara García
11:20-11:45 Parallel Multi-Objective Optimization for High-Order Epistasis Detection. Daniel Gallego-Sánchez, José M. Granado-Criado, Sergio Santander-Jiménez, Álvaro Rubio-Largo and Miguel A. Vega-Rodríguez
11:50-13:10 Lunch
13:10-15:00 SESSION 2: Hardware accelerators in Bioinformatics
Session Chair: José M. Granado-Criado
13:10-13:35 Configuring Concurrent Computation of Phylogenetic Partial Likelihoods: Accelerating Analyses using the BEAGLE Library. Daniel L. Ayres and Michael P. Cummings
13:35-14:00 Accelerating FaST-LMM for Epistasis Tests. Héctor Martínez, Sergio Barrachina, Maribel Castillo, Enrique S. Quintana-Ortí, Jordi Rambla De Argila, Xavier Farré and Arcadi Navarro
14:00-14:25 Pipelined Multi-FPGA Genomic Data Clustering. Rick Wertenbroek, Enrico Petraglio and Yann Thoma
14:25-14:50 First Experiences Accelerating Smith-Waterman on Intel's Knights Landing Processor. Enzo Rucci, Carlos Garcia, Guillermo Botella, Armando De Giusti, Marcelo Naiouf and Manuel Prieto-Matias
15:00-15:20 Afternoon Coffee
15:20-17:00 SESSION 3: Heterogeneous and distributed computing in Bioinformatics
Session Chair: José M. Granado-Criado
15:20-15:45 Power-performance Evaluation of Parallel Multi-objective EEG Feature Selection on CPU-GPU Platforms. Juan José Escobar, Julio Ortega, Antonio Francisco Díaz, Jesús González and Miguel Damas
15:45-16:10 Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks. Andreia Sofia Teixeira, Pedro T. Monteiro, João A. Carriço, Francisco C. Santos and Alexandre P. Francisco
16:10-16:35 PPCAS: Implementation of a Probabilistic Pairwise Model for Consistency-based Multiple Alignment in Apache Spark. Jordi Lladós, Fernando Guirado and Fernando Cores
16:35-17:00 Accelerating Exhaustive Pairwise Metagenomic Comparisons. Esteban Pérez-Wohlfeil, Oscar Torreno and Oswaldo Trelles


WORKSHOP ORGANIZERS


Miguel A. Vega-Rodríguez, University of Extremadura, Spain (mavega@unex.es)
José M. Granado-Criado, University of Extremadura, Spain (granado@unex.es)
Alvaro Rubio-Largo, University Nova of Lisbon, Portugal (arl@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
Beatriz Paniagua, Kitware, USA
César Gómez-Martín, University of Extremadura, Spain
David L. González-Álvarez, 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, AOIFES, Spain



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