PBio 2016
 

PBio 2016

4th International Workshop on Parallelism in Bioinformatics

August 23, 2016 - Grenoble, France
to be held as part of
Euro-Par 2016 (proceedings published by Springer LNCS)

 
 

GENERAL SCOPE


This is the 4th edition of this international workshop, the previous editions were organized as part of:


This year we organize the fourth edition of this international workshop as part of the prestigious conference Euro-Par 2016 (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 ISSUE


The authors of the best workshop papers, accepted and presented in PBio 2016, will be invited to submit properly extended and improved versions of their papers to a special issue in the journal Cluster Computing (Springer).


CLUS



Cluster Computing (Springer)

Impact Factor: 1.510, Quartile Q1

ISSN: 1386-7857

 





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


PBio 2016 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 should be written in English. Submissions in PDF format should not exceed 12 pages in the Springer LNCS style, which can be downloaded from the Springer Web site. The 12 pages limit is a hard limit. It includes everything (text, figures, references) and will be strictly enforced by the submission system. Complete LaTeX sources must be provided for accepted papers. Papers should be typeset using the single column format.

All submitted papers will be peer-reviewed by PBio's technical program committee. 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=europar2016ws, please select Track "Parallelism in Bioinformatics (PBio)".

Accepted and presented papers will be included into the workshop proceedings, published by Springer in the ARCoSS/LNCS series. Authors of accepted papers will have to sign a Springer copyright form.

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.



IMPORTANT DATES


Paper Submission Deadline: May 6th, 2016 May 20th, 2016 (extended)
Acceptation Notification: June 17th, 2016
Camera-Ready Submission: July 22nd, 2016
Workshop at Euro-Par 2016: August 23rd, 2016



PBIO PROGRAM


The PBio program can be found below, as part of the Euro-Par 2016 program.


Tuesday, August 23rd 2016
8:30-10:30 SESSION 1: Multithreaded computing in Bioinformatics
Session Chair: Sergio Santander-Jiménez
8:30-9:00 Performance Analysis and Optimization of SAMtools Sorting. Nathan T. Weeks and Glenn R. Luecke
9:00-9:30 Optimized Execution Strategies for Sequence Aligners on NUMA Architectures. Josefina Lenis and Miquel Angel Senar
9:30-10:00 High Performance Small RNA Detection with Pipelined Task Parallel Computation Model. Linqiang Ouyang and Jin H. Park
10:00-10:30 Improving Multiobjective Phylogenetic Searches by Using a Parallel Epsilon-Dominance Based Adaptation of the Firefly Algorithm. Sergio Santander-Jiménez and Miguel A. Vega-Rodríguez
10:30-11:00 Break
11:00-12:30 SESSION 2: Cluster computing in Bioinformatics
Session Chair: Sergio Santander-Jiménez
11:00-11:30 Seamless HPC Integration of Data-intensive KNIME Workflows via UNICORE. Richard Grunzke, Florian Jug, Bernd Schuller, René Jäkel, Eugene Myers and Wolfgang E. Nagel
11:30-12:00 Improving Bioinformatics Analysis of Large Sequence Datasets Parallelizing Tools for Population Genomics. Javier Navarro, Gonzalo Vera, Sebastián Ramos-Onsins and Porfidio Hernández
12:00-12:30 A Framework for Accessible Cluster-enabled Epistatic Analysis. Alex Upton, Johan Karlsson and Oswaldo Trelles
12:30-14:00 Lunch
14:00-16:00 SESSION 3: Heterogeneous computing in Bioinformatics
Session Chair: Sergio Santander-Jiménez
14:00-14:30 Improving Memory Accesses for Heterogeneous Parallel Multi-objective Feature Selection on EEG Classification. Juan José Escobar, Julio Ortega, Jesús González and Miguel Damas
14:30-15:00 Architecture for the Execution of Tasks in Apache Spark in Heterogeneous Environments. Estefanía Serrano, Javier Garcia Blas, Jesus Carretero and Monica Abella
15:00-15:30 Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs. Daniel Jünger, Christian Hundt, Jorge González-Domínguez and Bertil Schmidt
15:30-16:00 A Data Partitioning Model for Highly Heterogeneous Systems. Siham Tabik, Gloria Ortega, Ester M. Garzón and D. Suárez
16:00-16:30 Break
16:30-17:30 SESSION 4: Multi-level parallelism in Bioinformatics
Session Chair: Sergio Santander-Jiménez
16:30-17:00 Two-level Parallelism to Accelerate Multiple Genome Comparisons. Óscar Torreño Tirado and Oswaldo Trelles
17:00-17:30 Evaluation of Parallel Differential Evolution Implementations on MapReduce and Spark. Diego Teijeiro, Xoan C. Pardo, David R. Penas, Patricia Gonzalez, Julio R. Banga and Ramón Doallo


WORKSHOP ORGANIZERS


Miguel A. Vega-Rodríguez, University of Extremadura, Spain (mavega@unex.es)
Sergio Santander-Jiménez, University of Extremadura, Spain (sesaji@unex.es)
Alvaro Rubio-Largo, University Nova of Lisbon, Portugal (arl@unex.es)



PROGRAM COMMITTEE (in Alphabetical Order)


Antonio Gómez-Iglesias, Texas Advanced Computing Center, 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

José M. Granado-Criado, 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



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