PBio 2014

Second International Workshop on Parallelism in Bioinformatics

September 26, 2014 - Madrid, Spain
to be held as part of
IEEE Cluster 2014 (proceedings published by IEEE)



Due to the success of the previous edition of the workshop (see PBio 2013, as part of ACM EuroMPI 2013, and the special issue in the journal Parallel Computing), this year we organize the second edition of this international workshop as part of the prestigious conference IEEE Cluster 2014 (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 cluster-based approaches, but we welcome any technique based on: multicore 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 2014, will be invited to submit properly extended and improved versions of their papers to a special issue in the journal Concurrency and Computation: Practice and Experience (Wiley). This special issue can be found here.


Concurrency and Computation: Practice and Experience (Wiley)

Impact Factor: 0.845, Quartile Q2

ISSN: 1532-0626



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:

  • Cluster computing in Bioinformatics.
  • Data-intensive Bioinformatics (including Big Data storage and processing).
  • Parallel and distributed algorithms in Bioinformatics.
  • Workload partitioning strategies in Bioinformatics.
  • Memory-efficient algorithms in Bioinformatics.
  • Parallel tools and applications in Bioinformatics.
  • Multicore computing in Bioinformatics.
  • Supercomputing in Bioinformatics.
  • Cloud/Grid/P2P computing in Bioinformatics.
  • Volunteer computing in Bioinformatics.
  • Hardware accelerators (GPUs, FPGAs, etc.) in Bioinformatics.
  • Green 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; 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 DNA computing; etc.


PBio 2014 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 not exceeding 9 pages in English. The paper must be formatted according to the IEEE Xplore format for publication. The usage of LaTeX for preparation of the contribution as well as the submission in camera ready format is strongly recommended. Style files can be found at http://www.ieee.org/conferences_events/conferences/publishing/templates.html. All submissions will be evaluated on their originality, technical soundness, significance, presentation, and interest to the workshop attendees. Papers shall be submitted electronically via EasyChair, see https://www.easychair.org/conferences/?conf=pbio2014.

Submission implies the willingness of at least one of the authors to register and present the work associated with the paper submitted. The author of a paper in the PBio workshop has two alternatives: s/he can make a full registration (with access to the whole IEEE Cluster conference and gala dinner) or only workshop registration (very economical, but without the previous coverage). Please, see IEEE Cluster registration for all the details.

All submitted papers will be reviewed by PBio's technical program committee. All accepted papers of registered authors will be included in the workshop proceedings published by IEEE. Authors of accepted papers will be required to submit the IEEE Copyright Form.


Submission Deadline: May 15th, 2014 May 31st, 2014 (extended)
Acceptation Notification: June 30th, 2014
Camera-Ready Submission: July 25th, 2014
Workshop at IEEE Cluster 2014: September 26th, 2014


The PBio program can be found below, as part of the IEEE Cluster 2014 program.

Friday, September 26th 2014
09:30-11:00 SESSION 1: Cluster computing and optimization in Bioinformatics
Chair: Sergio Santander-Jiménez
09:30-09:50 Predicting Protein-Protein Interactions based on Rotation of Proteins in 3D-Space. Samaneh Aghajanbaglo, Sobhan Moosavi, Maseud Rahgozar and Amir Rahimi
09:50-10:10 A Hybrid OpenMP and OpenMPI Approach to Geometrical Motif Search in Proteins. Marco Ferretti, Mirto Musci and Luigi Santangelo
10:10-10:30 Applying OpenMP-based Parallel Implementations of NSGA-II and SPEA2 to Study Phylogenetic Relationships. Sergio Santander-Jiménez and Miguel A. Vega-Rodríguez
10:30-10:50 Feature Selection in High-Dimensional EEG Data by Parallel Multi-objective Optimization. Dragi Kimovski, Julio Ortega, Andrés Ortiz and Raúl Baños
11:00-11:30 Coffee Break
11:30-13:00 SESSION 2: Hardware accelerators in Bioinformatics
Chair: Sergio Santander-Jiménez
11:30-11:50 Smith-Waterman Algorithm on Heterogeneous System: A Case Study. Enzo Rucci, A. de Giusti, M. Naiouf, G. Botella, C. García and M. Prieto-Matias
11:50-12:10 High-Performance X-Ray Tomography Reconstruction Algorithm based on Heterogeneous Accelerated Computing Systems. Estefania Serrano, Guzman Bermejo, Javier Garcia Blas and Jesus Carretero
12:10-12:30 Anisotropic Nonlinear Diffusion for Filtering 3D Images in Structural Biology on GPUs. Siham Tabik and L. Felipe Romero
12:30-12:50 Multi-GPU Acceleration of DARTEL (Early Detection of Alzheimer). Pedro Valero-Lara
13:00-14:30 Lunch Break
14:30-16:00 SESSION 3: Big data and scalable computing in Bioinformatics
Chair: Sergio Santander-Jiménez
14:30-14:50 Job Scheduling in Hadoop with Shared Input Policy and RAMDISK. Aprigio Bezerra, Porfídio Hernández, Antonio Espinosa and Juan Carlos Moure
14:50-15:10 Support for Bioinformatics Applications through Volunteer and Scalable Computing Frameworks. Felipe Gutierrez, Danilo Azevedo, Marcos Barreto and Rodrigo Zucoloto
15:10-15:30 Evaluating Grasp-based Cloud Dimensioning for Comparative Genomics: a Practical Approach. Rafaelli Coutinho, Lúcia Drummond, Yuri Frota, Daniel de Oliveira and Kary Ocaña
15:30-15:50 A Scalable Framework for Large-Scale Analysis of Gene-Gene Interactions. Moez Ben Haj Hmida and Yahya Slimani
16:00-16:30 Coffee Break


Miguel A. Vega-Rodriguez, University of Extremadura, Spain (mavega@unex.es)
Sergio Santander-Jimenez, University of Extremadura, Spain (sesaji@unex.es)
David L. Gonzalez-Alvarez, University of Extremadura, Spain (dlga@unex.es)
Jose M. Chaves-Gonzalez, University of Extremadura, Spain (jm@unex.es)


Antonio Gomez-Iglesias, CSIRO - Commonwealth Scientific & Industrial Research Organisation, Australia

Maria Arsuaga-Rios, CERN, Switzerland

Sonia M. Almeida-Luz, Polytechnic Institute of Leiria, Portugal

Francisco Prieto-Castrillo, NECSI (New England Complex Systems Institute), Cambridge, MA, USA

Miguel Cardenas-Montes, CIEMAT, Spain

Jose M. Granado-Criado, University of Extremadura, Spain

Marisa da Silva Maximiano, Polytechnic Institute of Leiria, Portugal

Alvaro Rubio-Largo, University of Extremadura, Spain

Maria Boton-Fernandez, CETA-CIEMAT, Spain

Victor Berrocal-Plaza, University of Extremadura, Spain

Alejandro Hidalgo-Paniagua, University of Extremadura, Spain

Jose M. Lanza-Gutierrez, University of Extremadura, Spain