In Bioinformatics, we can find a variety of problems which are affected by huge processing times and memory 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 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 MPI-based approaches, but we welcome any technique based on: multicore and cluster computing, supercomputing, grid computing, cloud computing, hardware accelerators as GPUs, FPGAs, or Cell processors, etc.
JOURNAL SPECIAL ISSUE
The authors of the best workshop papers, accepted and presented in PBio 2013, were invited to submit extended and improved versions of their papers to a special issue in the journal Parallel Computing (Elsevier). This special issue can be found here.
Parallel Computing (Elsevier)
Impact Factor: 1.890, Quartile Q1
Parallel Computing is an international journal presenting the practical use of parallel computer systems, including high performance architecture, system software, programming systems and tools, and applications. Within this context the journal covers all aspects of high-end parallel computing.
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:
- MPI implementations in Bioinformatics.
- Parallel and distributed algorithms in Bioinformatics.
- Workload partitioning strategies in Bioinformatics.
- Memory-efficient algorithms in Bioinformatics.
- Parallel tools and applications in Bioinformatics.
- Multicore and cluster computing in Bioinformatics.
- Supercomputing in Bioinformatics.
- Grid/Cloud/P2P computing in Bioinformatics.
- Volunteer computing in Bioinformatics.
- Hardware accelerators (GPUs, FPGAs, Cell processors, etc.) in Bioinformatics.
With regard to the Bioinformatics problems, many different alternatives exist: 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.
PAPER SUBMISSION, REGISTRATION, AND PUBLICATION
PBio 2013 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 6 pages in English. The paper must be formatted according to double-column ACM ICPS proceedings style. 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.acm.org/publications/icps-instructions/. All submissions will be evaluated on their originality, technical soundness, significance, presentation, and interest to the workshop attendees.
Submission implies the willingness of at least one of the authors to register (please, see EuroMPI registration) and present the work associated with the paper submitted. 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 ACM Digital Library. Authors of accepted papers will be required to submit an online ACM Copyright Form. Authors will be contacted by ACM requesting this information. Papers shall be submitted electronically via EasyChair, see http://www.easychair.org/conferences/?conf=eurompi2013, please select Track "International Workshop on Parallelism in Bioinformatics".
March 29th, 2013 April 12th, 2013 (extended)
Acceptation Notification: May 11th, 2013
Camera-Ready Submission: June 15th, 2013
Workshop at EuroMPI 2013: September 17th, 2013
Miguel A. Vega-Rodríguez, University of Extremadura, Spain (email@example.com)
David L. González-Alvarez, University of Extremadura, Spain (firstname.lastname@example.org)
Sergio Santander-Jiménez, University of Extremadura, Spain (email@example.com)
Jose M. Chaves-González, University of Extremadura, Spain (firstname.lastname@example.org)
Antonio Gómez-Iglesias, CSIRO - Commonwealth Scientific & Industrial Research Organisation, Australia
María Arsuaga-Ríos, CERN, Switzerland
Sónia M. Almeida-Luz, Polytechnic Institute of Leiria, Portugal
Miguel Cárdenas-Montes, CIEMAT, Spain
José M. Granado-Criado, University of Extremadura, Spain
Francisco Prieto-Castrillo, CETA-CIEMAT, Spain
Marisa da Silva Maximiano, Polytechnic Institute of Leiria, Portugal
Álvaro Rubio-Largo, University of Extremadura, Spain
María Botón-Fernández, CETA-CIEMAT, Spain
Víctor Berrocal-Plaza, University of Extremadura, Spain
Alejandro Hidalgo-Paniagua, University of Extremadura, Spain
José M. Lanza-Gutiérrez, University of Extremadura, Spain