2nd International Workshop on
High Performance Bioinformatics and Biomedicine (HiBB)
August 30th, 2011, Bordeaux, France
held in conjunction with
August 30th - September 2nd, 2011
DEADLINE EXTENDED: papers due by July 10, 2011
CALL FOR PAPERS
High-throughput technologies (e.g. microarray and mass spectrometry) and clinical diagnostic tools (e.g. medical imaging) are producing an increasing amount of experimental and clinical data. In such a scenario, large scale databases and bioinformatics tools are key tools for organizing and exploring biological and biomedical data with the aim to discover new knowledge in biology and medicine.
High-performance computing may play an important role in many phases of life sciences research, from raw data management and processing, to data analysis and integration, till data exploration and visualization. In particular, at the raw data layer, Grid infrastructures may offer the huge data storage needed to store experimental and biomedical data, while parallel computing can be used for basic pre-processing (e.g. parallel BLAST) and for more advanced analysis (e.g. parallel data mining). In such a scenario, novel parallel architectures (e.g. e.g. CELL processors, GPUs, FPGA, hybrid CPU/FPGA) coupled with emerging programming models may overcome the limits posed by conventional computers to the mining and exploration of large amounts of data.
At an higher layer, emerging biomedical applications need to use in a coordinated way both bioinformatics tools, biological data banks and patient’s clinical data, that require seamless integration, privacy preservation and controlled sharing. Service Oriented Architectures and semantic technologies, such as ontologies, may allow the building and deployment of the so called “collaboratories”, where experimental research may be conducted by remote scientists in a collaborative way.
The goal of HiBB is to bring together scientists in the fields of high performance computing, computational biology and medicine to discuss, among the others, the organization of large scale biological and biomedical databases and the parallel implementation of bioinformatics algorithms and biomedical applications. Furthermore, the use of novel parallel architectures and dedicated hardware to implement bioinformatics and biomedical algorithms will be discussed.
TOPICS OF INTEREST
The workshop is seeking original research papers presenting applications of parallel and high performance computing to biology and medicine. Topics of interest include, but are not limited to:
- Large scale biological and biomedical databases
- Data integration and ontologies in biology and medicine
- Parallel bioinformatics algorithms
- Parallel visualization and exploration of biomedical data
- Parallel visualization and analysis of biomedical images
- Computing environments for large scale collaboration
- Scientific workflows in bioinformatics and biomedicine
- (Web) Services for bioinformatics and biomedicine
- Grid Computing for bioinformatics and biomedicine
- Peer-To-Peer Computing for bioinformatics and biomedicine
- Emerging architectures and programming models (e.g. Cell, GPUs) for bioinformatics and biomedicine
- Parallel processing of bio-signals
- Modeling and simulation of complex biological processes
AUGUST 30, 2011
SESSION I - Bioinformatics and Systems Biology
09:30-09:40 Opening remarks - Mario Cannataro, University of Catanzaro, Italy
9:40-10:20 On Parallelizing On-Line Statistics for Stochastic
Biological Simulations, Marco Aldinucci, Mario Coppo, Ferruccio
Damiani, Maurizio Drocco, Eva Sciacca, Salvatore Spinella, Massimo
Torquati and Angelo Troina, Department of Computer Science, University
of Torino and Department of Computer Science, University of Pisa,
10:20-11:00 Scalable Sequence Similarity Search and Join in Main
Memory on Multi-Cores, Astrid Rheinländer and Ulf Leser, Department of
Computer Science, Humboldt-Universitat Berlin, Germany
11:00-11:30 -- Break --
SESSION 2 - Software Platforms for High Performance Bioinformatics
11:30-12:10 Enabling Data and Compute Intensive Workflows in
Bioinformatics, Gaurang Mehta, Ewa Deelman, James Knowles, Ting Chen,
Ying Wang, Jens Vöckler, Steven Buyske and Tara Matise,
USC Information Sciences Institute, Keck School of Medicine of USC,
University of Southern California, and Rutgers University, USA.
12:10-12:50 Homogenizing Access to Highly-Consuming Biomedical
Applications throughout a Web-Based Interface, Luigi Grasso, Nuria
Medina Medina, Rosana Montes and María Del Mar Abad Grau, Dept.
Lenguajes y Sistemas Informaticos - CITIC, Universidad de Granada,
12:50-13:00 Discussion and comments
13:00-14:30 -- Lunch --
SESSION 3 - Tutorial
14:30-15:45 Tutorial on Distributed Management and Analysis of Omics
Data, Mario Cannataro, University of Catanzaro, Italy
15:45-16:00 Closing remarks and discussion, Mario Cannataro,
University of Catanzaro, Italy
PAPER SUBMISSION, REGISTRATION AND PUBLICATION
We invite original previously unpublished contributions. Submission implies that at least one author will register for the workshops at Euro-Par 2011 and present the paper in the workshop session, if accepted.
Full papers should not exceed 10 pages in the Springer LNCS style.
Paper submission has to be performed by using the HiBB EasyChair submission server.
In case of problems, authors may send their manuscript in PDF to the workshop chair: cannataro AT unicz.it.
Papers accepted for publication must also be supplied in source form (Latex or Word).
All accepted and presented papers will be included in the Workshops proceedings, that will be published in a separate Springer LNCS Euro-Par 2010 Workshop volume after the conference. Deadline for submitting camera
Authors of accepted papers will be required to sign up a Springer copyright form.
JOURNAL SPECIAL ISSUE
At the end of the workshop, we plan to invite the best 4-6 papers of the workshop for a special section on an international journal.
Full papers submission: July 10, 2011 (Deadline Extended)
Decision Notification: July 15, 2011
Final papers due: August 5, 2011
Workshop session: August 30, 2011
Final review comments: October 1, 2011
Camera ready papers for EuroPar Workshop Proceedings: October 15, 2011
Mario Cannataro, University Magna Grćcia of Catanzaro, Italy
PROGRAM COMMITTEE (TO BE CONFIRMED)
- Pratul K. Agarwal, Oak Ridge National Laboratory, USA
- David A. Bader, College of Computing, Georgia University of Technology, USA
- Ignacio Blanquer; Universidad Politécnica de Valencia, Valencia, Spain
- Daniela Calvetti, Case Western Reserve University, USA
- Werner Dubitzky, University of Ulster, UK
- Ananth Y. Grama, Purdue University, USA
- Concettina Guerra, University of Padova, Italy
- Vicente Hernández, Univ. Politécnica de Valencia, Spain
- Salvatore Orlando, University of Venezia, Italy
- Omer F. Rana, Cardiff University, UK
- Richard Sinnott; National e-Science Centre, University of Glasgow, Glasgow, United Kingdom
- Fabrizio Silvestri, ISTI-CNR, Italy
- Erkki Somersalo, Case Western Reserve University, USA
- Paolo Trunfio, University of Calabria, Italy
- Albert Zomaya, University of Sydney, Australia