[BiO BB] ACM-BCB 2nd Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio)

Mario Cannataro cannataro at unicz.it
Sat Apr 27 11:52:55 EDT 2013

       I apologize for any cross-posting of this announcement.
                  2nd International Workshop on
  Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio)

       held in conjunction with ACM BCB 2013 - ACM Conference on
    Bioinformatics, Computational Biology and Biomedical Informatics
                        September 22-25, 2013
                         Washington DC, USA

                 DEADLINE: MAY 30, 2013
                        * * * CALL FOR PAPERS * * *

Due to the availability of high-throughput platforms (e.g. next generation
sequencing, microarray and mass spectrometry) and clinical diagnostic
tools (e.g. medical imaging), a recent trend in Bioinformatics and
Biomedicine is the increasing production of experimental and clinical
Considering the complex analysis pipeline of the biomedical research, the
bottleneck is more and more moving toward the storage, integration, and
analysis of experimental data, as well as their correlation and
integration with publicly available data banks.

While Parallel Computing and Grid Computing may offer the computational
power and the storage to face this overwhelming availability of data,
Cloud Computing is a key technology to hide the complexity of computing
infrastructures, to reduce the cost of the data analysis task, and
especially to change the overall model of biomedical research and health

Grid infrastructures may offer the data storage needed to store the huge
experimental and biomedical data, while parallel computing can be used for
basic pre-processing (e.g. parallel BLAST, mpiBLAST) and for more advanced
analysis (e.g. parallel data mining). In such a scenario, novel parallel
architectures (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

On the other hand, these technologies yet require great investments by
biomedical and clinical institutions and are based on a traditional model
where users often need to be aware and face different management problems,
such as hardware and software management, data storage, software
ownership, and not scalable costs (different professional-level
applications in the biomedical domain have high starting costs that
prevent many small laboratories to use them).

The Cloud Computing technology, that is able to offer scalable costs and
increased reachability, availability and easiness of application use, and
also the possibility to enforce collaboration among scientists, is already
changing the business model in different domains and now it starts to be
used also in the bioinformatics (see for instance the recent JCVI Cloud
Bio-Linux initiative) and biomedical domains.  However, many problems
remain to be solved, such as availability and safety of the data,
privacy-related issues, availability of software platforms for rapid
deployment, execution and billing of biomedical applications.

The goal of ParBio is to bring together scientists in the fields of high
performance and cloud computing, computational biology and medicine, to
discuss, among the others, the organization of large scale biological and
biomedical databases, the parallel/service-based implementation of
bioinformatics and biomedical applications, and problems and opportunities
of moving biomedical and health applications on the cloud.

The workshop will focus on research issues, problems and opportunities of
moving biomedical and health applications on the cloud, as well as on the
opportunity to define guidelines and minimum requirements for a Biomedical
Cloud. Moreover, the workshop will discuss about parallel and distributed
management and analysis of molecular and clinical data, that more and more
need to be integrated and analysed in a joint way.

The main themes and research topics will regard the applications of
parallel and high performance computing to biology and medicine, as well
as Cloud Computing opportunities and problems for bioinformatics and
biomedical applications

- Large scale biological and biomedical databases
- Data integration and ontologies in biology and medicine
- Integration and analysis of molecular and clinical data
- Parallel bioinformatics algorithms
- Parallel visualization and exploration of omics and clinical data
- Parallel visualization and analysis of biomedical images
- Computing environments for large scale collaboration
- Scientific workflows in bioinformatics and biomedicine
- Emerging architectures and programming models for bioinformatics and
- Parallel processing of bio-signals
- Modeling and simulation of complex biological processes
- Cloud Computing for bioinformatics and biomedicine
- Cloud Computing for health systems
- Privacy issues for Cloud-based biomedical applications
-  (Web) Services for bioinformatics and biomedicine
- Grid Computing for bioinformatics and biomedicine
- Peer-To-Peer Computing for bioinformatics and biomedicine

The workshop will take place on (To Be Announced).
It is scheduled as full-day.
The program is not available yet.

ParBio 2013 welcomes original submissions that have not been published and
that are not under review by another conference or journal. Papers should
not exceed 10 pages in ACM template on 8.5 x 11 inch paper (see ACM
templates - http://www.acm.org/sigs/publications/proceedings-templates).
All submissions will be evaluated on their originality, technical
soundness, significance, presentation, and interest to the conference
Submission implies the willingness of at least one of the authors to
register and present the work associated with the paper submitted. All
submitted papers will be reviewed by ParBio’s technical program committee.
All accepted papers of registered authors will be included in the workshop
proceedings published by ACM digital libraries. Authors of selected papers
may be invited to adapt their papers for their publication in several
journals. Authors of accepted papers will be required to submit an online
ACM Copyright Form. Authors will be contacted by ACM requesting this
information. Authors should submit papers using the Easy Chair System

Paper submission: May 30, 2013
Notifications sent to authors: July 15, 2013
Camera-ready papers due: August 1, 2013
Conference: September 22-25, 2013

Mario Cannataro, University Magna Græcia of Catanzaro, Italy


1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA
2. David A. Bader, College of Computing, Georgia University of Technology,
3. Ignacio Blanquer; Universidad Politécnica de Valencia, Valencia, Spain
4. Vincent Breton, CNRS/IN2P3, LPC Clermont-Ferrand, France
5. Marian Bubak; AGH Krakow PL and University of Amsterdam NL
6. Rajkumar Buyya, University of Melbourne, Melbourne, Australia
7. Umit Catalyurek, The Ohio State University, USA
8. Tim Clark, Harvard Medical School, USA
9. Giuseppe Di Fatta, University of Reading, UK
10. Werner Dubitzky, University of Ulster, UK
11. Ananth Y. Grama, Purdue University, USA
12. Concettina Guerra, University of Padova, Italy
13. Pietro Hiram Guzzi, University Magna Græcia of Catanzaro, Italy
14. Vicente Hernández, Univ. Politécnica de Valencia, Spain
15. Pilar Herrero, Universidad Politecnica de Madrid, Madrid, Spain
16. Kamer Kaya, The Ohio State University, USA
17. Maria Mirto, University of Salento, Italy
18. Salvatore Orlando, University of Venezia, Italy
19. Maria S. Perez, Universidad Politecnica de Madrid, Madrid, Spain
20. Richard Sinnott, University of Melbourne, Melbourne, Australia
21. Fabrizio Silvestri, ISTI-CNR, Italy
22. Tony Solomonides, University of West of England, Bristol, UK
23. Roberto Tagliaferri, University of Salerno, Italy
24. Paolo Trunfio, University of Calabria, Italy
25. Albert Zomaya, University of Sydney, Australia

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