1st International Workshop on
Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio)



held in conjunction with ACM Conference on
Bioinformatics, Computational Biology and Biomedicine (ACM-BCB)

 October 7-10, 2012
Orlando, Florida, USA






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 data.

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 provision.


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 data.


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 biomedicine

-           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 2012 welcomes original submissions that have not been published and that are not under review by another conference or journal.  Papers should not exceed 8 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 attendees.

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 (https://www.easychair.org/conferences/?conf=parbio2012).




Paper submission: DEADLINE EXTENDED TO JULY 18, 2012

Notifications sent to authors: August 8, 2012

Camera-ready papers due: August 16, 2012

Conference: October 7-10, 2012



Mario Cannataro, University Magna Gr�cia of Catanzaro, Italy



  1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA
  2. David A. Bader, College of Computing, Georgia University of Technology, USA
  3. Ignacio Blanquer; Universidad Polit�cnica 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. Tim Clark, Harvard Medical School, USA
  8. Giuseppe Di Fatta, University of Reading, UK
  9. Werner Dubitzky, University of Ulster, UK
  10. Ananth Y. Grama, Purdue University, USA
  11. Concettina Guerra, University of Padova, Italy
  12. Pietro Hiram Guzzi, University Magna Gr�cia of Catanzaro, Italy
  13. Vicente Hern�ndez, Univ. Polit�cnica de Valencia, Spain
  14. Pilar Herrero, Universidad Politecnica de Madrid, Madrid, Spain
  15. Maria Mirto, University of Salento, Italy
  16. Salvatore Orlando, University of Venezia, Italy
  17. Maria S. Perez, Universidad Politecnica de Madrid, Madrid, Spain
  18. Richard Sinnott, University of Melbourne, Melbourne, Australia
  19. Fabrizio Silvestri, ISTI-CNR, Italy
  20. Tony Solomonides, University of West of England, Bristol, UK
  21. Roberto Tagliaferri, University of Salerno, Italy
  22. Paolo Trunfio, University of Calabria, Italy
  23. Albert Zomaya, University of Sydney, Australia