Workshop 17-BILIS

International Workshop on High Performance Computing Systems

for Bioinformatics and Life Sciences

(BILIS 2012)


As part of

The International Conference on High Performance Computing & Simulation (HPCS 2012) or

July 2 – July 6, 2012

Madrid, Spain

Extended Submission Deadline: March 14, 2012


Incorporating new advancements of Information Technology (IT) in general and High Performance Computing (HPC) in particular in the domain of Life Sciences and Biomedical Research continues to receive tremendous attention of researchers, biomedical institutions and the rest of the biomedical community. Although medical instruments have benefited a great deal from the technological advances of the couple of decades, the impact of integrating IT advancements in addressing critical problems in biomedical research remains limited and the process of penetrating IT tools in the medical profession continues to be a very challenging problem. For example, the use of electronic medical records and Hospital Information Systems in improving health care remains fragmented. Similarly, the use of advanced computational tools seamlessly in the biomedical research cycle continues to be minimal.

Due to the computational intensive problems in life sciences, the marriage between the Bioinformatics domain and high performance computing is critical to the advancement of Biosciences. In addition, the problems in this domain tend to be highly parallelizable and deal with large datasets, hence using HPC is a natural fit. The Bioinformatics domain is rich in applications that require extracting useful information from very large and continuously growing sequence of databases. Most methods used for analyzing DNA/Protein sequences are known to be computationally intensive, providing motivation for the use of powerful computational systems with high throughput characteristics.

In the current Information age, further progress of Medical Sciences requires successful integration with Computational and Information Sciences. The workshop attempts to attract innovative ways of how such integration can be achieved via Bioinformatics and Biomedical Informatics research, particularly in taking advantage of the new advancements in HPC systems. The focus of data analysis and data mining tools in biomedical research highlights the current state of research in the key biomedical research areas such as bioinformatics, medical informatics and biomedical imaging. Addressing performance concerns in managing and accessing medical data, while facilitating the ability to integrate and correlate different biomedical databases remains an outstanding problem in biomedical research. The amount of available biomedical data continues to grow in an exponential rate; however, the impact of utilizing such resources remains minimal. The development of innovative tools in HPC environments to integrate, analyze and mine such data sources is a key step towards achieving large impact levels.

The workshop focuses on topics related to the utilization of HPC systems and new models of parallel computations in problems related to Biomedical Informatics, along with the use of data integration and data mining tools to support biomedical research and Health Care.

The Workshop topics include (but are not limited to) the following:

    • HPC for the Analysis of Biological Data

    • Bioinformatics Tools for Health Care

    • Parallel Algorithms for Bioinformatics Applications

    • Algorithms and Tools for Biomedical Imaging and Medical Signal Processing

    • Energy Aware Scheduling Techniques for Large Scale Biomedical Applications

    • HPC for analyzing Biological Networks

    • Next Generation Sequencing and Advanced Tools for DNA Assembly

    • HPC for Gene, Protein/RNA Analysis and Structure Prediction

    • Identification of Biomarkers

    • Biomedical Visualization Tools

    • Efficient Clustering and Classification Algorithms

    • Correlation Networks in Biomedical Research

    • Data Mining Techniques in Biomedical Applications

    • Heterogeneous Data Integration

    • HPC systems for Ontology and Database Integration

    • Pattern Recognition and Search Tools in Biological and Clinical Databases

    • Ubiquitous Medical Knowledge Discovery and Exchange

    • HPC for Monitoring and Treatment Facilities

    • Drug Design and Modeling

    • Computer Assisted Surgery and Medical Procedures

    • Remote Patient Monitoring, Homecare Applications

    • Mobile and Wireless Healthcare and Biomedical Applications


You are invited to submit original and unpublished research works on above and other topics related to HPC for Bioinformatics, Healthcare and Life Sciences. Submitted papers must not have been published or simultaneously submitted elsewhere. Submission should include a cover page with authors' names, affiliation addresses, fax numbers, phone numbers, and authors email addresses. Please, indicate clearly the corresponding author and include up to 6 keywords from the above list of topics and an abstract of no more than 400 words. The full manuscript should be at most 7 pages using the two-column IEEE format. Additional pages will be charged additional fee. Please include page numbers on all preliminary submissions to make it easier for reviewers to provide helpful comments.

Submit a PDF copy of your full manuscript via email to the Workshop organizer at

Only PDF files will be accepted. Each paper will receive a minimum of three reviews. Papers will be selected based on their originality, contributions, relevance, technical clarity and presentation. Authors of accepted papers must guarantee that their papers will be registered and presented at the workshop. Accepted papers will be published in the conference proceedings which will be made available at the time of the meeting.

If you have any questions about paper submission or the workshop, please contact the organizer.


Extended Paper Submissions: ------------------------- March 14, 2012

Acceptance Notification: ----------------------------- March 27, 2012

Camera Ready Papers and Registration Due: ------------- April 25, 2012

Conference Dates: ---------------------------------- July 2 – 6, 2012


Prof. Hesham H. Ali

Department of Computer Science

College of Information Science and Technology

University of Nebraska at Omaha

Omaha, NE 68182 USA

Phone: +1 (402) 554-3623

Fax: +1 (402) 554-3284


International Program Committee:

All submitted papers will be rigorously reviewed by the workshop technical program committee members following similar criteria used in HPCS 2012.

    • Dhundy Bastola, UNO Bioinformatics Core Facility, University of Nebraska - Omaha, Nebraska, USA

    • Sanjukta Bhomwick, University of Nebraska - Omaha, Nebraska, USA

    • Young-Rae Cho, Dept of Computer Science, Baylor University, Texas, USA

    • Alexander Churbanov, Nebraska Center of Virology, University of Nebraska-Lincoln, Nebraska, USA

    • Kathryn Dempsey, University of Nebraska Medical Center (UNMC), Omaha, Nebraska, USA

    • Xutao Deng, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA

    • Huimin Geng, Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA

    • Pietro Hiram Guzzi, School of Computer Science and Biomedical Engineering, University of Catanzaro, Italy

    • Mahantesh Halappanavar, Pacific Northwest National Lab, Richland, Washington, USA

    • Ying Liu, School of Information Science and Engineering, Graduate University of Chinese Academy of Sciences, Beijing, China

    • Jason Rafe Miller, J. Craig Venter Institute (JCVI), Rockville, Maryland, USA

    • Daniel Quest, Oak Ridge National laboratory, Knoxville, Tennessee, USA

For information or questions about Conference's paper submission, tutorials, posters, workshops, special sessions, exhibits, demos, panels and forums organization, doctoral colloquium, and any other information about the conference location, registration, paper formatting, etc., please consult the Conference’s web site at or contact one of the Conference's organizers.

If you have any questions about the HPCS 2012 conference paper submission, please contact Conference Program Chair: Waleed W. Smari, Voice: +1 (937) 681-0098, Email: