Workshop 16-BILIS

International Workshop on High Performance Computing Systems

for Bioinformatics and Life Sciences

(BILIS 2015)


As part of

The International Conference on High Performance Computing & Simulation (HPCS 2014) or

July 20 – July 24, 2015

The Hilton Amsterdam Hotel

Amsterdam, The Netherlands

Extended Submission Deadline: April 24, 2015

Submissions could be for full papers, short papers, poster papers, or posters


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.

Moreover, high-throughput wet lab platforms such as next generation sequencing, microarray and mass spectrometry, are producing a huge amount of experimental "omics" data. The increasing availability of omics data poses new challenges to bioinformatics applications that need to face in a semi-automatic way an overwhelming availability of raw data. Main challenges regard: 1) the efficient storage, retrieval and integration of experimental data; 2) their efficient and high-throughput preprocessing and analysis; 3) the building of reproducible "in silico" experiments; 4) the integration of analysis results with pre-existing knowledge usually stored into ontologies.

As the storage, preprocessing and analysis of raw experimental data is becoming the main bottleneck of the analysis pipeline, parallel computing is playing an important role in all steps of the life sciences research pipeline, from raw data management and processing, to data integration and analysis, and to data exploration and visualization. Moreover, Cloud Computing is becoming the key technology to hide the complexity of computing infrastructures, to reduce the cost of the data analysis task, and especially to change the overall business model of biomedical research and health provision.

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 In such a scenario, large-scale distributed databases and parallel bioinformatics tools are key tools for organizing and exploring biological and biomedical data with the aim to discover new knowledge in biology and medicine.

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 computing and cloud computing 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 BILIS 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

  • Ontologies in Biology and Medicine

  • Integration and Analysis of Molecular and Clinical Data

  • Parallel Bioinformatics Algorithms

  • 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

  • Cloud Computing for Bioinformatics, Medicine, and Health Systems


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. For Regular papers, please submit a PDF copy of your full manuscript, not to exceed 8 double-column IEEE formatted pages, and include up to 6 keywords and an abstract of no more than 400 words. Additional pages will be charged additional fee. Submission should include a cover page with authors' names, affiliation addresses, fax numbers, phone numbers, and all authors email addresses. Please, indicate clearly the corresponding author(s). Short papers (up to 4 pages), poster papers and poster (please refer to for posters submission details) will also be accepted. Please specify the type of submission you have. 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 to the symposium paper submission site at Acknowledgement will be sent within 48 hours of submission. If the submission is for a poster paper or short paper, indicate that as well on the manuscript and in the form's Notes field.

Only PDF files will be accepted, uploaded to the workshop submission link above. Each paper will receive a minimum of three reviews. Papers will be selected based on their originality, relevance, significance, technical clarity and presentation. Submission implies the willingness of at least one of the authors to register and present the paper, if accepted. At least one of the authors of each accepted paper will have to register and attend the HPCS 2015 conference to present the paper at the workshop.


Accepted papers will be published in the Conference proceedings. Instructions for final manuscript format and requirements will be posted on the HPCS 2015 Conference web site. It is our intent to have the proceedings formally published in hard and soft copies and be available at the time of the conference. The proceedings is projected to be included in the IEEE Digital Library and indexed in all major indexing services accordingly.

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


Extended Paper Submissions: ---------------------------- April 24, 2015

Acceptance Notification: ---------------------------------- May 04, 2015

Camera Ready Papers and Registration Due by: ------- May 14, 2015

Conference Dates: ----------------------------------------- July 20 – 24, 2015


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


Prof. Mario Cannataro

Informatics and Biomedical Engineering

University "Magna Græcia" of Catanzaro

Viale Europa (Località Germaneto)

88100 Catanzaro, Italy

Phone: +39 0961-369 4100

Fax: +39


International Program Committee*:

All submitted papers will be rigorously reviewed by the workshop technical program committee members following similar criteria used in HPCS 2015.

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

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

  • Marian Bubak, AGH University of Science and Technology, Kraków, Poland

  • 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

  • Giuseppe Di Fatta, University of Reading, U.K.

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

  • Pietro Hiram Guzzi, University of Catanzaro, Italy

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

  • David Hill, Computer Science & Modeling Laboratory, Blaise Pascal University, Cedex, France

  • Ying Liu, Graduate University of Chinese Academy of Sciences, Beijing, China

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

  • Maria Mirto, Centro Euro-Mediterraneo sui Cambiamenti Climatici (CMCC), Italy

  • Daniel Quest, Mayo Clinic - Rochester, Minnesota, USA

  • Richard Sinnott, University of Melbourne, Australia

  • Roberto Tagliaferri, University of Salerno, Italy

(*The TPC is pending and will be confirmed shortly.)

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 URL: or or contact one of the Conference's organizers.