[hpc-announce] Second Workshop on HPC Applications in Precision Medicine @ ISC 2018 - CFP Open

Sunita Chandrasekaran sunisg123 at gmail.com
Sun May 13 14:20:08 CDT 2018

Second Notice

Call For Abstracts – Deadline Extended

Second Workshop on HPC Applications in Precision Medicine

Thursday,  June 28, 2018

As part of

ISC High Performance 2018


Frankfurt, Germany

*Important Dates:*

*Priority Consideration Abstract Submission Date:               May 28,

*Last Date for Submission:
                                                    June 07, 2018*

            June 28, 2018

Submission URL: https://easychair.org/conferences/?conf=hapm18

*Workshop Abstract*

High-performance computing has become integral to the future success of
precision medicine. Catalyzed by the dramatic increase in the amount of
data available through advanced next generation sequencing and advanced
imaging techniques, new approaches are in development to address the
complexities of understanding and modeling biology. When coupled with
long-standing computational chemistry and biology techniques used in drug
discovery, an exciting frontier emerges for innovation as the communities
join. The use of deep learning to develop data driven models combined with
exascale capabilities to explore and validate models, adds an exciting
dimension for the future of both HPC and precision medicine. The HPC
Applications in Precision Medicine workshop aims to bring together the
computational and life sciences communities to share experiences, examine
current challenges, and explore future opportunities for applications of
high-performance computing in precision medicine.

In the workshop, we bring together individuals from across the globe with
interests in the use of HPC applications in precision medicine to share
insights, experiences and showcase new capabilities in this rapidly
evolving field.

*Target Audience*

The workshop is expected to attract those developers, researchers, and
vendors with technologies and solutions holding potential to address
problems in precision medicine and seeking potential collaborators to work
with. The workshop also draws individuals from the breadth of precision
medicine application areas spanning research to clinical application in
areas including drug discovery, preclinical validation, diagnostics, health
monitoring, precision biomarker development, prevention and early
detection, treatment determination and population studies, interested in
the computational and data challenges and opportunities created in
precision and predictive medicine.

*Call for Abstracts*

The workshop is seeking submissions of *extended abstracts* for papers that
will enable any of the following as applied to precision medicine:

   - Bring awareness of new high-performance computational technologies,
   - Provide insight into novel HPC methodologies and approaches,
   - Share innovative and valuable data resources,
   - Broaden awareness with case and application studies, and
   - Develop opportunities for community collaboration, both nationally and

Submitted *extended abstracts* will be reviewed and selected for
presentation in the HPC Applications of Precision Medicine Workshop.
Abstracts selected for presentation will be invited to have papers included
in an anticipated special journal issue for the workshop.  Aiming to
provide broad visibility and access to submissions at this workshop, a
preliminary agreement has been arranged with BMC Bioinformatics to present
the accepted workshop submissions in special journal issue following the

Candidate topic areas for the HPC Applications in Precision Medicine may

*Precision Medicine Research and Clinical Applications*

Disease Specific Predictive Models

Therapeutic Development

Toxicity Modeling

Next Generation Sequencing Analysis

Single Cell Sequencing

Proteomics, Genomics, and Metabolomics

Flow Cytometry

High-throughput Screening

Multi-modal Biological Imaging

Structural Biology

Biological-scale Molecular Dynamics

Protein-protein Interaction

Cellular Signaling

Cell-level Predictive Modeling

Imaging and Digital Pathology

Pharmacodynamic Modeling

Pharmacogenomic Modeling and Analysis

Electronic Health and Medical Records

mHealth and Health Sensor Networks


Systems Biology

Biological Ensemble Models

*Computational Approaches*

High-performance Parallel Computing

Cloud Computing

Exascale and Extreme-scale Computing

Machine and/or Deep Learning

Cognitive Computing

Data Integration and Delivery

Data Sharing and Model Interchange

Image Processing

Heterogeneous Computing (GPGPU, FPGA, etc.)

Programming Models


Uncertainty Quantification

Multi-scale Predictive Modeling

Integrated Systems Simulations

Integration Frameworks

Computational Workflows

Information and Data Security

Automata and Finite State Machines

Novel Mathematical and Statistical Models

Data Science and Analytics

Graph and/or Network Analysis

Model Validation and Verification

*Submission Guidance*

Authors are invited to submit *extended abstracts* for papers in English
structured as preliminary technical papers from *two to four *letter size
pages (not including bibliography). A preliminary bibliography should be
included and use the IEEE format for conference proceedings. Submissions
not conforming to these guidelines may be returned without consideration or

Extended abstracts will be reviewed and judged on alignment to workshop
aims, originality, technical strength, correctness, quality of presentation
and interest to workshop attendees. Submitted abstracts may incorporate
unpublished new advances, insight and/or original research findings.

Submissions received after the due date, exceeding the prescribed length,
or not appropriately structured will be considered at lower priority for
potential inclusion in the workshop, and are also at risk of being returned
without review.

In submitting the extended abstract, the authors acknowledge that at least
one author of an accepted submission will register for and attend the

Preliminary *extended abstracts* submitted for consideration should be
submitted electronically as PDF documents at:


Instructions for submitting final versions of papers to be included in the
special journal issue will be shared with authors of the extended abstracts
selected for presentation at the workshop.

*Workshop Organizing Committee*

The initial workshop organizing committee has spearheaded the
identification of presenters from both Europe and US. The committee was
strongly supported by colleagues in identifying the slate of presenters for
the initial workshop in 2017 and has support for the same in developing the
program for the 2018 workshop.

Thomas Steinke – Zuse Institute Berlin

Sunita Chandrasekaran – University of Delaware

Patricia Kovatch – Mount Sinai Icahn School of Medicine

Eric Stahlberg – Frederick National Laboratory for Cancer Research

The workshop organizing committee has established a growing program
committee to support the organizers in developing the 2018 workshop
program, including review and selection of submitted papers.

*Workshop Program Committee*

Guy Robison, Cancer Research University of Cambridge, UK

Bertil Schmidt, University of Mainz, Germany

Erin Crowgey, Nemours Children Hospital

Guido Juckeland, HZDR, Germany

Paul Macklin, Indiana University, USA

Jonathan Ozik, Argonne National Lab

Prasanna Balaprakash, Argonne National Lab

Kshitij Srivatsava, Oak Ridge National Lab

Fernanda Foertter, Nvidia

Dave Richards, Oak Ridge National Lab

Martin Herbordt, Boston University

Ted Slater, Cray
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