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Track 3 - April 21 – 23, 2015

Cloud Computing  

Riding Cloud to Next-Generation Computing

Life scientists agree that the shift to cloud is both necessary and practical. Adoption has been greater than anyone expected and users continue to find novel ways and contexts in which to apply it. Track 3 explores the rapid growth and progressive maturation of cloud as well as evolving provider and user experiences.

Final Agenda

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Tuesday, April 21

7:00 am Workshop Registration and Morning Coffee

8:00 – 11:30 Recommended Morning Pre-Conference Workshops*

An Embarrassment of Riches: Choosing and Implementing Cloud Infrastructure

12:30 – 4:00 pm Recommended Afternoon Pre-Conference Workshops*

Large-Scale NGS Analysis Using Globus Genomics

* Separate registration required

2:00 – 6:30 Main Conference Registration



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5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing


Wednesday, April 22

7:00 am Registration Open and Morning Coffee



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9:00 Benjamin Franklin Awards and Laureate Presentation

9:30 Best Practices Awards Program

9:45 Coffee Break in the Exhibit Hall with Poster Viewing



10:50 Chairperson’s Opening Remarks

Dave Peterson, Executive Director, Vendor & Third Party Assurance, National IT Compliance, Kaiser Permanente Information Technology



Krista Woodley, Director, Information Technology, Biogen

We provide insight on how to best manage SaaS-based projects in a regulated world, by discussing best practices for Lifecycle management, change control, security management and IT risk management. IT and business project teams will have a clear understanding of how to optimize their IT deployments in this new cloud-based environment.

11:30 Rethinking Cloud Security: You Can’t Control What You Can’t See

Kevin Gilpin, CTO, Conjur, Inc.

As more companies adopt DevOps programs and build new infrastructure, the quantity and sensitivity of data being processed outside of the traditional IT stack are growing. Few organizations know where the access points into this information are, or how to secure them. We outline best practices for establishing visibility and control in this new space, drawing real-world examples from environments large and small.

OKTA12:00 pm Security in the Cloud: How AMAG Protects Company Data with Multi-factor Authentication

Nathan McBride, Vice President, IA & Chief Cloud Architect, AMAG Pharmaceuticals

To stay competitive and deliver world-class care, organizations such as yours are increasingly adopting cloud and mobile-first IT strategies. These trends come with significant security and access management challenges. In this presentation, Nate McBride, VP of IT and Chief Cloud Architect at AMAG Pharmaceuticals will discuss AMAG's move to the cloud and their deployment strategy for securing data with multi-factor authentication.

12:30 Session Break

Silicon Mechanics12:40 Luncheon Co-Presentation I: Are Your Researchers Paying Too Much for Their Cloud-Based Data Backups?

Dirk Petersen, Scientific Computing Manager, Fred Hutchinson Cancer Research Center (FHCRC)

Joe Arnold, President and Chief Product Officer, SwiftStack

Considering deploying a multi-petabyte storage-as-a-service offering in your research environment? Learn how an industry-leading software-defined object storage solution, architected by SwiftStack and Silicon Mechanics, helped shift hundreds of users to an object-based workflow for their archival data. With an emphasis on cost efficiencies, scalability, and manageability, see how this implementation at Fred Hutchinson Cancer Research Center (FHCRC) is continually evolving across new use cases and access methods.

Amazon logo1:10 Luncheon Co-Presentation II: Running Scalable and Cost Effective High-Throughput Sequencing Data Analysis on Amazon Web Services

Cory Funk, Ph.D., Research Scientist, Institute for Systems Biology

Dmitry Pushkarev, Ph.D., CEO and Founder, ClusterK

Here we present work by the Institute for Systems Biology, in collaboration with ClusterK and AWS, to run large cohort RNA-Seq comparative data analysis on the AWS Spot Market. We will showcase the SNAPR algorithm for transcriptome analysis, as well as highlight the advanced features of the ClusterK products that make full use of AWS Spot instances that resulted in significant cost savings over on-demand pricing.

1:40 Session Break



1:50 Chairperson’s Remarks

Jonas S. Almeida, Ph.D., Professor and CTO, Biomedical Informatics Department, SUNY Stony Brook

1:55 Web Computing as Commodity Supercomputing for User-Facing Genomics Applications

Jonas S. Almeida, Ph.D., Professor and CTO, Biomedical Informatics Department, SUNY Stony Brook

Recently, web computing (computing distributed to web clients, typically web browsers) has been the object of both academic and commercial attention as an extreme low-cost, high-distribution, high-availability model for supercomputing. Genomics applications are particularly suitable for this model of cloud computing. There is, as always, a price to pay: some core sequence analysis algorithms need to be re-identified.

2:25 Chameleon: A Large-Scale, Reconfigurable Experimental Environment for Cloud Research

Kate Keahey, Senior Fellow, Computation Institute, University of Chicago and Argonne National Laboratory; Principal Investigator, Chameleon

Chameleon is a large-scale, reconfigurable testbed for next-generation cloud computing research, established under the NSFCloud program. This talk describes the types of experiments it will support, the exciting hardware and software capabilities we will provide for cloud computing research, as well as the timeline in which these capabilities will be provided.

Seagate2:55 Leveraging the Cloud to Safeguard Genomic Data and Ensure Its Availability

Tyna Callahan, Senior Manager, Healthcare Products & Strategy, E-Vault - Seagate Systems

The sheer volume of data that must be retained today is massive—as is the responsibility to keep it intact, and to keep private information out of the wrong hands. Storage experts from Iron Mountain and Seagate CSS will discuss the key considerations for developing a storage strategy that leverages object storage in the cloud to ensure data availability, data integrity, data security and privacy.

Cleversafe3:10 Web-Scale: The Genomic Data Commons Project  

Piers D. Nash, Director, Business Development and Outreach, University of Chicago

Learn how using a web-scale data hub dramatically speeds up the pace of medical research by housing cancer genomic data. The Genomic Data Commons, a first of its kind facility established by the University of Chicago will not only centralize genomic data, but also harmonize it, enabling collaboration and engagement between researchers.

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing

BIOVIA4:00 Simulating the Behavior of a Living Human Heart

Karl D’Souza, SIMULIA Virtual Human Modeling

Given the prevalence of cardiovascular disease, major efforts are underway to understand cardiac function, design effective treatments, and accelerate the approval process. However, the lack of realistic simulation models and adequate computational resources has limited the use of in-silico methods to predict in-vivo drug or device performance. In response, Dassault Systemes is developing high fidelity multiphysics and multiscale models of the human heart and leveraging cloud computing. We present progress on this project to date.

4:15 Selected Oral Poster Presentation: Accurate HLA Genotyping to 3-field Level from Whole-Genome Sequencing Data Analyzed by Omixon Target HLA in G3’s GLOBAL Clinical Study

Robert Pollok, Ph.D., Field Application Scientist, Omixon, Inc.

Successful characterization of HLA genes allows for more positive organ transplant outcomes and disease associations. Omixon, working with the Global Genomics Group, is validating NGS methods on HLA genes using Whole Genomic Sequencing, targeted amplifications and non-sequencing-based HLA typing methods to build confidence in using NGS with HLA genes.

4:30 Using Cloud Computing to Improve the Accuracy and Probability of Success of Drug Discovery

Ed Addison, Ph.D., CEO, Corporate, Cloud Pharmaceuticals, Inc.

Cloud computing combined with Moore’s Law has provided an unprecedented opportunity for “in silico” drug discovery. The presentation explores why this approach got a bum rap in the past, how this has changed, accurate binding prediction, machine learning, use of QSAR, efficient search and property filtering.

5:00 Creating Customized Research Computing Environments on Cloud, While Addressing Needs for Faster Data Transfer, and a High Performance Parallel File System

Jason Stowe, CEO, Cycle Computing

Cloud provides researchers the ability to create customized computing environments for drug design and life sciences. But with that flexibility, come challenges. This session will review successful enterprise & start-up use cases to highlight how people are using cloud - in production - today. It will also offer a vision into how to address other needs like faster data transfer speeds, a high performance parallel file system (Lustre), and encryption/security.

5:30 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing

6:30 Close of Day


Thursday, April 23

7:00 am Registration Open and Morning Coffee



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10:00 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced



10:30 Chairperson’s Remarks

Jason Tetrault, Associate Director, Business and Information Architect, R&D IT, Biogen

10:40 Next-Generation Sequencing and Cloud Scale: A Journey to Large-Scale Flexible Infrastructures in AWS

Jason Tetrault, Associate Director, Business and Information Architect, R&D IT, Biogen

Biogen has built burst capabilities for large-scale NGS processing and collaboration with our partners. This extension of our infrastructure capability allows us to be more nimble, process more data and scale as needed. It also gives us unique options as we work with collaborators at scale. Of course, because it is NGS data, doing it securely is important.

11:10 Data Communications in BSL-3 and BSL-4 Containment: Safety, Compliance and Security

John McCall, Director, Information Technology and Telecommunications, National Emerging Infectious Diseases Laboratories, Boston University

Innovative solutions for BSL-3 and BSL-4 facilities address the asset tracking, personnel monitoring and worker communication problems associated with personal protective equipment and physical environment design. I scope out what it takes to plan and roll out a wireless networking and voice-over-IP system that meets safety, security and compliance requirements at Boston University’s National Emerging Infectious Disease Laboratory.

Aspera11:40 Breaking the Classical Barriers to Collaboration and Scientific Discovery - Distance and Data Size

Michelle Munson, President and CEO, Aspera, an IBM Company

Life sciences organizations need to dramatically reduce analytics time and speed up clinical interventions, but most still rely on shipping physical disks due to inherent problems with existing networks and transfer protocol inefficiencies. Spending days to transport data is not a viable option, this session will explore technology infrastructure for file transfer that will catalyze the transition from 1GbE to 10GbE and beyond.

12:10 pm Session Break

12:20 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:20 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing



1:55 Chairperson’s Remarks

John M. Conley, J.D., Ph.D., William Rand Kenan, Jr. Professor of Law, University of North Carolina, Chapel Hill; Counsel, Robinson Bradshaw & Hinson



Taha A. Kass-Hout, M.D., MS, Chief Health Informatics Officer, CTO and Director, Office of Informatics and Technology, FDA

OpenFDA was the first innovation created by Taha Kass-Hout, M.D., MS, upon joining FDA as the first Chief Health Information Officer in March 2013. OpenFDA was launched on June 2, 2014, allowing software developers, researchers and the public to tap into adverse events for drugs and medical devices; recalls, for drugs, devices and foods; and labeling for products on the market.

2:30 Global Developments in Privacy and Data Security Law

John M. Conley, J.D., Ph.D., William Rand Kenan, Jr. Professor of Law, University of North Carolina, Chapel Hill; Counsel, Robinson Bradshaw & Hinson

The international legal climate governing privacy and data security is changing. The European Union is in the midst of a fundamental shift in its approach. The U.S. still lacks a national data law, so the states and individual federal agencies are groping toward a strategy. This presentation focuses on the impact of these ongoing changes on genomics, bioinformatics and health research.

3:00 PANEL DISCUSSION: Achieving Much-Needed Innovation while Hurdling the Barriers of Stringent Regulation

Moderator: John M. Conley, J.D., Ph.D., William Rand Kenan, Jr. Professor of Law, University of North Carolina, Chapel Hill; Counsel, Robinson Bradshaw & Hinson


Dana Caulder, Senior Software Engineer, Bioinformatics and Computational Biology, Genentech

Chris Dwan, Assistant Director, Research Computing and Data Services, Broad Institute of MIT and Harvard

Sanjay Joshi, CTO – Life Sciences, Emerging Technologies Division, EMC

Taha A. Kass-Hout, M.D., MS, Chief Health Informatics Officer, CTO and Director, Office of Informatics and Technology, FDA

Dave Peterson, Executive Director, Vendor & Third Party Assurance, National IT Compliance, Kaiser Permanente Information Technology

Vas Vasiliadis, Director, Products, Computation Institute, University of Chicago and Argonne National Laboratory

The growth in patient healthcare and life sciences innovations can be attributed to technology enhancements like cloud computing, big data analytics and mobile applications, but may conflict with increasing regulatory compliance demands to ensure protection of healthcare life and quality as well as patient data privacy and security. This panel of esteemed technology solution providers and regulators debates real-world challenges and how regulation must also innovate at technology’s pace.

4:00 Conference Adjourns

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  • Making the World's Knowledge Computable
  • Bioinformatics in the Cloud
  • The Application of Text Analytics to Drug Safety Surveillance

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