Bio IT World Expo 2016  
Bio IT World Expo 2016

Track 3: Cloud Computing 


Final Agenda: 

Track 3 provides focused research presentations, real world use cases and individual experiences with cloud computing. Themes include HPC in the Cloud, value of cloud computing studies, cloud vendors/providers, non cloud solutions that provide what the cloud does, performance benchmarking, security models, and tools and frameworks for data analysis.



7:00 am Workshop Registration and Morning Coffee

8:00 - 4:00 pm Pre-Conference Workshops*

Recommended workshop: (W11) Cloud Computing
*Separate Registration Required.

2:00 - 6:00 Main Conference Registration

4:00 Event Chairperson’s Opening Remarks

Cindy Crowninshield, RD, LDN, Conference Director, Cambridge Healthtech Institute

Sponsored by
Isilon Systems
4:05 Keynote Introduction

Chris Blessington, Life Sciences Solutions Architect, Isilon

Plenary Keynote

4:15 Making the World’s Knowledge Computable

StephenWolframStephen Wolfram, Ph.D., CEO, Wolfram Research; Creator of Wolfram|Alpha




Sponsored by

5:00 Welcome Reception in the Exhibit Hall and Poster Viewing




Wednesday, April 13

7:00 am Registration and Morning Coffee

8:00 Event Chairperson’s Opening Remarks

Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute

Sponsored by
8:05 Keynote Introduction
Grant Stephen, CEO, Tessella, Inc.

Plenary Keynote

8:15 Interacting with Complex Information Landscapes: Integration and Next Generation User Interfaces

Bryn RobertsBryn Roberts, Ph.D., Global Head, Informatics, Pharma Research and Early Development, F. Hoffmann-La Roche Ltd.





8:45 Benjamin Franklin Award/Presentation: Jonathan Eisen, Ph.D., Professor, Genome Center, University of California, Davis

9:10 Best Practices Awards Program

Sponsored by

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


High Performance Computing
and Data Analysis Pipeline

Sponsored by
Model Metrics
10:50 Chairperson’s Remarks

Jason Hanley, Director, Life Sciences, Model Metrics




11:00 Featured Presentation
HPC Trends from the Trenches (Joint with Tracks 1 - 3)

Chris Dagdigian, Founding Partner, Director, Technology, BioTeam, Inc.

This talk will review some of the BioTeam’s recent work with biotech, pharmaceutical, government and enterprise clients. As an independent consulting firm, the BioTeam is able to see how HPC problems in life science informatics have been approached by organizations of varying type and size. We will address common problems and observed trends in computing, workflows and data movement, along with details on particularly clever solutions observed in production environments around the world.

11:30 High-Throughput Analysis Pipelines on the Cloud

Toby Bloom, Ph.D., Director , Informatics, Genome Sequencing, Broad Institute

Cloud computing is often suggested as a solution to the next-gen sequencing data deluge. Running high-throughput pipelines on very large volumes of data introduces some interesting challenges not seen in smaller applications on the cloud. The Broad production sequencing analysis pipeline is an example of such a high-throughput application. We discuss our experiences porting that pipeline to the Amazon cloud, the challenges we encountered, and the solutions we utilized. We will also compare the requirements of this application, designed to process large numbers of runs concurrently, with the requirements of many next-gen users to process a single run at a time on the cloud.

Sponsored by
Omixon small
12:00 pm Easy-to-Use, Customized Next-Generation Sequencing Data Pipelines on Cloud Computing

Attila Berces, Ph.D., CEO, Omixon

We demonstrate Omixon’s fully automated, easy-to-use, custom built data analysis pipelines to solve customers’ problems on Amazon Web Services. We demonstrate applications in genome variant analysis and human exome analysis.

Sponsored by
Cycle Computing
12:15 A Viable Alternative to In-House Compute Clusters: Real Results from Life Science Use Cases in the Cloud

Jason Stowe, Founder and CEO, Cycle Computing, LLC

 Sponsored by
12:30 Luncheon Presentation
Experiencing LifeScope™ Genomic Analysis Software through the Cloud
Nicholas D. Socci, Ph.D., Assistant Director, Bioinformatic Core, Computational Biology Center, Memorial Sloan Kettering Cancer Center 
LifeScope™ Cloud offers customers an alternative to buying and maintaining the computer infrastructure typically required for second-generation sequencing data analysis. Dr. Socci will describe his experience of using LifeScope™ Genomic Analysis Software through the Cloud, and will focus on how LifeScope™ can be used for analyzing targeted resequencing data generated from AB SOLiD™ Sequencing instruments from Life Technologies.


Next-Generation Sequencing on the Cloud

1:40 Chairperson’s Remarks

Andrew Su, Ph.D., Associate Director of Bioinformatics, Genomics Institute of the Novartis Research Foundation


1:45 Critical Components for Cloud-Computing

Angel Pizarro, Director, ITMAT Bioinformatics Facility, Institute for Translational Medicine & Therapeutics, University of Pennsylvania

To facilitate using second generation sequencing for interrogating diseases, cloud computing providers promise instant access to vast amounts of computational resources on a pay-as-you-go basis. However, orchestrating loosely coupled system components into a cohesive high-throughput computational resource is a challenge. This talk will cover the critical components that need to be in place to be successful on the cloud.

2:15 Scalability of Genome Assemblers for Cloud and HPC Computing Environments

C. Victor Jongeneel, Ph.D., Director, Bioinformatics & Biomedical Informatics, Natl. Center for Supercomputing Applications, Inst. for Genomic Biology, University of Illinois at Urbana-Champaign

While cloud computing is gaining acceptance in the biological community, high-end HPC has not yet been fully embraced. This presentation will demonstrate the applicability of a diversity of computational fabrics (cloud, HPC, and HPC in a cloud) for de novo genome assembly using Velvet and ABySS, two applications with widely different characteristics. It will be based on real use cases and performance benchmarks.

Sponsored by
BT small
2:45 Cloud Computing: Beyond the Hype and Headlines

Neil Lock, IT Services Program Director, BT Global Services

This presentation explores what lies beyond the cloud. As so much of the debate, hype and headlines about cloud computing has focused on technology, we will look rather at why pharma organisations should focus on the benefits of cloud services and how it can drive performance in R&D. We will discuss what organisations need to do to make cloud solutions work for them along with the how and why.

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing

3:45 BioGPS – Crowdsourcing the Development of a Gene Annotation Portal

Andrew Su, Ph.D., Associate Director of Bioinformatics, Genomics Institute of the Novartis Research Foundation

The landscape of online, gene-centric annotation databases is highly fragmented, spanning hundreds or thousands of individual web sites. To better navigate and organize these resources, we developed BioGPS (, a gene annotation portal that aggregates gene annotation data within a single framework. BioGPS focuses on two key concepts: user customizability and community extensibility. To maximize the addition of new functionality and the efficiency of our development, we currently host significant sections of our data and application in the cloud.

4:15 Dynamically Scalable, Accessible Analysis for High-Throughput Sequence Data

Enis Afgan, Ph.D., Postdoctoral Researcher, Departments of Biology and Mathematics & Computer Science, Emory University

High-throughput sequencing has transformed biomedical research, however making sense of this resource requires sophisticated computational tools. The Galaxy project seeks to make these tools available to a wide audience of researchers, while ensuring that analyses are reproducible and can be communicated transparently. The Galaxy framework provides a consistent accessible user interface for complex tools; however, many such tools require significant computational resources. Here we describe Galaxy cloud, which allows researchers to instantiate an analysis environment which can be scaled up and down on demand as needed, using nothing more than a web browser.

Sponsored by

4:45 Understand How your Workloads can Leverage a Trusted Cloud Environment
John Hanrahan, Director, EMC Consulting Life Science & Healthcare Practice
Cloud computing allows life sciences business and IT leaders to build a trusted, secure, reliable and  cost effective IT environment. We will provide a unique perspective on how to determine what data workloads can and should be moved to the cloud, protocols on how to control "acceptable use" and how to ensure secure information-sharing practices are in place with applicable controls. This session will discuss how we analyze your collaboration, high performance and other workloads and our approach to defining a cloud strategy.

Sponsored by
5:00 Cloud Computing in Support of Biomedical Research and Clinical Care
Mark Adams, Ph.D., Principal, Booz Allen Hamilton 
This talk will present how Booz Allen has worked with a range of clients in the biomedical research and care spaces to leverage cloud computing as a key part of implementing solutions for a variety of challenging problems.  We will present how Booz Allen has developed and implemented a private cloud infrastructure, secured and validated for identifiable health data.  We will then present how the team has developed an open source set of tools which provide for semantically-enabled query and analysis in Hadoop databases.  We will finally discuss how these components have been used to rapidly and cost-effectively carry out significant clinical and biomedical research activities for several clients.

5:15 Best of Show Awards in the Exhibit Hall

6:15 Exhibit Hall Closes


Thursday, April 14

8:45 Event Chairperson’s Opening Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

Sponsored by
BT small
8:50 KEYNOTE PANEL: Keynote Introduction A special plenary session featuring a series of succinct, forward-looking presentations by:

Ken Buetow, Ph.D., Associate Director, Bioinformatics and Information Technology, National Cancer Institute

Debra Goldfarb, Senior Director, Strategy, Microsoft

Martin D. Leach, Ph.D., Executive Director, MRL IT for Discovery & Pre-Clinical Sciences, Merck & Co.

Mark Boguski, M.D., Ph.D., Founder, Resounding Health Incorporated

Jamie Heywood, Co-founder and Chairman, PatientsLikeMe
Yury Rozenman, Global Head of Marketing, Pharmaceutical and Life Sciences Sector, BT Global Services

10:30 Coffee Break in the Exhibit Hall with Poster Competition


Pharma & Healthcare Perspective
on the Cloud

Sponsored by
HP sm 
10:55 Chairperson’s Remarks

David Medina, Worldwide Life Science and Pharma Segment Executive, HP Enterprise Business

11:00 Cloud Computing Concepts Applied in Pharma R&D

Rick Franckowiak, IT Director, Johnson and Johnson Global R&D Delivery Services

Tom Messina, IT Manager, Johnson and Johnson Global R&D Delivery Services

A session to share lessons learned and approaches in applying cloud computing concepts in a pharmaceutical research and development environment. Specific real world use cases will be highlighted. There will be discussion on future opportunities as well as current challenges in reaching further adoption including strategic issues such as security, technical integration, platform readiness, cost and service support.

11:30 Genome Era Medicine and HealthCare Disruptive Technology

Dennis P. Wall, Ph.D., Assistant Professor of Pathology, Beth Israel Deaconess Medical Center & Director, Computational Biology Initiative, Center for Biomedical Informatics, Harvard Medical School

Using a novel translational and clinical science ‘cloud’ computing platform, we created mathematical models that reflect patient populations and the use of personalized medicine by testing preventative health care for individuals based on their specific medical, family, and genetic characteristics. This presentation will discuss the objectives, serious medical practice barriers, outcomes and future effort of a series of pilot projects.

Sponsored by
Cambridge Semantics small
12:00 pm Applying Technologies Designed for the Cloud to Transform Pharma and Healthcare

Steven Kludt, Vice President Marketing, Cambridge Semantics

By applying Semantic technologies designed from the ground up for the cloud, computational capabilities of the cloud can be combined with next generation data management in the cloud. Current processes become radically cheaper and faster to implement while new solutions and levels of collaboration are being developed that were not possible before. This session will present new ways of thinking about leveraging data in the cloud and the architectural and governance challenges they present. Use cases will be presented in pharma with discussions of next steps being explored.

Sponsored by
12:15 Scale-Out Storage for High Performance Bioinformatics in the Cloud
Anand Babu Periasamy, CTO & Co-Founder, Gluster
Gluster and RightScale Cloud Management enable bioinformatics companies to focus on research and forget about IT by leveraging the automation and massive scalability capabilities of the Amazon public cloud.  Best practices, recommendations, and use cases on managing research data in the cloud will be discussed.

12:30 Luncheon in the Exhibit Hall with Poster Viewing

2:00 Exhibit Hall Closes


Collaboration and Security on the Cloud

1:55 Chairperson’s Remarks

William Tulskie, CEO and CTO, Healthcare IT, Inc.

2:00 Research Collaboration in the Cloud: How NCI and Research Partners are Using Digital Identities to Accelerate Medical Advances

Cindy Cullen, SSBB, CISM, CISSP, CTO, SAFE BioPharma Association

The National Cancer Institute, the private sectors [Bristol-Myers Squibb & Sanofi Aventis], and SAFE BioPharma Association are piloting a process to use federated trust to access, digitally sign and exchange documents, eliminating use of paper-based forms in research projects associated with oncology drug development and clinical trials. The goal is faster, lower cost delivery of medical advances to patients.

2:30 Elastic-R, a Ubiquitous Data Analysis Workbench for IaaS-Style Clouds

Karim Chine, Director, Cloud Era Ltd., Cambridge, UK

The success of EC2 announces the emergence of a new era in scientific computing and data analysis. Bringing that era for research still requires new software that would bridge the gap between the cloud and the scientists’ tools. Elastic-R enables anyone, using a standard Web browser, to work virtually and collaboratively with mainstream scientific computing environments without memory or computing constraints.

Sponsored by
caBIG logo
3:00 caBIG® in the Cloud

William Tulskie, CEO and CTO, Healthcare IT, Inc.

Access to applications for collecting patient outcomes and related research data is enabling innovations in personalized healthcare. As cloud-based offerings mature, these data and applications are becoming easier and more economical to implement. The Support Service Provider program within caBIG® offers a fully functional enterprise class cloud environment tuned to the specialized security and availability requirements for healthcare and clinical research applications and data. This session will present case study examples of current implementations that demonstrate innovative cloud-based support for biomedical research.

3:30 The Atlas Cloud Computing Infrastructure for Organizing and Querying Multiomics Data (Joint with Tracks 1-5)

Misha Kapushesky, Ph.D., Functional Genomics Team Leader, EBI, Cambridge, UK

The Expression Atlas is a cloud computing based distributed infrastructure for organizing and querying multiomics data. Built upon the open-source Expression Atlas project at the EBI in partnership with the pharmaceutical industry, the Atlas provides a scalable solution that can be easily deployed on in-house servers or accessed remotely in the cloud. Learn how the Atlas deals with secure processing and combined analysis and integration of public/private transcriptomic and proteomic data, with an emphasis on our novel pipeline for next-generation sequencing data processing and reporting.

4:00 Conference Adjourns

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Platinum Sponsors


Cycle Computing logo small

DDN Storage  

Elsevier R&D Solutions


 IBM Logo Illumnia logo  

Intel Logo  

Precision for Medicine


 Seven Bridges Genomics

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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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