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Track 3: Cloud Computing 

Track 3 focuses on integrated data infrastructure and information management leveraging Cloud-based technologies. It will showcase simple turnkey cloud-based applications for small businesses/labs and portable healthcare, as well as collaborative efforts that integrate semantics, AI and statistics for intelligent information retrieval from big data on the fly.


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Final Agenda


TUESDAY, APRIL 9

7:00 am Workshop Registration and Morning Coffee

8:00 Pre-Conference Workshops*

Beyond the Cloud: Improving the R&D Innovation Process through Cloud Services

Cloud Computing in Hospital Data Management and Integration


*Separate Registration Required

2:00 - 7:00 pm Main Conference Registration

4:00 Event Chairperson’s Opening Remarks

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

4:05 Keynote Introduction

Kevin Brode, Senior Director, Health & Life Sciences, Americas Hitachi Data Systems


» 4:15 PLENARY KEYNOTE 

Do Network Pharmacologists Need Robot Chemists?

Andrew HopkinsAndrew L. Hopkins, DPhil, FRSC, FSB, Division of Biological Chemistry and Drug Design, College of Life Sciences, University of Dundee





 OKTA 

10 Minute Welcome to the Reception!

Mike Nolte, Regional Sales Manager – East, Okta

 

Cycle Computing logo
OKTA
5:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Drop off a business card at the CHI Sales booth for a chance to win 1 of 2 iPads® or 1 of 2 Kindle Fires®!*

*Apple® is not a sponsor or participant in this program



WEDNESDAY, APRIL 10

7:00 am Registration and Morning Coffee

8:00 Chairperson’s Opening Remarks

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

8:05 Keynote Introduction

Sanjay Joshi, CTO, Life Sciences, EMC Isilon


» 8:15 PLENARY KEYNOTE 

Atul ButteAtul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children's Hospital; Co-founder, Personalis and Numedii





 


8:55 Benjamin Franklin Award & Laureate Presentation

9:15 Best Practices Award Program

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


Risk and Strategy for Pharma in the Cloud 

10:50 Chairperson’s Remarks

Jason Stowe, CEO, Cycle Computing

11:00 Pharma Disruptors: A Real-World Look Into How Cloud Computing Can Impact Your Business

Nathan McBride, Vice President, IT, AMAG Pharmaceuticals

The IT Team at AMAG Pharmaceuticals ignored the trends and created a scalable enterprise cloud model and eliminated their data center in the process. This came with a realized reduction of over 60% in costs with only five personnel in IT. Today, AMAG continues to push the boundaries of innovation with the cloud model they have constructed.

11:30 Use of Cloud Services and Application Virtualization within Roche Research and Early Development

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

Thomas Kandl, Global Head Scientific Computing Services, Pharma Research and Early Development Informatics, F. Hoffmann-La Roche Ltd.

The use of Cloud services is growing rapidly due to a number of advantages, including lower costs, ability to scale, enabling mobility and support for external collaboration. Similarly, application virtualization has significant cost and time benefits, and provides the ability to manage large numbers of applications across diverse devices and operating systems.

BT Global Services logo medium 12:00 pm Beyond the Cloud: How Cloud Services Can Drive Performance in Pharma R&D

David Brown, CTO, BT Life Sciences, BT Global Services

As so much of the debate about cloud computing has focused on technology, this presentation will look at why pharma 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.

Aspera 12:30 Luncheon Presentation I: Big Data in the Cloud: A New Age of Collaboration for Life Sciences

Richard Heitmann, Vice President, Marketing, Aspera

Life science researchers have a new range of cloud-enabled tools to simplify workflows and greatly enhance the transport, analysis, transformation, and sharing of big data. While the inherent advantages of cloud computing are numerous, the bottlenecks of cloud infrastructure have prevented its adoption in the life sciences field. New technologies and cloud architectures have overcome these technical challenges, enabling scale-out transfer, analysis and sharing of next-gen sequencing and large volumes of scientific data, often between far-flung collaborators. This innovation enabled genomic data to be transported at a sustained rate of almost 10 Gbps over a new link connecting prominent US and China research and education networks and is also used by cloud-based bio-informatics platform from BGI and BT Life Sciences.

IBM small logo 1:00 Luncheon Presentation II: The Convergence of Big Data Analytics with HPC Cloud 

Jeff Karmiol, Senior Product Manager, Platform Computing, HPC Cloud, IBM

Life science research continues to push the boundaries for more compute cycles and is looking to high performance computing (HPC) cloud technology for best practices in managing these environments. We now see the rapid evolution of HPC for big data analytics and a convergence of big data analytics with HPC cloud. This presentation will talk about how cloud technology can be used to provision, flex and manage multiple multi-tenant analytics and high performance computing clusters within a shared pool of cloud resources while meeting the needs of the most demanding compute-intensive and big data workloads.  


Cloud for Collaboration 

1:40 Chairperson’s Remarks

Jason Stowe, CEO, Cycle Computing

1:45 Next-Generation Bioinformatics Cloud Infrastructure for Global Collaboration

Theodore Omtzigt, Ph.D., CEO and Founder, Stillwater Supercomputing Inc.

With the proliferation of NGS instruments at core facilities the collected genome information will become distributed. To leverage the collective information large data sets need to be shared among a growing set of research teams and geographically dispersed organizations. We describe our automated cloud computing solution that seamlessly connects core facilities and research teams.

2:15 Genestack Platform for Bioinformatics R&D

Misha Kapushesky, Ph.D., CEO, Genestack Limited

Genestack Platform is a universal collaborative ecosystem for bioinformatics research and development. It allows users to store and share large data sets securely within and across organizations, with free access to public data from major databases. The platform includes open-source and proprietary genomics applications, working together independent of file formats. For developers an SDK, APIs and a marketplace are provided.

Cycle Computing logo 2:45 Utility Supercomputing: Revolutions in Computational Sciences and Genomics

Jason Stowe, CEO, Cycle Computing

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


NGS Analysis in the Cloud 

3:45 Integrated Research Data management and Analysis in NGS using Globus Online, Galaxy and Amazon Web Services

Ravi Madduri, Fellow, Computation Institute, University of Chicago; Project Manager, Math and Computer Science Division, Argonne National Lab

In this talk we will present a robust, scale on-demand solution that provides end-to-end research data management for Next-Gen Sequencing Analysis using Galaxy, Globus Online and Amazon Web Services. The emphasis is on providing the researcher with a high degree of flexibility to inspect, customize, and configure NGS analysis tools and workflows, and share findings with collaborators.

4:15 Whole Genome Sequencing Data Analysis in the Cloud

Kurt Prenger, IT Senior High Performance Computing Analyst, Application Services Research & Development, Johnson & Johnson

By utilizing cloud resources and open source toolsets, our team was able to reduce the time taken to process 50 Whole Human Genomes from ~3 years sequentially on a local machine to ~3 days in the cloud. The coordination between processing steps was automated to limit the need for manual intervention, and basic checkpoints were created to determine if steps were completing correctly.

Annai Systems4:45 Kickstarting the Worldwide Genome Web

Dan Maltbie, CTO, Annai Systems Inc.

Genomics has triggered a transformative change: the world is now embracing genomics for the advancement of biological research, and more particularly for personalized medicine. Projects such as The Cancer Genome Atlas, The 1000 Genomes Project, and the International Cancer Genome Consortium are a few examples of this fundamental shift. What is needed to foster and accelerate these advancements is a system of interlinked "big data" genomics content (and other data types) that is globally accessible through a secure Internet, similar to the way the original Worldwide Web (WWW) originated and grew, from isolated prototype solutions to a global ubiquitous web.  This talk will present how Annai Systems is kickstarting the Worldwide Genome Web. 

5:15 Best of Show Awards Reception in the Exhibit Hall

6:15 Exhibit Hall Closes


Thursday, April 11

Intel Logo7:00 am Breakfast Presentation Panel: Enabling Technology. Leveraging Data. Transforming Medicine.

Panelists:

Samuel Aronson, Executive Director, IT, Partners HealthCare Center for Personalized Genetic Medicine
Sanjay Joshi, CTO, Life Sciences, EMC Isilon
Glen Otero, Life Sciences HPC Solution Architect, Dell
Ketan Paranjape, Global Director, Healthcare & Life Sciences, Intel Corp.
Toby Bloom, Director, Informatics, Genomics Platform at Broad Institute

As we arrive at the $1000 genome, we find the fundamental problems have shifted... it is no longer about shrinking the cost of sequencing but the explosive growth of big data: the downstream analytics with rapidly evolving parameters, data sources and formats; the storage, movement and management of massive datasets and workloads; and perhaps most paradoxical of all, the challenge of articulating the results and translating the latest findings directly into improving patient outcomes.  Please join Intel and our distinguished panel to discuss how collaborating with a broad range of ecosystem partners to develop innovative solutions to seemingly intractable problems emerging in healthcare and life sciences today is driving us towards the vision of personalized medicine. 

 

» FEATURED PRESENTATION 

8:00 Featured Presentation Introduction

Geoffrey Noer, Senior Director, Product Marketing, Panasas

8:10 Trends in the Trenches 2013

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

HPC Trends in the Trenches is one of the most popular presentations of the Expo! This talk will present how common HPC problems in life science informatics have been approached by organizations of varying type and size. We will discuss observed trends in computing, workflows and data movement, along with details on particularly clever solutions observed in production environments around the world.


Open Innovation 

8:45 Chairperson’s Opening Remarks

Richard Heitmann, Vice President, Marketing, Aspera

8:50 Virtual Screening of 4.5 Billion Compound-Target Pairs Using AutoDock Vina on Google Exacycle

James Swetnam, Visiting Research Scientist, Cloud Platforms, Google

The current trend in scientific computing is toward low-cost distributed systems of commodity hardware. Using Google Exacycle, we computed 4.5 billion compound-target energy scores between 538,501 compounds and 8,300 receptor conformations corresponding to 589 unique targets using AutoDock Vina. To our knowledge, this is the largest virtual screen ever performed.

9:20 Computing in the Sky: MOON Computing + Cloud Computing

Wu Feng, Ph.D., Elizabeth & James Turner Associate Professor, Computer Science, Electrical & Computer Engineering, Virginia Bioinformatics Institute, Virginia Tech

Project MOON (MapReduce On Opportunistic eNvironments) proactively harvests the unused compute cycles of volatile computing resources and combines them with a small number of dedicated computing resources to provide the illusion of a robust supercomputer. This substantially enhances the return on investment on institutional computing resources.

BGI 9:50 Challenges in the Era of Big Genomic Data and Our Practices in BGI 

Xing Xu, Ph.D., Director, Cloud Computing Products, BGI

While the amount of next generation sequencing (NGS) data grows exponentially, effective genomic data transferring, sharing, processing, and management encounter substantial scientific and technical challenges. In this session, we will share BGI’s practice and experience how we handle these challenges in ultrafast data transfer, cloud computing, algorithm development with different HPC frameworks (Hadoop and GPU) and data management (iRODS).

10:20 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

10:45 Plenary Keynote Panel Chairperson’s Remarks

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

10:50 Plenary Keynote Panel Introduction

Yury Rozenman, Head of BT for Life Sciences, BT Global Services

Niven R. Narain, President & CTO, Berg Pharma


» PLENARY KEYNOTE PANEL 

11:05 The Life Sciences CIO Panel

Panelists:
Remy Evard, CIO, Novartis Institutes for BioMedical Research
Martin Leach, Ph.D., Vice President, R&D IT, Biogen Idec
Andrea T. Norris, Director, Center for Information Technology (CIT) and Chief Information Officer, NIH
Gunaretnam (Guna) Rajagopal, Ph.D., VP & CIO - R&D IT, Research, Bioinformatics & External Innovation, Janssen Pharmaceuticals
Cris Ross, Chief Information Officer, Mayo Clinic
Matthew Trunnell, CIO, Broad Institute of MIT and Harvard


12:15 pm Luncheon in the Exhibit Hall with Poster Viewing


Panel Session:Building the IT Architecture of the New York Genome Center 

2:00 Closing Featured Panel Session Introduction

Wanmei Ou, Senior Product Strategist, Oracle Health Sciences

2:10 Panel Session: Building the IT Architecture of the New York Genome Center

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

Chris Dwan, Acting Senior Vice President, Information Technology and Research Computing, New York Genome Center

Jim Harding, CTO, Sabey Corporation

Sanjay Joshi, CTO, Life Sciences, EMC Isilon Storage Division

Robert B. Darnell, M.D., Ph.D., President & Scientific Director, New York Genome Center

George Gosselin, CTO, Computer Design & Integration LLC

 

In 2011, a consortium of 11 major academic and medical organizations in and around New York announced the creation of the New York Genome Center (NYGC). Under the direction of Robert B. Darnell, the NYGC aspires to be a world-class genomics and medical research center, and is currently undergoing construction in the heart of Manhattan. NYGC management has the opportunity to design and create a state-of-the-art IT and data management infrastructure to handle, store and share the output from what will rapidly become one of the world’s foremost genome sequencing facilities. This series of talks will describe the thinking that went into the design, creation and construction of the NYGC’s IT infrastructure and entire data management strategy.

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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