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2014 Archived Content

Cloud Computing 

Service providers and users have different definitions of what “the cloud” is. Currently, options range from public clouds to private clouds to hybrid clouds. As with many new services, adoption of next-generation technology may be much greater than anyone expects, as users find novel ways and contexts in which to apply it. Track 3 explores the rapid growth and continuing maturation of the cloud as well as evolving provider and user experiences.

Final Agenda


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TUESDAY, APRIL 29


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 to Replace On-Premises HPC for Next-Generation Sequence Analysis
Analyzing NGS Data in Galaxy

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

IT & Informatics in Support of Collaboration
Running a Local Galaxy Instance and Externalization

*Separate Registration Required. Click here for detailed information.


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 PLENARY KEYNOTE SESSION 

Click here for detailed information. 


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

 

 


WEDNESDAY, APRIL 30

7:00 am Registration Open and Morning Coffee

8:00 Chairperson's Opening Remarks

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


8:05 PLENARY KEYNOTE SESSION 

Click here for detailed information. 


9:00 Benjamin Franklin Award & Laureate Presentation

9:30 Best Practices Awards Program

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


Collaborations 

10:50 Chairperson's Remarks

Ravi K. Madduri, Fellow, Computation Institute, University of Chicago; Project Manager, Mathematics and Computer Science Division, Argonne National Laboratory

11:00 tranSMART – A Rapidly Evolving Community-Driven Open Source Platform for Translational Research

Michael Braxenthaler, Ph.D., Global Head, Strategic Alliances, F. Hoffmann-La Roche; VP, Industry Relations, tranSMART Foundation

One year after its inception, the tranSMART Foundation releases version 1.2 of the open source translational research platform tranSMART. Major new features across all key functional areas were contributed by many members of a vibrant community spanning academic, not-profit and commercial sectors. We present a success story for pre-competitive collaborative efforts.

11:30 Improving Multi-Organization Collaboration Using the Best the World Has to Offer

Andrew Porter, Director, IT Architecture, Merck

In today’s environment, successful life science organizations are looking outside their four walls to engage the best resources available. EngageZone is a collaboration platform powered by a secure cloud-based life sciences identity hub which allows companies across the industry to utilize a shared infrastructure to facilitate better collaboration while delivering improved usability, ease of deployment, security of intellectual property, and information accountability.

12:00 pm New Cloud-Based Workflows Power Global Life Science Innovation

Michelle Munson, President, CEO & Co-Founder, Aspera

Cloud-based tools for life sciences are driving innovation and enabling advancements like never before. High-speed transport technology was the first step in removing the inherent bottlenecks of cloud infrastructure. Now life sciences workflows have been transformed. High-speed transport and powerful, high-performance cloud computing sit behind a new generation of transport, analysis, transformation and sharing of big data.


12:40 Luncheon Presentation I: Bringing the Big Brain Computer to the Cloud: SGI UV for Cloud-Based Genomics Workflows
James Reaney, Director, Research Markets, SGI  

Building on years of experience with Cyclone™, SGI announces a new collaborative project to bring cloud-based computational resources to genomics workflows worldwide. SGI will showcase several of its computational and storage technologies in the project but chief among these is the SGI UV platform: the “Big Brain” supercomputing system which already powers several large genomics research facilities worldwide. A brief, high-level overview of the project and its collaborative approach will be given, along with a discussion of the initial goals and anticipated benefits for researchers.


1:10 Luncheon Presentation II: Embrace the Inevitable: Six Imperatives to Prepare Your Company for Cloud Computing
Vadim Parizher, Senior Director of Enterprise Architecture, Allergan
In today’s digital economy, speed and agility are the keys to winning in business. This session outlines Allergan, Inc.’s (NYSE: AGN) journey from a traditional on-premise IT landscape into a Hybrid IT environment and the role Cloud computing has played in enabling a “second” speed delivery capability. This session will detail experiences, lessons learned, and required changes – including the requirements for identity management - as part of this evolution and share specific challenges in the Pharmaceutical industry. 


Healthcare and Security 

1:50 Chairperson's Remarks

R. Mark Adams, Ph.D., CIO, Good Start Genetics

1:55 Riding the Cloud to Big Data Analytics in and for Healthcare

Nitesh Chawla, Ph.D., Associate Professor, Computer Science and Engineering, University of Notre Dame

Faced with unsustainable costs and huge amounts of under-utilized data, healthcare needs more efficient practices, research and tools to harness the full benefits of personal health and healthcare-related data. In this talk, I will present the foundations of work that takes a Big Data approach, leveraging cloud computing, towards population health management and personalized healthcare.

2:25 Bursting through to the Cloud – Migrating On-Premises High-Performance Computing to the Cloud in a Clinically Validated, HIPAA-Regulated Setting

R. Mark Adams, Ph.D., CIO, Good Start Genetics

High-performance computing is a critical component of the emerging clinical next-generation sequencing field. This talk addresses the processes involved with taking a custom-developed, in-house pipeline supporting a unique exon-capture NGS approach and acquiring/developing the necessary refinements, tools and processes to implement a clinically validated system in the cloud.


2:55 Gov't, Pharma, and BioTech Case Studies: Implementing Cloud for Computational Life Sciences 
Jason Stowe, CEO and Founder, Cycle Computing
From HIPAA, to Genomics, and Drug Design, this session will review Science-on-Cloud implementations, and provide thoughts on future directions. Case studies will represent a variety of applications, and workload sizes from 128 cores, up to runs of more than 156,000 cores. Bring your questions about Cloud HPC, your thinking caps, and we'll review several real examples from the past year. 

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

4:00 GenoSpace – Integrated Data Services for Genomic Medicine Delivery

Niall O'Connor, Head, Engineering, GenoSpace

Genomic data generation has become a commodity and the challenge of managing, analyzing and interpreting results for clinically actionable findings remains a growing problem. We present a secure cloud-based data architecture and service model that integrates vast, disparate knowledge collections. It empowers pathologists, clinicians and patients to harness precision medicine’s promise.

4:30 New Approaches around Security and Cloud-Based Orchestration of Genomic Workflows

Charles Schmitt, Ph.D., CTO, RENCI, University of North Carolina at Chapel Hill

Executing genomic workflows in the cloud allows convenience and financial savings over traditional approaches. But users must deal with issues of security and potentially complex workflow orchestration to take full advantage of cloud offerings. We present work from NSF- and NIH-funded projects that provide a cloud-based trust fabric to securely execute cloud-based genomic workflows.

5:00 Enabling Secure Global Genomics Data Exchanges

Stuart Young, Director, Bioinformatics, Annai Systems

Research and healthcare organizations are facing the challenge of finding and exchanging genomic information. Annai Systems provides a solution: Annai-GNOS, a Repository as a Service platform that provides secure access to conduct metadata searches and execute encrypted, accelerated downloads of genomic information. GNOS enables global genomic data exchanges of public and private partners to increase the use and value of genomic information.

5:15 Sponsored Presentation (Opportunity Available)

5:30 - 6:30 Best of Show Awards Reception in the Exhibit Hall


THURSDAY, MAY 1

7:00 am Registration Open

7:00 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Chairperson’s Opening Remarks

Kevin Davies, Ph.D., Vice President Business Development & Publisher C&EN, American Chemical Society; Founding Editor, Bio-IT World


8:05 PLENARY KEYNOTE SESSION 

Click here for detailed information. 


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


NGS Analysis 

10:30 Chairperson's Opening Remarks
Jason Stowe, CEO and Founder, Cycle Computing 

10:35 Implementations of Cloud-Based Pipelines for Large-Scale DNA-Seq and RNA-Seq Data Analyses

Shanrong Zhao, Ph.D., Senior Scientist, Informatics, Johnson & Johnson

Due to reduced sequencing costs, more NGS data are produced by small research groups. Data storage and CPU resources required for large-scale whole-genome sequencing and RNA-Seq data analyses are too large for many individual laboratories to provide. To meet these challenges, we developed Rainbow and Stormbow: cloud-based software packages for large-scale DNA-Seq and RNA-Seq analyses.

10:55 Analyzing DNA-Seq Data Using DRAW: Lessons Learned from Using Amazon EC2 for Next-Generation Sequencing Studies

Li-San Wang, Ph.D., Assistant Professor, Pathology and Laboratory Medicine, University of Pennsylvania

DNA-Seq studies pose enormous challenges to many researchers who have limited access to dedicated IT support or high-performance computing. Cloud computing is a promising solution to address these needs. This talk covers our experience using the DNA Resequencing Analysis Workflow (DRAW) software to process >800 samples and our strategy to use Amazon EC2 effectively for DNA-Seq analysis.

PodcastLogo

11:15 Globus Genomics: An End-to-End NGS Analysis Service on the Cloud for Researchers and Core Labs

Ravi K. Madduri, Fellow, Computation Institute, University of Chicago; Project Manager, Mathematics and Computer Science Division, Argonne National Laboratory

We describe the Globus Genomics platform. Globus Genomics provides an integrated platform for end-to-end data management using Globus Online and scalable analysis using the Galaxy framework and Amazon Web Services. We will walk through case studies of researchers and core labs at various universities that are leveraging the service to meet their rapidly growing genomics analysis needs.

11:35 Technology Advancements in High Density Compute and Storage that Power the Next Generation of Cloud Infrastructure

Brian Corn, Vice President, Marketing, Thinkmate

Thinkmate solutions accelerate discovery while reducing TCO, expanding scalability and enabling business continuity. Exciting new solutions from names like Intel, Supermicro, and Western Digital will be covered. This presentation is a “must see” for any attendees involved in hardware infrastructure design, testing, and procurement.

12:15 pm Luncheon Presentation I: Turn-Key RNA-Seq Analysis for the Biologist Using the Maverix Analytic Platform
Dan Kearns, Director, Software Development, Maverix Biomics, Inc. 
Studies leveraging RNA-seq data are commonly limited by the tools, infrastructure, and trained bioinformaticians necessary to process, interpret and manage the data. The Maverix Analytic Platform addresses these challenges through a unique environment designed for biologists. This cloud-based platform leverages best-in-class tools and provides an integrated UCSC-genome browser endpoint to enable visualization and interpretation of results. 

12:45 Luncheon Presentation II: Biotech Self-Service Agility in Public and Private Clouds
Dennis Faucher, Director, Presales, AdvizeX Technologies, a Rolta Company
Biotech requires fast time to market with high quality, high compliance and lowered cost.  The correct mix of private and public cloud enables: reduced costs to significantly lower Total Cost of Ownership (TCO), on-demand application and service provisioning in hours rather than weeks, increasing business agility, supporting business growth and accelerating time-to-market, and increased service levels and business continuity via an in-built disaster recovery capability. 

1:15 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing


Pharma Strategies 

1:55 Chairperson’s Remarks
Jason Stowe, CEO and Founder, Cycle Computing 

2:00 Data Sciences: Cloud Compute and New Graph Compute Models

Jeremy Chambers, Senior Data/IT Architect, Data Science, R&D IT, Biogen Idec

2:30 SHERPA: A Service to Utilize ScienceCloud for Integration of Collaboration Data at Sanofi

James Connelly, Ph.D., Head, Research Data Management, Sanofi

In recent years, there has been a great increase in collaborative research that requires integration and analysis of compound and bioactivity data from multiple sources. This is necessary to enable efficient cycle time for compound optimization and effective project decisions. ScienceCloud/HEOS was an ideal platform to enable secure collaborative data sharing in a “Cloud” and to facilitate pipelining of data to and from our internal data systems. At Sanofi, we have built a service, called SHERPA, to support drug discovery research projects data sharing with external collaborators. Expansion is also planned to support Biologics Research.

3:00 From Nebula to Cloud: A Critical Assessment of Cloud Technologies in R&D Informatics

Alain Nanzer, Ph.D., Global Head, Safety and Development Workflows, Pharma Research and Early Development Informatics (pREDi), F. Hoffmann-La Roche Ltd.

Migration of R&D computer systems and services to “The Cloud” are considered an important step to reduce costs while increasing flexibility, availability and service quality. The presentation will assess a series of cloud implementations in R&D informatics to define the success of these projects along the predicted gains. A special focus will be put on cloud implementations in regulated environments.

3:30 PANEL DISCUSSION: Optimizing Cloud Computing for Scientific Research

Moderator: Jason Stowe, CEO and Founder, Cycle Computing

Jeremy Chambers, Senior Data/IT Architect, Data Science, R&D IT, Biogen Idec

James Connelly, Ph.D., Head, Research Data Management, Sanofi

Ravi K. Madduri, Fellow, Computation Institute, University of Chicago; Project Manager, Mathematics and Computer Science Division, Argonne National Laboratory

Alain Nanzer, Ph.D., Global Head, Safety and Development Workflows, Pharma Research and Early Development Informatics (pREDi), F. Hoffmann-La Roche Ltd.

Thomas Schilling, Ph.D., IT Portfolio Manager, R&D, Bayer Business Services GmbH

In this big data age, researchers rely more heavily on cloud computing to store, share and analyze data. It is thus important to understand the options, potential uses and best practices for optimizing this technology. This panel of IT infrastructure experts, software development pros and end users will address the possibilities and perils of working in the cloud, now and in the future.

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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