2018 Archived Content
Track 5: Cloud Computing

Cloud computing has become the platform enterprises turn to for their application analysis as well as data storage. Data-intensive life scientists from biological researchers to biopharmaceutical organizations realize this practicality and necessity. Thus, adoption has been greater than anyone expected and users continue to expand applications. Through case studies, Track 5 explores the rapid growth and progressive maturation of cloud as well as evolving provider and user experiences.

Tuesday, May 15

7:00 am Workshop Registration Open (Commonwealth Hall) and Morning Coffee (Foyer)

8:0011:30 Recommended Morning Pre-Conference Workshops*

W6. An Intro to Blockchain in Life Sciences

W7. Containerizing Applications and Workflows for Large-Scale Reproducible Science

12:304:00 pm Recommended Afternoon Pre-Conference Workshops*

W8. Automating Data Analysis with Excel

* Separate registration required.

2:006:30 Main Conference Registration Open (Commonwealth Hall)

4:00 PLENARY KEYNOTE SESSION (Amphitheater & Harborview 2)

5:007:00 Welcome Reception in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

Wednesday, May 16

7:00 am Registration Open (Commonwealth Hall) and Morning Coffee (Foyer)

8:00 PLENARY KEYNOTE SESSION (Amphitheater & Harborview 2)


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

Cityview 1

10:50 Chairperson’s Remarks

Lance Smith, Associate Director, IT, Celgene

11:00 APIs All the Way Down: Security and Compliance with Cloud Automation

David Bernick, Director of Technology Operations, Data Sciences, Broad Institute

Deploying to a cloud and keeping data safe is one thing. Enabling developers to move at rapid speed, maintain compliance and provide for safe collaboration is another. We explore how Broad does DevOps and DevSecOps in the cloud.

11:30 Making a Case for Private Cloud: Using OpenStack in Research and Early Development

Albion Baucom, MSc, Team Lead, IT, Invitae

Using OpenStack private cloud over the past 6 years, we have gained many insights into the operations, management, use cases and governance of this type of data center resource in a scientific application development setting. In this talk, we discuss our journey with vendors, benefits to our business as well as successes and challenges encountered along the way.


12:00 pm Solving Practical Challenges for Futuristic Workloads

Jason Stowe, Principal Group Program Manager, Azure Specialized Compute, Microsoft

This talk shares lessons from over a decade of helping customers adopt cloud for traditional HPC workloads as well as new *omics and AI workloads. Learn lessons from cloud adopters including how to achieve the governance you need to accelerate life sciences innovation.

12:30 Session Break

12:40 Luncheon CO-PRESENTATION I: Genomic
Pipelines: Short and Long-Term Strategies for Efficiencies and Scale

Ron Bianchini, CEO and President, Avere Systems

Adam Kraut, Director of Infrastructure and Cloud Architecture, BioTeam, Inc.

The cloud provides a strategic advantage for genomic pipeline analysis and big science. This presentation will focus on factors leading to successful cloud missions and the vital role of file systems and support of POSIX applications. Examine real-world hybrid cloud use cases. Gain insights into how to leverage the cloud to enable research for both short- and long-term advantage.

1:10 Luncheon Presentation II: Analyzing Genomic Data at Scale with Google Cloud

Jonathan Sheffi, Product Manager, Genomics & Life Sciences, Google Cloud

Google Cloud enables scientists to change the way they perform research and collaborate with one another. This presentation will highlight how Google Cloud is accelerating life sciences research and finding new ways to innovate.

1:40 Session Break

Cityview 1

1:50 Chairperson’s Remarks

Scott Jeschonek, Director, Cloud Services, Avere Systems

1:55 Protecting Genome Data Privacy and Security in the Cloud

Shuang Wang, PhD, Assistant Professor, Department of Biomedical Informatics, University of California, San Diego

The outsourcing of genome data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years. In this presentation, we overview the privacy risks that are associated with genome data and discuss technical solutions to safeguard genome data analysis in the cloud.

2:25 It’s Raining Exomes: Cloud-Enabled Genomics – Handling >250k Samples

John Penn, MSc, Manager, NGS Data Analysis, Regeneron Genetics Center, Regeneron

Processing, structuring, and analyzing the data for 250k+ exomes requires a scalable and customizable compute framework. Cloud computing provides the adaptable infrastructure to quickly and facilely adjust, add, and modify tools, processes and frameworks to address any and all challenges that arise in the mass production of genomic data.


2:55 Orion: Delivering Drug Design and Discovery Workfloes in the Cloud

Andy Maynard, Senior Applications Scientist, OpenEye Scientific

Orion is OpenEye's cloud-based drug discovery platform. It unites highly optimised methods for computational drug discovery, developed in the course of delivering innovative scientific solutions to pharmaceutical R&D for over two decades, with the scale, reliability, and cost-effectiveness of cloud computing. Built cloud-native from the ground up, Orion offers collaborative drug discovery and design capabilities on an unprecedented scale.

3:10 Tibanna - Workflow Automation and Monitoring Solution at 4DNucleome Data Coordination and Integration Center

Soohyun Lee, PhD, Senior Bioinformatics Scientist, Department of Biomedical Informatics, Harvard Medical School

Automated execution of genomic workflows on the cloud requires standardization of workflows, real-time monitoring, metadata handling and data-dependent resource optimization. We introduce Tibanna, a cloud-based workflow management system designed to meet these goals, specifically tailored for the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC). Tibanna executes containerized workflows described in Common Workflow Language (CWL).

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

Cityview 1

4:00 Collaborative Simulation Development Accelerated by Cloud-Based Computing and Software as a Service Model

Howard J. Stamato, MS, Consultant; formerly Associate Director, Drug Product Science and Technology, Bristol-Myers Squibb

Collaborative development of simulations can be enabled by cloud-based computing capability and flexible access to software. Faster development and consumption of models is expected from having a system in which to share the right information in the right context. A system like this has been proposed for a consortium of pharmaceutical companies and is expected to bring advantages and further efficiencies to delivering medicines for patients.

4:30 Lessons and Questions from Multiple Journeys to Cloud Analytics: An Open Discussion

This is an open panel discussion with members from different companies comparing experiences from different journeys. We hope to make this as interactive as possible, as we discuss lessons learned, flexibility needs, things to watch out for, and open questions.

Lovisa Afzelius, PhD, Senior Vice President, Cogen Therapeutics

Sebastien Lefebvre, Senior Director, Data Analytics & Decision Support, Alexion Pharmaceuticals

Valerie Smith, IT Director, Global Head of R&D, Clinical, and Regulatory IT, Alkermes

Jason Tetrault, Global Head, Data Engineering and Emerging Technology, Takeda Pharmaceuticals

Aspera_IBM BW 5:00 Overcoming the Challenges of Sharing and Migrating Large Data Sets in Healthcare and Life Sciences

David Mostardi Senior Engineer, IBM Aspera

Healthcare & research are experiencing unprecedented growth in data. Legacy file sharing & cloud migration tools rely on technology that can’t handle such size and volume. Learn through real-world use cases how IBM Aspera accelerates R&D cycles, speeds data workflows, and impacts clinical and research outcomes by leveraging multi-cloud and on premises solutions.

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


7:0010:00 Bio-IT World After Hours @Lawn on D
 **Conference Registration Required. Please bring your conference badge, wristband, and photo ID for entry.   

Thursday, May 17

7:30 am Registration Open (Commonwealth Hall) and Morning Coffee (Foyer)

8:00 PLENARY KEYNOTE SESSION & AWARDS PROGRAM (Amphitheater & Harborview 2)

9:45 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced (Commonwealth Hall)

Cityview 1

10:30 Chairperson’s Remarks

Duncan R. MacCannell, PhD, CSO, Office of Advanced Molecular Detection, National Center for Emerging & Zoonotic Infectious Diseases, Centers for Disease Control and Prevention

10:40 A Cloud-Based Bioinformatics Solution for Infectious Disease Diagnostics     

Manoj Dadlani, MEng, CEO, CosmosID

Currently many pathogens escape detection in samples when traditional assays, such as culture and PCR, are employed. It is critical to develop unbiased, timely methods of pathogen detection. This presentation describes our success utilizing such facile methods for infectious disease research with various pilot studies including necrotizing fasciitis, infective endocarditis, urinary tract infections, and wound infections. Methods of metagenomic identification and antimicrobial resistance profiling will be presented.

11:10 Cloud-Based Asynchronous Virtual Tumor Board (VTB) to Operationalize and Scale the Democratization of Precision Oncology

Edik Blais, PhD, Computational Biologist, Perthera, Inc.

Since 95% of cancer patients are treated in the community, the ability to provide a leading-edge, scalable precision medicine workflow is of critical importance. We have developed a scalable, asynchronous Virtual Tumor Board (VTB) that can bring together patients’ clinical and molecular data along with clinical evidence to the fingertips of the clinician for precision treatment planning.

11:40 Pathogen Genomics in Public Health

Duncan R. MacCannell, PhD, CSO, Office of Advanced Molecular Detection, National Center for Emerging & Zoonotic Infectious Diseases, Centers for Disease Control and Prevention

Microbial genomics is playing a rapidly increasing role in public health, from detecting and responding to outbreaks, to providing better data for disease surveillance, to monitoring the impact of vaccines, to developing a new generation of diagnostics. This presentation provides an overview of how next-generation sequencing is transforming infectious disease public health in the United States.

12:10 pm Session Break

 IDBS12:20 Luncheon Presentation I: Developing A Digital Transformation Roadmap to Future-Proof Your R&D Organization And Fuel Scientific Innovation

Scott Weiss, PhD, Vice President, Product Strategy, IDBS

Join Dr. Scott Weiss for this session as he illustrates the ways digital is transforming R&D; how it delivers value in scientific organizations, and what you need to do to prepare for this transformation in your organization. Learn how digital capabilities can be applied across R&D to enable future success, advance innovation and ensure compliance.

Amazon Web Services12:50 Luncheon Presentation II: Biotech-in-a-Box: Turn-Key Cloud Infrastructure for Enterprise-Grade Research

Elliot Menschik, MD, PhD, Healthcare and Life Science Ventures, Amazon Web Services

This talk introduces the AWS Biotech Blueprint, a toolset enabling biotechs to rapidly establish enterprise-grade research environments in the cloud, supporting both wet and computational labs. Optimized out-of-the-box for security, resilience and regulatory compliance, it further automates the installation and integration of leading scientific applications under the customer’s direct control. The talks will include illustrations drawn from successful customer deployments.

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



1:55 Sponsor Introduction

Scott Jeschonek, Director, Cloud Services, Avere Systems

2:054:00 Panel Session: BioTeam Town Hall: 2018 Bio-IT Trends

Chris Dwan, Senior Technologist and Independent Life Sciences Consultant (Moderator)

Ari Berman, PhD, Vice President and General Manager of Consulting Services, BioTeam, Inc.

Tanya Cashorali, Founder, TCB Analytics

Kristen Cleveland, PMP, Director of Operations, BioTeam, Inc.

Chris Dagdigian, Co-Founder and Senior Director, Infrastructure, BioTeam, Inc.

Karl Gutwin, PhD, Senior Scientific Consultant, BioTeam, Inc.

Adam Kraut, Director of Infrastructure and Cloud Architecture, BioTeam, Inc.

Since 2010, the “Trends in the Trenches” presentation, given by Chris Dagdigian, has been one of the most popular annual traditions on the Bio-IT Program. The intent of the talk was to deliver a candid (and occasionally blunt) assessment of the best, the worthwhile, and the most overhyped information technologies (IT) for life sciences. The presentation tried to recap the prior year by discussing what has changed (or not) around infrastructure, storage, computing, and networks. This presentation has helped scientists, leadership, and IT professionals understand the basic topics involved in supporting data intensive science. In 2017, the “Trends in the Trenches” presentation evolved and expanded from 60 minutes to 120 minutes and featured more content, speakers, and interactive discussion. We will continue this format for 2018, featuring short focused podium talks on current trends related to computing, storage/data transfer, networks, cloud, and managing successful IT projects. An interactive Q&A moderated discussion with the audience follows. Come prepared with your questions and commentary for this informative and lively session.

4:00 Conference Adjourns

Exhibit Hall and Keynote Pass

Data Platforms and Storage Infrastructure