Cloud Computing

Cloud computing has become the platform enterprises utilize for their application of analyzing, storing, processing, exploring, and sharing dynamic data. These data-intensive life scientists from biological researchers to biopharmaceutical organizations demand this practicality and necessity. Thus, adoption has been greater than anyone expected, and users continue to expand applications. Through case studies, the Cloud Computing track explores the rapid growth and progressive maturation of cloud, as well as evolving provider and user experiences and challenges. Some of these challenges include how to handle new equipment pumping data into the cloud when most internal tools run locally, reproduce processes and new workflows, accelerate research, and find new ways to collaborate, remove data storage and processing bottlenecks, and make significant business impact across R&D in enabling large-scale modeling and simulation. How will these activities be impacted by the evolution of quantum computing methods, and eventually computers?

Tuesday, October 6

PLENARY KEYNOTE PROGRAM

10:00 am

Welcome Remarks

Cindy Crowninshield, Executive Event Director, Cambridge Healthtech Institute
Scott Parker, Director of Product Marketing, Marketing, Sinequa
10:15 am

NIH’s Strategic Vision for Data Science

Susan K. Gregurick, PhD, Associate Director, Data Science (ADDS) and Director, Office of Data Science Strategy (ODSS), National Institutes of Health
Rebecca Baker, PhD, Director, HEAL (Helping to End Addiction Long-term) Initiative, Office of the Director, National Institutes of Health
11:05 am

LIVE Q&A: Session Wrap-Up Panel Discussion

Panel Moderator:
Ari E Berman, PhD, CEO, BioTeam Inc
11:25 am Lunch Break - View Our Virtual Exhibit Hall
11:55 am Recommended Pre-Conference Workshops*
W1: Data Management for Biologics: Registration and Beyond
W2: A Crash Course in AI: 0-60 in Three
W3: Data Science Driving Better Informed Decisions

*Separate registration required. See workshop page for details.

1:55 pm Refresh Break - View Our Virtual Exhibit Hall
2:15 pm Recommended Pre-Conference Workshops*
W4: Digital Biomarkers and Wearables in Pharma R&D and Clinical Trials
W5: AI-Celerating R&D: Foundational Approaches to How Emerging Technologies Can Create Value
W6: Dealing with Instrument Data at Scale: Challenges and Solutions

*Separate registration required. See workshop page for details.

4:15 pm Close of Day

Wednesday, October 7

APPLYING CLOUD FOR MEGA-SCALE GENOMICS

9:00 am

The Road from Data Commons to Data Ecosystems: Challenges, Opportunities, and Emerging Best Practices

Robert Grossman, PhD, Frederick H. Rawson Distinguished Service Professor in Medicine and Computer Science; Director, The Jim and Karen Frank Center for Translational Data Science, University of Chicago

There are now several large-scale data commons supporting the biomedical research community and the beginnings of data ecosystems. In this talk, we discuss some of the emerging best practices around data ecosystems, as well as some of the challenges and opportunities. We also discuss some case studies of data commons and data ecosystems developing using the open source Gen3 data platform.

9:20 am

Harnessing Cloud for Mega-Biobanks: Efficient Computing with Sensible Data Governance

Saiju Pyarajan, PhD, Director, Center for Data and Computational Sciences, VA Boston Healthcare System; Faculty, Harvard Medical School

Multiple initiatives are currently underway for setting up large biobanks with associated clinical and molecular data. With more than 800,000 samples already collected and genotyped, the Million Veteran Program (MVP), promises a unique opportunity to perform genomic analysis at scale for meaningful interpretation of results with better confidence. This talk will discuss the infrastructure that facilitates genomic research in MVP, as well as the challenges in scaling data, analytics, security, and data governance.

Abhay Kini, Director of Product Management, Marketing, IDBS

No business is immune to change. This presentation will highlight how the right blend of best practices and technology can provide researchers the tools needed to facilitate and accelerate their digital transformation.

10:00 am Coffee Break - View Our Virtual Exhibit Hall

CLOUD COMPUTING: INFRASTRUCTURE

10:20 am

Evaluating Distributed Computing Infrastructures: An Empirical Study Comparing Hadoop Deployments on Cloud and Local Systems

Devipsita Bhattacharya, PhD, Assistant Professor, Information Security & Digital Forensics, University at Albany, State University of New York

This talk discusses current cloud-based distributed computing options and presents results from a study that compared cost and performance of cloud systems and in-house deployments. It is intended not only as an evaluation of infrastructural choices, but also proposes a metric framework that can serve as a baseline for researchers and practitioners examining distributed infrastructures on cloud.

10:40 am

Reproducible Software Stacks Everywhere – Cloud, Containers and OnPrem

John Dey, Senior HPC Systems Engineer, Fred Hutchinson Cancer Research Center

The Hutch uses EB for building software containers and all software for our computer cluster. Our software stack is published and citable and we share our work with the global community of EasyBuild users.

Jer-Ming Chia, Principal Program Manager, Microsoft
Scott Jeschonek, Principal Program Manager, Azure, Microsoft

COVID-19 research represents the type of unplanned and extemporaneous projects that places strain on internal HPC capacity. In this segment, we discuss the building blocks needed to build supercomputing-class HPC environments on Azure, and how these help our partners with their Covid-19 research.

11:30 am LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
John Dey, Senior HPC Systems Engineer, Fred Hutchinson Cancer Research Center
Jer-Ming Chia, Principal Program Manager, Microsoft
Panelists:
Robert Grossman, PhD, Frederick H. Rawson Distinguished Service Professor in Medicine and Computer Science; Director, The Jim and Karen Frank Center for Translational Data Science, University of Chicago
Scott Jeschonek, Principal Program Manager, Azure, Microsoft
Abhay Kini, Director of Product Management, Marketing, IDBS
Saiju Pyarajan, PhD, Director, Center for Data and Computational Sciences, VA Boston Healthcare System; Faculty, Harvard Medical School
11:50 am Lunch Break - View Our Virtual Exhibit Hall
11:55 am Interactive Breakout Discussions

Consider joining a breakout discussion group. These are informal, moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.

Michael Riener, President, RCH Solutions

Join us for a lively discussion among prominent pharma leaders, and learn:

Why, when & how to implement a public Cloud for your computing needs

Challenges and opportunities when setting and managing stakeholder expectations

Critical keys to success to realize the best outcomes

To learn more about RCH Solutions, visit our Virtual Booth

Joe Donahue, Managing Director, Life Sciences, Accenture

Hosted by Joe Donahue, Managing Director, Life Sciences, Accenture

 

Participants include: 

Andreas Matern, Head of Digital Translational Medicine, Sanofi

John Quackenbush, Professor of Computational Biology and Bioinformatics; Harvard T.H. Chan School of Public Health

Seungtaek Lee, VP, Strategic Partnerships and AI RWE Head of CoE; ConcertAI

Preston Keller, PhD, MBA, President & CCO, PercayAI

Philip Payne, PhD, Becker Professor and Chief Data Scientist, Washington University in St. Louis

 

Jeff Evernham, VP of Customer Solutions, Consulting, Sinequa

Most large scale analysis of clinical trial data only leverages part of the picture, ignoring unstructured data and limiting findability across all the information collected throughout multiple disparate data sources.  This roundtable will discuss leveraging a cognitive platform to combine all data from multiple sources into one unified view using a single entry point to the data.

 

Sasha Paegle, Life Science Business Development, Dell Technologies

Evaluating, optimizing and benchmarking of next generation sequencing (NGS) methods are essential for clinical, commercial and academic NGS pipelines. Optimizations for speed and accuracy often require making trade-offs relative to other constraints. Join this roundtable to discuss benchmarking strategies, trade-offs, and the value of benchmarking genomics tools and applications. 

PLENARY KEYNOTE PROGRAM

Michael Schwartz, Head, Product Marketing, Marketing, Benchling

The life science industry has forged ahead with a new generation of therapeutics. A new R&D paradigm is required to develop scientific platforms, manage data complexity, and orchestrate progress across specialized teams. Digital solutions and data ecosystems are at the heart of this, but require both structure and adaptability to thrive in the modern life science R&D environment.

12:30 pm KEYNOTE PRESENTATION & PANEL DISCUSSION:

Game On: How AI, Citizen Science, and Human Computation Are Facilitating the Next Leap Forward

Allison Proffitt, Editorial Director, Bio-IT World

While the precision medicine movement augurs for better outcomes through targeted prevention and intervention, those ambitions entail a bold new set of data challenges. Various panomic and traditional data streams must be integrated if we are to develop a comprehensive basis for individualized care. However, deriving actionable information requires complex predictive models that depend on the acquisition and integration of patient data on a massive scale. This picture is further complicated by new data streams emerging from quantified self-tracking and health social networks, both of which are driven by experimentation-feedback loops. Tackling these issues may seem insurmountable, but recent advancements in human/AI partnerships and crowdsourcing science adds a new set of capabilities to our analytic toolkit. This session describes recent work in online collective systems that combine human and machine-based information processing to solve biomedical data problems that have been otherwise intractable, and an information processing ecosystem emerging from this work that could transform the landscape of precision medicine for all stakeholders. Pietro will open with a framing talk, followed by short presentations from each panelist, ending with a moderated Q&A discussion by Allison with speakers and attendees. 

Panelists:
Seth Cooper, PhD, Assistant Professor, Khoury College of Computer Sciences, Northeastern University
Lee Lancashire, PhD, CIO, Cohen Veterans Bioscience
Pietro Michelucci, PhD, Director, Human Computation Institute
Jérôme Waldispühl, PhD, Associate Professor, School of Computer Science, McGill University
1:55 pm Refresh Break - View Our Virtual Exhibit Hall

CLOUD COMPUTING: APPLICATIONS

2:10 pm

Mass Spectrometry Data Processing in the Cloud: From Biological Samples to Digital Results Using Cloud Computing

Felipe Albrecht, PhD, Bioinformatics and Computer Scientist, Pharma Research and Early Development, F. Hoffmann-La Roche

In this presentation, we show how we are using cloud technologies for: (i) processing MS data through a cloud-based ETL pipeline for extracting features; (ii) analyzing MS data using in-house tools developed for Windows system in a cloud environment; and (iii) storing and organizing MS data and its metadata in a cloud-based Data Lake. The Data Lake allows researchers to access and explore the MS data through a convenient web interface, using metadata and data parameters, as well as the extracted data features. Finally, we present how our system uses the extracted features for automatic System Suitable Tests analysis, thus informing the researchers about the status and expected performance of the MS instruments.

2:50 pm Refresh Break - View Our Virtual Exhibit Hall
3:10 pm

Automating Molecular Modeling in the Cloud

Sam DeLuca, PhD, Director of Engineering Cyrus Biotechnology

Cyrus Biotechnology has developed a set of tools and research practices that allow us to rapidly develop complex molecular modeling procedures, automate the execution of those procedures and deliver them to our research team and to external customers as API based products.  This presentation will describe the architecture of cloud-native system that allows us to accomplish this as well as our approach to software engineering and scientific research.

Rob Lalonde, VP and GM - Cloud, Univa Corporation

Cloud computing allows life science researchers and organizations unprecedented access to compute capacity to improve their time to results. This session will look at cloud computing trends in life sciences and HPC in general and discuss various alternatives for cloud migration.

 

Jess Gordon, Senior Director, Software Engineering, Illumina

Learn how Illumina is enabling researchers, scientists, and informaticists to gain more insight on their genomic and multi-omic data with a new, flexible cloud-based platform. This platform allows researchers to store and manage data at scale, analyze data through custom and published workflows with high efficiency, and collaborate with users.

4:00 pm LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
Felipe Albrecht, PhD, Bioinformatics and Computer Scientist, Pharma Research and Early Development, F. Hoffmann-La Roche
Panelists:
Sam DeLuca, PhD, Director of Engineering Cyrus Biotechnology
Rob Lalonde, VP and GM - Cloud, Univa Corporation
Jay Patel, Product Manager, Software & Informatics, Illumina
4:20 pm Bio-IT Connects - View Our Virtual Exhibit Hall
5:00 pm Close of Day

Thursday, October 8

TRENDS FROM THE TRENCHES - 10TH ANNIVERSARY!

9:00 am KEYNOTE PRESENTATION & PANEL DISCUSSION:

Trends from the Trenches

Kevin Davies, PhD, Executive Editor, The CRISPR Journal; Founding Editor, Bio-IT World

The “Trends from the Trenches” will celebrate its 10th Anniversary at Bio-IT! Since 2010, the “Trends from 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 is 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 has helped scientists, leadership, and IT professionals understand the basic topics related to computing, storage, data transfer, networks, and cloud that are involved in supporting data-intensive science. In 2020, Chris will give the “Trends from the Trenches” presentation in its original “state-of-the-state address” followed by guest speakers giving podium talks on relevant topics. An interactive Q&A moderated discussion with the audience follows. Come prepared with your questions and commentary for this informative and lively session. To stay connected with Trends from the Trenches updates after today and all year, sign up for BioTeam's newsletter here: https://bit.ly/33uO0OY 

Panelists:
Vivien R. Bonazzi, PhD, Managing Director & Chief Biomedical Data Scientist, Deloitte Consulting LLP
Tim Cutts, PhD, Head of Scientific Computing, Wellcome Sanger Institute
Chris Dagdigian, Senior Director, BioTeam Inc.
Kjiersten Fagnan, PhD, CIO, Data Science & Informatics, Lawrence Berkeley National Laboratory
Matthew Trunnell, Data Commoner-at-Large; Executive Director, Pandemic Response Commons; Former Vice President and Chief Data Officer, Fred Hutchinson Cancer Research Center
Paul Speciale, Chief Product Officer, Product Management, Scality

Biotechnology companies are facing new challenges in the amount of data that needs processing for genomics analysis. What used to be Terabytes of data is now petabytes of data and beyond. This data needs to be collected, analyzed, processed and then ultimately retained for compliance and research purposes - resulting in massive data storage and management challenges, unsolvable by legacy technology solutions. Our session will explain how to leverage new all-flash storage and hybrid-cloud solutions to make genomics analysis run quantum leaps faster than before.

10:55 am Session Break
11:30 am Lunch Break - View Our Virtual Exhibit Hall
11:35 am Interactive Breakout Discussions

Consider joining a breakout discussion group. These are informal, moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.

Timothy Gardner, CEO, Riffyn, Inc.

How do you use data / digitization today to drive scientific discovery / product development?

What are you greatest scientific pain points / gaps that are not being met by digitization?

What kinds of outcomes do you believe digital tools could help you achieve?

 

Scott Jeschonek, Principal Program Manager, Microsoft Azure

Welcome to this discussion group on the growth of demand for HPC in scientific research. We are looking forward to a lively forum. We'll start by looking at three related topics:

- What events trigger demand in your organization? How has the current pandemic impacted resources?

- What could make scale and collaboration more accessible to more researchers?

- Share a recent experience of shifting workloads to manage HPC capacity.

Greg DiFraia, General Manager, Americas, Executive Team, Scality
Shailesh Manjrekar, Head of AI and Strategic Alliances, Executive Team, WekaIO

In this session we’ll discuss how to provide researchers with performance and scale in genomics & research analytics, to drive results at a price point that’s economically viable on public & private cloud.

11:35 am

Breakout: NGS Pipeline Optimizations

Tristan J Lubinski, PhD, Sr Scientist, Next Generation Sequencing Informatics, AstraZeneca Pharmaceuticals; Co-organizer, Boston Computational Biology and Bioinformatics (BCBB)
Howard Marks, Technologist Extraordinary and Plenipotentiary, VAST Data

Storage solutions we’ve been using force bioinformaticists to make trade-offs between the capacity and low-cost of disk and the performance of flash. This results in complex tiering configurations that only deliver performance for a small slice of the data. In this session, we will review how advancements in technology enable VAST Data to revolutionize the cost of all-flash and allows bioinformatists faster analysis across larger datasets for deeper insights.

PLENARY KEYNOTE PROGRAM

12:00 pm

Welcome Remarks

Cindy Crowninshield, Executive Event Director, Cambridge Healthtech Institute
Juergen A. Klenk, PhD, Principal, Deloitte Consulting LLP
12:15 pm

Toward Preventive Genomics: Lessons from MedSeq and BabySeq

Robert C. Green, Professor & Director, G2P Research, Genetics & Medicine, Brigham & Womens Hospital
12:40 pm

AI in Pharma: Where We Are Today and How We Will Succeed in the Future

Natalija Z. Jovanovic, PhD, Chief Digital Officer, Sanofi
1:05 pm

LIVE Q&A: Session Wrap-Up Panel Discussion

Panel Moderator:
Vivien R. Bonazzi, PhD, Managing Director & Chief Biomedical Data Scientist, Deloitte Consulting LLP
Juergen A. Klenk, PhD, Principal, Deloitte Consulting LLP
1:25 pm Happy Hour - View Our Virtual Exhibit Hall
2:00 pm Close of Conference





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