Original Agenda
We are actively working with our speakers to confirm their availability for the virtual event. Initial response from our speakers has been very positive, and we are optimistic we will have the new programs ready to share here soon.

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 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?

Final Agenda

Monday, october 5

9:00 am - 5:00 pm Hackathon*

*Pre-registration required.

Tuesday, october 6

7:30 am Workshop Registration Open and Morning Coffee

8:30 am - 3:30 pm Hackathon*

*Pre-registration required.

8:30 - 11:30 am Recommended Morning Pre-Conference Workshops*

W5. Giving the Personalized Digital Health Ecosystem a FAIRshake

Avi Ma’ayan, PhD, Professor, Department of Pharmacological Sciences; Director, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai

Daniel Clarke, Data Scientist, Ma'ayan Lab, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai

12:30 - 3:30 pm Recommended Afternoon Pre-Conference Workshops*

W12. Cancer Genome Analysis

Jeffrey Rosenfeld, PhD, Manager, Biomedical Informatics Shared Resource and Assistant Professor of Pathology and Laboratory Medicine, Rutgers Cancer Institute of New Jersey; President, Rosenfeld Consulting LLC

*Separate registration required.

2:00 - 6:30 Main Conference Registration Open


4:00 Welcome Remarks

Cindy Crowninshield, RDN, LDN, Executive Event Director, Cambridge Healthtech Institute





4:05 Keynote Introduction

4:15 PLENARY KEYNOTE PRESENTATION: 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





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



Wednesday, october 7

7:30 am Registration Open and Morning Coffee


8:00 Welcome Remarks

Allison Proffitt, Editorial Director, Bio-IT World




8:05 Awards Program Introduction

J.W. Bizzaro8:10 Benjamin Franklin Award and Laureate Presentation

J.W. Bizzaro, Managing Director, Bioinformatics.org





Allison Proffitt8:35 Bio-IT World Innovative Practices Awards

Allison Proffitt, Editorial Director, Bio-IT World




8:45 Keynote Introduction

8:55 PANEL DISCUSSION: Game On: How AI, Citizen Science, and Human Computation Are Facilitating the Next Leap Forward

Seth CooperSeth Cooper, PhD, Assistant Professor, Khoury College of Computer Sciences, Northeastern University






Lee LancashireLee Lancashire, PhD, Chief Information Officer, Cohen Veterans Bioscience






Pietro Michelucci, PhD, Director, Human Computation Institute






Jérôme WaldispühlJérôme Waldispühl, PhD, Associate Professor, School of Computer Science, McGill University






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 talk 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.

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


10:50 Organizer’s Welcome Remarks

Cambridge Healthtech Institute

10:55 Chairperson’s Remarks

11:00 KEYNOTE PRESENTATION: The Road from Data Commons to Data Ecosystems: Challenges, Opportunities, and Emerging Best Practices

Grossman_RobertRobert Grossman, PhD, Frederick H. Rawson Distinguished Service Professor in Medicine and Computer Science; The Jim and Karen Frank Director, 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.

11:30 Harnessing Cloud for Mega-Biobanks: Efficient Computing with Sensible Data Governance

Pyarajan_SaijuSaiju 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.

Google-Cloud-New 12:00 pm Presentation to be Announced


12:15 Presentation to be Announced

12:30 Session Break

12:40 Luncheon Presentation I to be Announced

Microsoft_Azure 1:10 LUNCHEON PRESENTATION II: Bioinformatics Pipelines in Azure

Jer-Ming Chia, Principal Program Manager, Microsoft

Scott Jeschonek, Principal Program Manager, Azure, Microsoft

The lunch session will describe how to apply a typical bioinformatics pipeline on Microsoft Azure. Topics will include common workflow frameworks like Cromwell and Nextflow in Azure, data storage and access considerations, and a discussion about the advantages of leveraging the latest AMD EPYC based virtual machines in these pipeline architectures.

1:40 Session Break


1:50 Chairperson’s Remarks

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

1:55 Evaluating Distributed Computing Infrastructures: An Empirical Study Comparing Hadoop Deployments on Cloud and Local Systems**

Bhattacharya_DevipsitaDevipsita 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.

2:25 Reproducible Software Stacks Everywhere - Cloud, Containers and OnPrem

Dey_JohnJohn 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.


2:55 Supercharging Transformation Across the Life Science Value Chain

Partovi_ShezShez Partovi, MD, Director, Healthcare, Life Sciences, Genomics, Amazon Web Services

Learn how life science companies are working with AWS to transform their organizations, from creating labs of the future to enhancing clinical trials with artificial intelligence and machine learning, to developing digital therapeutics. Finally, hear how this transformation helps organizations drive top-line revenue and improve patient experiences.


3:10 Presentation to be Announced

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


4:00 Chairperson's Remarks

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

4:05 Managing Large-Scale Lab Data in Cloud

Moiseyenko_OlegOleg Moiseyenko, Senior Cloud Architect, Scientific Computing Systems, Bristol-Myers Squibb

In days of high-speed internet and cloud computing, life sciences organizations still face significant difficulties moving laboratory data from labs to cloud. This includes but is not limited to typical challenges usually associated with big data as well as data validations, choosing effective data ingest mechanism, establish-ing the right data tagging systems, indexing for metadata catalogs, applying propriety encryption, systems qualification, and petabyte-scale data enrichment as well as data archival. This presentation highlights Bristol-Myers Squibb Company’s approach to these problems.

4:25 Mass Spectrometry Data Processing in the Cloud: From Biological Samples to Digital Results using Cloud Computing

Albrecht_FelipeFelipe Albrecht, PhD, Bioinformatics and Computer Scientist, Pharma Research and Early Development (pRED), Roche Diagnostics GmbH

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.

4:45 Single Point of Truth for Target Identification and Validation – In-House Hosted OpenTargets

Liu_SeanSean Liu, PhD, Global Head, Scientific Assets & Decision Support, Scientific Informatics, Takeda Pharmaceuticals

Takeda has joined the Open Targets consortium and has installed the Open Targets platform on internal cloud platform to help our target discovery process. We will outline the motivation for this decision, give an overview of how we use the system and the benefits we derive from it.

5:05 Sponsored Presentation (Opportunity Available)




5:35 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing


6:45 End of Day

Thursday, october 8

7:30 am Registration Open and Morning Coffee


8:00 Organizer’s Remarks

Cindy Crowninshield, RDN, LDN, Executive Event Director, Cambridge Healthtech Institute




Robert Green8:15 Toward Preventive Genomics: Lessons from MedSeq and BabySeq

Robert Green, MD, MPH, Professor of Medicine (Genetics) and Director, G2P Research Program/Preventive Genomics Clinic, Brigham & Women’s Hospital, Broad Institute, and Harvard Medical School




Natalija Jovanovic9:00 AI in Pharma: Where We Are Today and How We Will Succeed in the Future

Natalija Jovanovic, PhD, Chief Digital Officer, Sanofi Pasteur




9:45 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced at 10:00





10:30 Organizer’s Remarks

Cambridge Healthtech Institute

10:35 Chairperson’s Remarks

10:40 Umbrella: Infrastructure-Enabling FAIR Data Management

Ryan Golhar, PhD, Senior Research Investigator, Bristol-Myers Squibb

Bristol-Myers Squibb had a need several years ago for an NGS data management and analysis platform.  Born out of that need, a home-grown platform was developed which has since transformed into an enterprise-wide platform, called NGS360.  NGS360 is an Amazon-based platform designed to enable users to easily manage and analyze NGS data.  The NGS360 platform can integrate with external applications using REST APIs and currently supports Illumina BaseSpace and the SevenBridges platform.  While NGS360 is focused on next-gen sequencing data, its capabilities enable it to work with any other assay types including image/pathology and mass-spec data. 

11:10 PEPSI-KOLA: A Data-Driven Approach to Find and Connect with Thought Leaders

Gupta_RishiRishi Gupta, PhD, Research Scientist, Information Research, AbbVie, Inc.

Within a Life Science organization, Key Opinion Leaders, or KOLs, are generally influential physicians or academic researchers who are respected and acknowledged as leaders in a subject area. In this work, we will showcase the KOL application utilized by business functions within AbbVie that uses several structured and unstructured data sources to evaluate each thought leader in qualitative and quantitative ways with the goal of optimizing selection and management.

11:40 Sponsored Presentation (Opportunity Available)

12:10 pm Session Break

AWS 12:20 LUNCHEON PRESENTATION I:  Pre-Competitive Tools for Accelerating Biotech R&D in the Cloud

Elliot Menschik, MD PhD, Global Head, Life Science Startups, Amazon Web Services
Karina Chmielewski, VP, Platform Operations, Third Rock Ventures

The convergence of data science, biology and chemistry has accelerated the need for robust cloud-based environments that support lab automation, informatics workflows, high-performance computation, machine learning, and cross-organizational collaborations. The Biotech Blueprint is a set of pre-competitive tools that speed turnkey creation of virtual R&D labs and streamline deployment of third-party open source and proprietary tools for research informatics, HPC and ML. We’ll discuss its latest features, roadmap and results from adoption by next-generation biotechs.

IDBS 12:50 Luncheon Presentation II to be Announced


1:20 Dessert Refreshment Break in the Exhibit Hall with Last Chance Poster Viewing


1:55 Chairperson’s Remarks

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



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


Bonazzi_VivienVivien Bonazzi, PhD, Chief Biomedical Data Scientist, Managing Director, Deloitte


Cutts_TimTim Cutts, PhD, Head, Scientific Computing, Wellcome Trust Sanger Institute


Fagnan_KjierstenKjiersten Fagnan, PhD, Chief Informatics Officer, Data Science and Informatics Leader, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory


Trunnell_MatthewMatthew Trunnell, Data Commoner-at-Larger; former Vice President and Chief Data Officer, Fred Hutchinson Cancer Research Center


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.

4:00 Close of Conference


**Presentations delivered via a live, interactive, video conferencing platform**

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