Data Visualization Tools

With a sharp increase in the volume and complexity of big datasets for research and drug discovery labs, data visualization is needed to clearly express the complex patterns. It is more important than ever to develop data visualization and exploration tools alongside the rest of the analytics, as opposed to later in the game. The Data Visualization Tools track will discuss new visualization tools, dashboards, and platforms, as well as ways that these tools can help solve problems, validate, and interpret the data science and artificial intelligence insights. How can your visualization methods be validated as to their ability to provide full analytic results that may extend well beyond 2 or 3 dimensions?

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

CREATING A NARRATIVE WITH YOUR DATA

9:00 am

The State of the Art in Visualizing Multivariate Networks

Carolina Nobre, PhD, PostDoc Fellow, Harvard University

Multivariate networks are made up of nodes and their relationships (links), but also data about those nodes and links as attributes. Most real-world networks are associated with several attributes, and many analysis tasks depend on analyzing both, relationships and attributes. Visualization of multivariate networks, however, is challenging, especially when both the topology of the network and the attributes need to be considered concurrently. In this state-of-the-art report, we analyze current practices and classify techniques along four axes: layouts, view operations, layout operations, and data operations. We also provide an analysis of tasks specific to multivariate networks and give recommendations for which technique to use in which scenario. Finally, we survey application areas and evaluation methodologies.

9:20 am

Visualizing the Clinical Research Landscape – And Why It Matters for Ethics, Efficiency, and Transparency

Spencer Hey, PhD, CSO at Prism Analytic Technologies and faculty at Harvard Medical School

In this talk, I will present three different pictures of clinical research landscapes–one depicting a single drug development trajectory; one depicting a family of development trajectories from drugs in the same class; and one depicting the entire research portfolio from ten pharmaceutical companies. I will argue that each of these pictures has something valuable to teach about how to make the research enterprise more efficient, transparent, and ethical.

9:40 am

Cellxgene VIP Unleashes Full Power of Interactive Analysis of Single Cell RNA-seq Data with Millions of Cells


Baohong Zhang, PhD, Head, Genome Informatics, Biogen

To meet the growing demands from scientists to effectively extract deep insights from single cell RNA-seq datasets, we developed cellxgene VIP, a frontend interactive visualization plugin to cellxgene framework, which directly interacts with in-memory data to generate a comprehensive set of plots in high resolution, perform advanced analysis, and make data downloadable for further analysis. It makes large scale scRNA-seq data visualization and analysis more accessible and reproducible with the potential to become an ecosystem for the scientific community to contribute even more modules to the Swiss knife of scRNA-seq data exploration tool. The source code is available at https://github.com/interactivereport/cellxgene_VIP. 

10:00 am Coffee Break - View Our Virtual Exhibit Hall
10:20 am

SeedMeLab - Data Management System: Search, Manage, Share, and Visualize Data

Amit Chourasia, Visualization Group Leader, University of California San Diego

SeedMeLab, a web-based data management system, comprises a modular set of building blocks that could be configured and customized in an extensible manner. It enables to host data on the web/intranet with access controls and pluggable identity management. The expressive and extensible file system allows data, its description, and its discussion to be collocated, which catalyzes discovery. It enables rich presentation and visualization that aids in making data more insightful. The built-in web services, coupled with extension API, make it a powerful platform to realize FAIR data compliance. Research teams or science applications could spin up SeedMeLab with their own branding and domain with customized file-system and presentation layout.

11:00 am LIVE Q&A:

Session Wrap-Up

Panel Moderator:
Spencer Hey, PhD, CSO at Prism Analytic Technologies and faculty at Harvard Medical School
Panelists:
Amit Chourasia, Visualization Group Leader, University of California San Diego
Carolina Nobre, PhD, PostDoc Fellow, Harvard University
Baohong Zhang, PhD, Head, Genome Informatics, Biogen
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

ANALYTIC AND VISUALIZATION TOOLS FOR IMPROVED DATA INSIGHTS

2:10 pm

The Global Substance Registration System (GSRS): An Essential Tool for Structuring Translational Clinical and Regulatory Data

Lawrence Callahan, PhD, Chemist, Global Substance Registration System/Office of Health Informatics, Office of Chief Scientist, FDA

The ISO IDMP is a set of standards developed by regulators and industry to structure medicinal product information in a consistent manner. The GSRS is freely distributed software, developed in collaboration with NIH/NCATS, that implements the substance standard. The GSRS defines substances in medicinal products and related substances, such as targets, metabolites, and impurities, and links these substances to products, clinical trials, applications, and adverse events.

2:30 pm

Offshoot Applications from the G-SRS Moonshot

Danny Katzel, Senior Software Engineer, National Center for Advancing Translational Science, NIH

While developing G-SRS, the NIH/NCATS team developed useful standalone tools to help streamline registration, curation, and regulation of medicinal ingredients. This presentation will cover three such projects: an image to chemical structure recognition program (molvec); an abstraction layer allowing cheminformatics software to switch between underlying informatics frameworks at runtime (molwitch); and Inxight:Drugs, which incorporates and unifies marketing, regulatory status, rigorous drug ingredient definitions, biological activity, and clinical use.

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

Clinical Data Visualizations to Drive Clinical and Biomarker Exploration Using Both Clinical Trial and Real-World Data

Philip Ross, PhD, Director, Clinical Data Utilization, Knowledge Science Research, Bristol-Myers Squibb

Exploratory visualizations generated from clinical trials and real-world data sources provide important insights into safety, efficacy, and biomarker responses to novel and standard-of-care treatments. Automation of data updates in near-real time increases the impact of this information on decision-making.

3:30 pm

Supporting Personalized Healthcare by Pooling and Integrating Diverse Types of Data

Ewa Jermakowicz, IT Business Partner, Scientific Decision Support Network, Roche

Truly personalized healthcare is possible only if we have access to meaningful, diverse and integrated data at scale. We are working on an E2E Engine that will allow us to FAIRify our clinical and molecular data from planning, through ingestion to re-use. We are creating a solution to pool clinical data with molecular, genomics and digital biomarkers for diverse therapeutic areas to fully capitalize on Roche scientific data. To address the diversity of the scientific data we leverage a Data Commons approach to process data from source systems in order to pool and share them with scientists.

4:00 pm LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
Lawrence Callahan, PhD, Chemist, Global Substance Registration System/Office of Health Informatics, Office of Chief Scientist, FDA
Panelists:
Ewa Jermakowicz, IT Business Partner, Scientific Decision Support Network, Roche
Danny Katzel, Senior Software Engineer, National Center for Advancing Translational Science, NIH
Philip Ross, PhD, Director, Clinical Data Utilization, Knowledge Science Research, Bristol-Myers Squibb
4:20 pm Bio-IT Connects - View Our Virtual Exhibit Hall
5:00 pm Close of Day

Thursday, October 8

SINGLE-CELL RNA-Seq DATA PLATFORMS, TOOLS, AND ANALYSIS

9:00 am

Embedding Single-Cell RNA-Seq Profiles in Non-Euclidean Spaces

Jiarui Ding, PostDoc Associate, Broad Institute

Single-cell RNA-Seq has become an invaluable tool for studying biological systems in health and diseases. We introduced scPhere, a scalable deep generative model to embed cells into low-dimensional hyperspherical or hyperbolic spaces, as a more accurate representation of the data. scPhere resolves cell crowding, corrects multiple, complex batch factors, facilitates interactive visualization of large datasets, and gracefully uncovers pseudotemporal trajectories.

9:20 am

Scaling scRNASeq Visualization to Unlimited Datasets with Cellxgene Gateway

Alok Saldanha, PhD, Technical Associate Director, NIBR Informatics, Novartis Institutes for Biomedical Research

Cellxgene Gateway is an open source tool (https://github.com/Novartis/cellxgene-gateway) which allows you to use the Cellxgene Server provided by the Chan Zuckerberg with multiple datasets. I will introduce this tool in the context of a typical single-cell RNA-Seq analysis workflow, and touch on deployment issues in an enterprise cloud with a budget.

9:40 am Coffee Break - View Our Virtual Exhibit Hall
10:00 am

LIVE Q&A: Session Wrap-Up Panel Discussion

Panel Moderator:
Alok Saldanha, PhD, Technical Associate Director, NIBR Informatics, Novartis Institutes for Biomedical Research
Panelists:
Jiarui Ding, PostDoc Associate, Broad Institute

VISUALIZING BUSINESS VALUE WITH VCs

10:20 am

Live Panel Discussion:  Visualizing Business Value with VCs

Panel Moderator:
Annastasiah M. Mhaka, PhD, Co-Founder & Convenor, AAIH; Founder, Mawambo

This panel is useful for startups and young companies to learn what VCs are looking for to invest in new platforms and technology. Topics to be addressed include: 1) Explore trends and lessons learned with regards to how AI and digital health platform developers are strategically partnering with BioPharma to accelerate business and asset value; 2) How to collaborate with pharmaceutical and technology companies when you are a startup; 3) What are VCs looking for?; 4) Discuss how software and platform developers are creating value around tools to secure capital, including key challenges and opportunities, and 5) Examine tangible case studies of what is working and what isn’t within this dynamic of stakeholders.

Panelists:
Navid Alipour, Co-Founder & Managing Partner, Analytics Ventures
Ardy Arianpour, CEO & Co-Founder, Seqster
Avantika Daing, Managing Director & Partner, Plum Alley Investments
Sean J. Cheng, PhD, Senior Investment Manager, Philips Ventures
Jessica J. Federer, Venture Affiliate Partner, Boston Millennia Partners
Michael Langer, Head of Search and Evaluation, Pear Therapeutics
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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