Software Applications and Services

As data generation increases, there is a need for workflows that are reproducible across infrastructures and empower scientists and researchers to apply cutting-edge analysis methods. One problem is scientific data are not centralized or standardized and are fragmented—from instrumentation to clinical research to legacy software. A second problem is critical validation of algorithms is commonly overlooked. There are real-world differences in data equivalence for integration and analysis, without adequate contextual information. A third problem is navigating vendor silos and deciding between all-in-one solutions or niche providers. The Software Applications and Services track explores these problems and how biopharma companies implementing solutions to drive data strategies and scientific decision-making by leveraging software tools and data platforms. Case studies will be presented on software tools to facilitate data manipulation, data analytics approaches, data methods and standards approaches, integration strategies, transparency, efficiency, security, and cost-effective solutions. What are critical approaches to validation of complex software development that will have to deal with missing/incomplete data, conflicting data, sparse data, etc.? These will become increasingly important as regulatory agencies evolve procedures and rules for implementation.

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

TOOLS, MODELS, AND SERVICES TO AUTOMATE AND OPTIMIZE DATA MANAGEMENT AND WORKFLOW PROCESSES

9:00 am

Harmonizing Lab Device and System Integration for Lab Workflow Automation

Andreas Steinbacher, PhD, Lead Discovery Informatics Data Management, Roche pRED Informatics

Lab device and system integration are too expensive, inflexible and time-consuming due to a lack of industry-wide standards. Instead of advocating for one specific software standard, this contribution suggests another way – a lab device integration ‘rule book’. The intention is to streamline the communication between instrument vendor, IT department, and lab scientist by defining different lab instrument complexity and integration levels.

9:20 am Session Break
9:40 am

Effectively Completing the Projects with Water-Agile-Fall Model

Gurpreet Kanwar, Senior Manager, Project Delivery Services, NAV CANADA

Water-Agile-Fall is a way to develop software without using full agile practices. It is the way to combine traditional planning in waterfall and execution in Agile way. Organizations are trying to execute agile practices but unable to give full control to project teams and prefer to have top down control similar to waterfall methodology. In this presentation you will learn the advantages and disadvantages of using Water-Agile-Fall, when Agile teams fall into Waterfall, hybrid model for executing projects with sample projects.

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

STANDARDS WITHIN THE CONTEXT OF TOOL DEVELOPMENT AND TEXT PROCESSING

10:20 am

Planet Microbe: A Modern Cyberinfrastructure Platform for FAIR Data and Tools.

Bonnie L. Hurwitz, PhD, Associate Professor, Biosystems Engineering, University of Arizona

Understanding the genomic content of the microbial communities from diverse ecosystems requires environmental contextual information; however, a lack of high-quality FAIR semantics to represent such information hinders the integration and annotation of existing data. Further, no standard exists to encapsulate multi-component marine metagenomic datasets and their annotation semantics within a machine-readable framework. Here we present a platform for FAIR data and tools called Planet Microbe that leverages ontology terms to annotate, standardize, and make each dataset's metadata findable, accessible, interoperable, and reusable (FAIR). This work pioneers a complete cyberinfrastructure system that not only includes the best available metadata-rich marine-omics datasets that are cleaned, standardized, and annotated but also allows for in-depth comparative analyses, via metadata searches and embedded computational tools (Apps).

10:40 am

Normalizing Regulatory Data Using Natural Language Processing (NLP)

Qais Y. Hatim, PhD, Visiting Associate, Office of Computational Science, FDA CDER co-presenting with David Milward, Dr., Senior Director, NLP Technology, Linguamatics, an IQVIA Company
David Milward, PhD, Senior Director, NLP Technology, Linguamatics

 

The FDA receives a high proportion of data as unstructured text. Natural Language Processing (NLP) is used to normalize information for further analysis or machine learning. A challenge is the variation in the ways that concepts are referred. Although there are a number of open source terminologies, not all are designed for text processing. We will describe some of the uses of text mining at the FDA, how to adapt terminologies, and how to extend coverage using machine learning.


 

Scott Weiss, VP, Product Strategy, IDBS

In this presentation, Scott Weiss, VP of Product strategy at IDBS, will take us through building an ecosystem that not only fills a need, but also fits into your lab’s workflows to drive R&D processes and ensure data is in an accessible and digestible format.

Subhadra R.V, Ph.D, Principal Domain Expert, Healthcare & Life Sciences, Persistent Systems
Sivasankar Ganesan, Data & Analytics Leader, Healthcare & Life Sciences, Persistent System

Personalized medicine and technology advances are transforming healthcare & disease management.  Data Analytics, integration of Genomics & Multi-omics, clinical and other diagnostic technologies make precision medicine a reality through informed decisions to precisely diagnose, treat, and prevent diseases.Learn how Persistent manages and analyses diverse data sets for actionable insights

11:30 am LIVE Q&A:

Session Wrap-Up

Panel Moderator:
Gurpreet Kanwar, Senior Manager, Project Delivery Services, NAV CANADA
Panelists:
Qais Y. Hatim, PhD, Visiting Associate, Office of Computational Science, FDA CDER co-presenting with David Milward, Dr., Senior Director, NLP Technology, Linguamatics, an IQVIA Company
Bonnie L. Hurwitz, PhD, Associate Professor, Biosystems Engineering, University of Arizona
Subhadra R.V, Ph.D, Principal Domain Expert, Healthcare & Life Sciences, Persistent Systems
Sivasankar Ganesan, Data & Analytics Leader, Healthcare & Life Sciences, Persistent System
Andreas Steinbacher, PhD, Lead Discovery Informatics Data Management, Roche pRED Informatics
Scott Weiss, VP, Product Strategy, IDBS
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

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.

 

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

 

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

TOOLS AND TOOLKITS FOR IMPLEMENTING FAIR DATA IN THE CLOUD

2:10 pm

Building a Toolkit for FAIR Implementation by Life Science Industry

Ian D. Harrow, PhD, Consultant Project Manager, Pistoia Alliance, Inc.

We report on building a new toolkit to help life science industry implement the FAIR (Findable, Accessible, Interoperable, Reusable) principles for data management and stewardship. It provides practical support by bringing together relevant methods for tools, training and managing change, which are illustrated by use cases mostly from life science industry. These elements are assembled together as one user-friendly and freely accessible website.

2:30 pm

BLAST, Pipelines and FAIR on the Cloud

Thomas L. Madden, Staff Scientist, Information Engineering, NCBI/NLM/NIH

A sequence similarity search often provides essential information about a DNA or protein sequence. With the rapidly expanding use of high-throughput sequencing, a few issues may occur for BLAST users. First, the need for searches may come in bursts, with many searches needing to be done at once and current resources unable to handle the load. Second, many searches are now part of a pipeline, which can be a powerful multiplier for bioinformatics tools, but is not straight-forward to maintain if it does not conform to FAIR (Findable, Accessible, Interoperable, and Reusable) principles. The cloud can help with the first problem, allowing a user to scale up the computational resources per their specific needs. Containerization and formal pipeline languages can help with the second issue, making pipelines more reproducible and easier to maintain. We discuss a containerized version of BLAST, usage with CWL, and a cloud infrastructure that includes databases hosted on cloud providers.

2:50 pm Refresh Break - View Our Virtual Exhibit Hall
Vasu Rangadass, PhD, CEO, L7 Informatics, Inc.
4:00 pm LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
Ian D. Harrow, PhD, Consultant Project Manager, Pistoia Alliance, Inc.
Panelists:
Thomas L. Madden, Staff Scientist, Information Engineering, NCBI/NLM/NIH
Vasu Rangadass, PhD, CEO, L7 Informatics, Inc.
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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