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.

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

Amir Lahav, ScD, Digital Health Innovation Consultant

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

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

W16. Dealing with Instrument Data at Scale: Challenges and Solutions

Rachana Ananthakrishnan, Head, Products, Globus, University of Chicago

Brigitte Raumann, Product Manager, Globus, University of Chicago

*Separate registration required.

2:00 - 6:30 Main Conference Registration Open

PLENARY KEYNOTE SESSION

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

PLENARY KEYNOTE SESSION

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

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

10:50 Organizer’s Welcome Remarks

Cambridge Healthtech Institute

10:55 Chairperson’s Remarks

11:00 AIDEAS Web: The New Generation Web Enabled Cheminformatics Platform

Gupta_RishiRishi Gupta, Principal Research Scientist, Data Science and Informatics, AbbVie, Inc.

The first part of the presentation will showcase the technology on which AIDEAS Web is built. The second part will focus on AIDEAS Lite which has enabled scientists across AbbVie by making several workflows seamless and easy to use. We will present a few examples to highlight the ability of AIDEAS to provide advanced scientific workflows within one of the best visual analytics frameworks that easily allows users to share information and define multiple analysis templates. Authors: Pierrick Chabot, Rishi Gupta.

11:30 Harmonizing Lab Device and System Integration for Lab Workflow Automation

Steinbacher_AndreasAndreas Steinbacher, PhD, R&D Informatics and Machine Learning/Artificial Intelligence Leader for Lab Automation, Roche Innovation Center Munich

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.

12:00 pm SeedMeLab - Data Management System: Search, Manage, Share and Visualize Data

Amit Chourasia, Visualization Group Leader, San Diego Supercomputer Center, UC San Diego

SeedMeLab is web-based data management system. It 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 filesystem and presentation layout.

12:30 Session Break

12:40 Luncheon Presentation I: Talk Title to be Announced

Holm-Nygaard_SaraSara Holm Nygaard, Global Product Manager, Intomics


IDBS 1:10 Luncheon Presentation II to be Announced

1:40 Session Break

TOOLS, MODELS, AND SERVICES TO AUTOMATE AND OPTIMIZE DATA MANAGEMENT AND WORKFLOW PROCESSES (CONT.)

1:50 Chairperson’s Remarks

Gurpreet Kanwar, MBA, PMP, Senior Manager, Project Delivery Service, NAV CANADA

1:55 SaaS Healthcare Platform that Enable Organizations to Drive Efficient Healthcare with Integrated Data

Arianpour_ArdyArdy Arianpour, CEO & Co-Founder, Seqster


2:25 Effectively Completing the Projects with Water-Agile-Fall Model

Gurpreet_KanwarGurpreet Kanwar, MBA, PMP, Senior Manager, Project Delivery Service, 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.

2:55 Next-Generation Bio-Data Management Systems

Vasu Rangadass, PhD, CEO, L7 Informatics, Inc.

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

IMAGE MANAGEMENT AND ANALYSIS SOLUTIONS

4:00 Chairperson’s Remarks

4:05 Icy2.0: A Newly Redesigned Open and Free Software for Bioimage Analysis

Olivo-Marin_Jean-ChristopheJean-Christophe Olivo-Marin, PhD, Head, BioImage Analysis Unit and Director, Institute Carnot Pasteur Microbes et Santé, Institut Pasteur

We present Icy2.0, which is a major evolution of our previous free and open software for bioimage analysis Icy. This release has three important features: 1) the ability to handle very large images (> 4Gb); 2) the possibility to process long sequences; and 3) a totally redesigned web site for improved interactions with the users community.

4:35 Image Management for Research: To What End

Whitehead_PaulPaul Whitehead, PhD, Head, IT Business Partner, Leads Discovery & Optimization, Bristol-Myers Squibb

Advanced digital microscopes have revolutionized biology and pharmaceutical research, generating massive volumes of images, including 3D and time series data. But scientists can’t study what they can’t measure. The need to quantify biological characteristics, such as cell count, or to calculate metrics such as drug occupancy, has driven a need to seamlessly ingest, annotate, share, analyze and archive image datasets. This project seeks to make image datasets easily discoverable, accessible, transformable, and analyzable, and to ensure that numeric datasets derived from image datasets are easily transferable to downstream data analysis platforms.

5:05 Presentation to be Announced


 

RedRiver

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

PLENARY KEYNOTE SESSION & AWARDS PROGRAM

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

 

 

DATA-DRIVEN STANDARDS

10:30 Organizer’s Remarks

Cambridge Healthtech Institute

10:35 Chairperson’s Remarks

10:40 It Takes a Village vs Field of Dream Approaches for Data-Driven Standards

Schriml_LynnLynn Schriml, PhD, Associate Professor, Epidemiology and Public Health Department and Institute of Genome Sciences, University of Maryland School of Medicine


11:10 iMicrobe Project and Potentially the NMDC and the Practicalities, Pain Points of Standards within the Context of Tool Development

Hurwitz_BonnieBonnie Hurwitz, PhD, Assistant Professor, Biosystems Engineering, University of Arizona


11:40 Sponsored Presentation (Opportunity Available)

12:10 pm Session Break

12:20 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

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

KEYNOTE PRESENTATION & PANEL DISCUSSION:
TRENDS FROM THE TRENCHES 2020

1:55 Chairperson’s Remarks

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


 

2:00 KEYNOTE PRESENTATION & PANEL DISCUSSION: Trends from the Trenches

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



Platinum Sponsors

accenture

BenchlingNEW

Elsevier-square

L7-informatics

linguamatics

Nutanix

PerkinElmer

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