Track 4: Software Applications and Services

Tools, Models, and Services to Automate and Optimize Digital Data Flow and Processes

May 4 - 5, 2022 ALL TIMES EDT

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, critical validation of algorithms, is commonly overlooked. There are real-world differences in data equivalence for integration and analysis, without adequate contextual information. The Software Applications and Services track explores how biopharma companies are driving 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, transparency, efficiency, security, and cost-effective solutions.

Tuesday, May 3

7:00 am Registration Open (Plaza Level Lobby)
8:00 am Recommended Pre-Conference Workshops and Symposium*

On Tuesday, May 3, 2022 Cambridge Healthtech Institute is pleased to offer nine pre-conference workshops scheduled across three time slots (8:00-10:00 am, 10:30 am-12:30 pm, and 1:45-3:45 pm) and a Symposium from 8:25 am-3:45 pm. All are designed to be instructional, interactive and provide in-depth information on a specific topic. They allow for one-on-one interaction and provide a great way to explain more technical aspects that would otherwise not be covered during the main conference tracks that take place Wednesday-Thursday.

*Separate registration required. See Workshop page and Symposium page for details.

3:45 pm Session Break and Transition to Plenary Keynote

PLENARY KEYNOTE LOCATION: 210 (Overflow 208)

PLENARY KEYNOTE PROGRAM

4:00 pm

Welcome by Conference Organizer

Allison Proffitt, Editorial Director, Bio-IT World
4:05 pm Innovative Practices Award
Mike Tarselli, PhD, Chief Scientific Officer, TetraScience
4:30 pm

Ask What IT Can Do for Bio...and What Bio Can Do for IT

George M. Church, PhD, Robert Winthrop Professor, Genetics, Harvard Medical School

IT for Bio: In May 2021, one haploid human genome (3.055 billion bp) was sequenced completely, but zero diploid. We have 7.7 billion diploid humans yet to be sequenced and correlated with their environments and traits in the Personal Genome Project. Plus, at least one genome from each of over 8.7 million eukaryotic species in the Earth Biogenome project. Plus, monitoring pathogenic and commensal bacteria, allergens, and viruses in the BioWeatherMap. Plus, ancient DNA. We are counting RNA molecules per cell in most (or all) cell types in humans, mice, and many other species throughout development and connectome (with imaging resolution up to 20 nm).   

Bio for IT: Reading and writing DNA has improved exponentially in cost (at least 60 million fold) and is increasingly used for storing non-biological data. The record for editing DNA in vivo is now 24,000 edits per cell and for storing data in vivo is about 1 terabyte per mouse. Enormous chemical and biological 'libraries' can perform 'Natural Computing' for tasks far beyond current von-Neumann silicon and quantum computers. The combination of these – machine learning + megalibraries (ML-ML) is already having commercial impact (e.g. Nabla, Manifold, Dyno, Patch). 

5:45 pm Welcome Reception in the Exhibit Hall with Poster Viewing (Auditorium/Hall C)
7:00 pm Close of Day

Wednesday, May 4

7:00 am Registration Open and Morning Coffee (Plaza Level Lobby)

PLENARY KEYNOTE ROOM LOCATION: 210

PLENARY KEYNOTE PROGRAM

8:00 am

Welcome by Conference Organizer

Allison Proffitt, Editorial Director, Bio-IT World
Zachary Powers, Chief Information Security Officer, Benchling
8:15 am

Accessing and Securing the Data that Drives Breakthroughs

Allison Proffitt, Editorial Director, Bio-IT World
Rachana Ananthakrishnan, Executive Director, Globus, University of Chicago
Ari E. Berman, PhD, CEO, BioTeam, Inc.
Jonathan C. Silverstein, Chief Research Informatics Officer & Professor, Biomedical Informatics, University of Pittsburgh
Rebecca F. Rosen, PhD, Director, Office of Data Science and Sharing, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health

Life sciences research is generating massive amounts of data that should be accessible to collaborators and colleagues to enable breakthrough discoveries. However, ensuring sensitive data are shared securely in a manner that protects patient privacy and complies with myriad regulations is a daunting task, which often slows the pace of research. Our panel of leading practitioners will share insights on the challenges and best practices of managing protected research data.

9:30 am Coffee Break in the Exhibit Hall with Poster Viewing (Auditorium/Hall C)

ROOM LOCATION: 310

DRIVING DIGITIZATION, WORKFLOWS AND SCIENTIFIC DECISION-MAKING

10:15 am Organizer's Remarks
10:20 am

Chairperson's Remarks

Gurpreet Kanwar, Senior Manager, Project Delivery Services, NAV CANADA
10:25 am

Managing Risks for Faster Delivery

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

Almost all technology projects face multiple risks that impact the project delivery across organizations. In this talk, you will learn the most important risks your technology projects can face and how strategies can be put in place to mitigate them and deliver as planned. Also learn the steps or process to manage risks to keep your projects on track. Good risk management means fewer issues, planned delivery and client confidence in your team to handle all uncertainties.

10:55 am

Validation as a Service: Value of Quality and DevOps to Early-Stage Drug Development

C. Jeffrey Weitz, Associate Director, Enterprise Applications, Frequency Therapeutics

The pace of innovation in software and informatics is greatly outpacing most IT organizations. With regulatory agencies finally catching up (e.g., Computer Software Assurance in the FDA), business must build robust pipelines for evaluating, designing, testing, and deploying new applications let alone emerging technologies. Companies large and small can unlock their data pipeline by blending continuous integration with continuous improvement. Quality and DevOps principles can accelerate change, de-risk, technology and deliver quality data. In this talk, I discuss how I attack this problem from the perspective of culture and organizational habits. Giving the audience the wherewithal to change their teams and companies’ mindsets will help them evaluate the plethora of DevOps tools I introduce to meet their specific needs.

11:25 am

Authorization (AuthZ) Engine Architecture for Distributed Systems

John Jacquay, Scientific Systems Engineer, BioTeam, Inc.

Authorization is a critical component of data systems that adhere to FAIR data principles. Distinct from authentication concerns (e.g. who is using the system), authorization engines answer the age-old data-governance question for data storage systems and applications: what information or resource(s) does the user have access to? Is the user permitted to perform an operation on this resource? In my talk titled "Authorization (AuthZ) Engine Architecture For Distributed Systems" I outline an ideal architecture for authorization engines in the context of distributed systems., including direction on avoiding common pitfalls relating to performance, capabilities, and architecture.

Jan Christopherson, Application Scientist, ChemAxon

Automated regulatory compliance is a necessity in substance management. As a consequence of the spread of psychoactive substance derivatives, regulators increasingly use generic compound definitions, challenging conventional compliance verification methods. To solve this we have developed a novel search technology harnessing Markush structure queries, which increases the reliability of checking procedures.
We exhibit benchmarks against MolPort’s 45.8m compounds, and highlight the native scalability and integrability of the ComplianceChecker SaaS solution.

12:25 pm Interactive Discussions

Interactive Discussions are informal, moderated discussions, allowing participants to exchange ideas and experiences and develop future collaborations around a focused topic. Each discussion will be led by a facilitator who keeps the discussion on track and the group engaged. For in-person events, the facilitator will lead from the front of the room while attendees remain seated. For virtual attendees, the format will be in an online networking platform. To get the most out of this format, please come prepared to share examples from your work, be a part of a collective, problem-solving session, and participate in active idea sharing. Please visit the Interactive Discussion page on the conference website for a complete listing of topics and descriptions.

Mike Jones, General Manager Americas, Do iT Lean
Michael Cattapan, Director, Software Engineering, AbbVie
Yann Danilovich, Head of Scientific Product Engineering, R&D, Takeda

Got Legacy? In this moderated session we will explore how Takeda and Abbvie are leveraging new technologies to speed up and simplify the delivery of new digital solutions to modernize their business. We will ask the audience to share their experience and learn how these companies are challenging the status quo.

12:55 pm Session Break and Transition to Luncheon Presentation
Terence Barnhart, Effectiveness and Transformation Executive, Biopharmaceutical Organizational Design, Novartis

A lot of people feel stuck.  No one seems to have the power to change the status quo, no matter their title.  Why does it take so much time, effort and money to bring new therapies to market? Why can’t we change it, despite careers of effort? Apparently, we can change it. The urgency of the pandemic and the Warp Speed program proved that our constraints are self-imposed. In fact, the path to speed has been known for decades. But we, as an industry don't implement those solutions. It's time to change that. This talk will attack the problem with remedies at different levels, and will end with a tangible action that you can implement tomorrow. Disrupters, we need you. Change never happens until enough people stop believing that they’re stuck.

1:50 pm Refreshment Break in the Exhibit Hall with Poster Viewing (Auditorium/Hall C)

TOOLS, MODELS AND SYSTEMS FOR DATA ANALYSIS, RISK AND COMPLIANCE MONITORING, AND OPTIMIZING DATA FLOW PROCESSES

2:35 pm

Chairperson's Remarks

Rishi R. Gupta, PhD, Associate Director, Data Science, Novartis Institute for Biomedical Research
2:40 pm

CO-PRESENTATION: The “NIBR”verse of Drug Discovery

Rishi R. Gupta, PhD, Associate Director, Data Science, Novartis Institute for Biomedical Research
Wilian Cortopassi, PhD, Senior Expert in Data Science (Principal Scientist), Novartis Institutes for BioMedical Research (NIBR)

Since 2017, The Novartis Institutes for BioMedical Research (NIBR) has pioneered the use of virtual reality (VR) for collaborative structure-based drug design. This has been enabled through a research partnership with Nanome, Inc., a VR software company specializing in immersive molecular design. With the advantages of interactive multi-user drug design demonstrated, we are now expanding our NIBR immersive virtual drug design world, named as “NIBR”verse, to all NIBR associates, independent of skillset, to interactively communicate from anywhere in a fully configurable and non-passive VR environment. The VR technology has seen a remarkable growth in recent years. Through the research partnership, the VR environment has evolved from a tool for collaborative protein/small molecule visualization, to a fully functional drug design platform for small molecules and proteins, that through its interactive and global reach provides a powerful 3D ideation platform. NIBR is currently using AutoFocus, an internal web-browser platform, as a main chemistry design application for NIBR with advanced 3D tools already available. This platform is being developed in collaboration with Discngine, which in turn is already a strategic partner with Nanome. In this talk, we will discuss our advancements in integrating AutoFocus and other internal drug design tools in the “NIBR”verse of drug discovery.

3:10 pm

Robust Automated and Interactive Protocols for NMR-Based Fragment Screening Using the CcpNmr Analysis Screen Programme

Geerten Vuister, PhD, Professor, Molecular & Cell Biology, University of Leicester

Nuclear Magnetic Resonance (NMR) is used in many stages of fragment-based drug discovery and design (FBDD), including for identifying lead drug-like molecules. In my presentation, I will document the role of NMR in FBDD and show how CcpNmr AnalysisScreen facilitates quality assessment of NMR data, and how robust and optimised workflows for automated rapid hit identification can be implemented, thus improving the speed, reliability, and reproducibility of the NMR-based FBDD process. AnalysisScreen is a modern, intuitive, and versatile biomolecular NMR software platform that enables easy analysis of the large datasets needed in the early process of drug discovery by NMR.

3:40 pm

Augmented Drug Design (Innovative Practices Award Winner)

Anna Berg Åsberg, Global Vice President R&D IT, AstraZeneca
Alla Bushoy, Engineering Lead, Augmented DMTA Platform, AstraZeneca

The Pharmaceutical industry is seeking to accelerate Drug Discovery through a renewed focus on the valuable data it has accumulated and find ways to use these data far more effectively through Artificial Intelligence and Machine Learning techniques that were previously impossible. Augmented Drug Design is the program driving AstraZeneca’s efforts in the Drug Design space with the aim of significantly reducing the time to develop candidate drugs. Built in conjunction with EPAM Systems, Amazon Web Services and Schrödinger, the Augmented Drug Design platform uses centralized data access guided by FAIR data principles and high-performance computational modeling coupled with AI/ML insights to provide our scientists with novel drug design capabilities. In the twenty months since program inception, these technologies have been deployed against 70% of our small molecule projects and have significantly impacted several areas including molecular ideation, library design decisions, synthetic route planning, patent research and writing and have already contributed to accelerations in the discovery pipeline. 

Kelly Bachovchin, PhD, Customer Engagement Scientist, Support, Collaborative Drug Discovery, Inc.

Collaborative Drug Discovery (CDD) provides a whole solution for today’s biological and chemical data needs, differentiated by ease-of-use and superior collaborative capabilities.  CDD Vault® software includes Activity & Registration, Visualization, Inventory, and ELN capabilities. Researchers can archive, mine, and securely collaborate within CDD Vault.  Collaborative hypothesis generation and evaluation allow multiple perspectives for multi-parameter optimization.

Matt Clifford, Director of Research and Innovation, IDBS

Leading-organizations-are-developing-next-generation digital-strategies, including-adopting AI&ML tools. AI tools are cherries on the top of the cake of well-designed architectures, organizational behaviors, as well as deep scientific learning, and many organizations are only partly adapted to take full advantage of the possibilities. I will discuss the importance of standardized data management, enterprise integration tools, and how to enable better science via built-in analysis capabilities in a regulatory compliant, secure and auditable cloud offering.

4:40 pm Best of Show Awards Reception in the Exhibit Hall with Poster Viewing (Auditorium/Hall C)
6:00 pm Close of Day

Thursday, May 5

7:30 am Registration Open and Morning Coffee (Plaza Level Lobby)

PLENARY KEYNOTE ROOM LOCATION: 210

PLENARY KEYNOTE PROGRAM

8:00 am Welcome by Conference Organizer
8:00 am

Welcome by Conference Organizer

Allison Proffitt, Editorial Director, Bio-IT World
Nate Raine, Director Data Custodians, Lifebit
8:15 am

Leveraging Large-Scale Human Data to Advance and Accelerate Drug Discovery

Shankar Subramaniam, PhD, Distinguished Professor of Bioengineering; Professor of Chemistry, Biochemistry and Nanotechnology; Adjunct Professor of Cellular & Molecular Medicine, University of California at San Diego

Advances in genomics technologies have led to generation of massive amounts of human data. This has catalyzed new insights into cellular processes in the normal and disease state and facilitated the search for safe and effective medicines. The UK Biobank, All of US and TopMed initiatives are exemplars of this approach. We highlight examples from our lab where meaningful insights have been obtained advancing our understanding of disease biology and its pharmacological application.

9:30 am Coffee Break in the Exhibit Hall with Poster Viewing (Auditorium/Hall C)

ROOM LOCATION: 310

DATA STANDARDS TO SUPPORT DATA LIQUIDITY

10:15 am Organizer's Remarks
10:20 am

Chairperson's Remarks

John M. Conley, PhD, William Rand Kenan Jr. Professor, Law, University of North Carolina
10:25 am

How Researchers Can Cope with the EU's New Restrictions on Data Transfers

John M. Conley, PhD, William Rand Kenan Jr. Professor, Law, University of North Carolina

In 2021, the European Union made major changes to its rules for international data transfers, changes that make it more much difficult to move research data out of the EU. Individual subject consent is getting heightened scrutiny, while use of the EU's Standard Contractual Clauses has become significantly more onerous, and impossible in some cases. This presentation will review these new roadblocks to research and explore the possibilities for overcoming them.

10:55 am

Opportunities for Researchers to Tap Standards-based Electronic Health Records Data

David Kreda, Consultant, Biomedical Informatics and Sync for Science, Harvard Medical School

The Cures Act Final Rule requires all certified EHR systems to deliver a minimum set of clinical data (U.S. Core Data for Interoperability) by API for single patient or in bulk using the HL7 Fast Health Interoperability Resources (FHIR) data standard. Researchers will be able to complement their existing clinical data capture methods, especially if they need to assemble a longitudinal account of their participants medical history in the cohort. Learn how to exploit this approach as well as how other aspects of Final Rule will give researchers additional flexibility for acquiring more than the minimum set of clinical data.

11:25 am

Leveraging HL7 FHIR to Streamline Clinical Research and Trials

Dan Gottlieb, Principal, Central Square Solutions

Collecting clinical data for research can be difficult, especially when that data is spread across multiple healthcare institutions. Researchers are often forced to resort to incomplete participant surveys, time consuming record requests, and costly and error prone data re-keying. The HL7 FHIR data standard, built into dozens of electronic health record systems (EHRs) and deployed at thousands of healthcare institutions, enables novel, automated approaches to obtaining this data. Learn how FHIR's patient facing interfaces, provider facing interfaces, and bulk interfaces can be used by researchers to quickly get the data they need.

Tamsin Mansley, Head of North American Operation, Optibrium

AI platform Cerella™ empowers discovery organisations, combining leading deep learning capabilities with an architecture designed for enterprise-level deployment. See how Cerella seamlessly integrates with frontend applications via a REST API, increasing adoption and augmenting existing workflows. Through a direct link to your corporate data infrastructure, Cerella automatically updates models and insights as new data become available, delivering proven technology and reducing the time and cost of drug discovery.

12:10 pm Sponsored Presentation (Opportunity Available)
12:25 pm Interactive Discussions (Sponsorship Opportunity)

Interactive Discussions are informal, moderated discussions, allowing participants to exchange ideas and experiences and develop future collaborations around a focused topic. Each discussion will be led by a facilitator who keeps the discussion on track and the group engaged. For in-person events, the facilitator will lead from the front of the room while attendees remain seated. For virtual attendees, the format will be in an online networking platform. To get the most out of this format, please come prepared to share examples from your work, be a part of a collective, problem-solving session, and participate in active idea sharing. Please visit the Interactive Discussion page on the conference website for a complete listing of topics and descriptions.

12:55 pm Session Break and Transition to Luncheon Presentation
1:05 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:50 pm Refreshment Break in the Exhibit Hall with Poster Viewing (Auditorium/Hall C)

ROOM CHANGE: 210

KEYNOTE PROGRAM: TRENDS FROM THE TRENCHES

2:35 pm

Trends from the Trenches

Chris Dagdigian, Senior Director, BioTeam, Inc.
Matthew Trunnell, Data Commoner
Adam Kraut, Director Infrastructure & Cloud Architecture, BioTeam, Inc.
Anna Sowa, PhD, Senior Scientific Consultant, BioTeam, Inc.
Michelle Bayly, PhD, Senior Scientific Consultant, BioTeam, Inc.

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, cloud, data science, and machine learning that are involved in supporting data-intensive science. In 2022, 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. 

4:10 pm Close of Conference





Submit Your Speaker Proposal

Modern Data Platforms and Storage Infrastructure