Track 3 - April 5 – 7, 2016

Software Applications & Services

Tools that Best Utilize Data to Drive Scientific Decision Making

Track 3 explores the technology and tools that are used to connect data, applications, people, processes, and partners to ensure available, reliable, and actionable information for scientific decision making. Case studies will be presented that address how life science organizations address common problems in utilizing data including analytics, methods and standards, using open source, semantic technology, using in-house vs. customized commercial platforms, transparency, efficiency, security, and cost-effective solutions.

Tuesday, April 5

7:00 am Workshop Registration and Morning Coffee

8:00 – 11:30 Recommended Morning Pre-Conference Workshops* Security Considerations for Virtual Research

12:30 – 4:00 pm Recommended Afternoon Pre-Conference Workshops* Growth Strategy: Leveraging Cloud Scalability to Enable Rapid Growth and Change

* Separate registration required

2:00 – 6:00 Main Conference Registration


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Precision for Medicine5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Wednesday, April 6

7:00 am Registration Open and Morning Coffee


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9:00 Benjamin Franklin Awards and Laureate Presentation

9:30 Best Practices Awards Program

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


10:50 Chairperson’s Opening Remarks

Jane Reed, Ph.D., Head of Life Science Strategy, Business Development, Linguamatics

11:00 Allotrope Foundation: Driving Metadata and Master Data Management through Improved Data Modeling with Semantic Technologies

Dana Vanderwall, Associate Director, Cheminformatics, Research Information Technology & Automation, Bristol-Myers Squibb; Vice Chair, Allotrope Board of Directors
Eric Little, Ph.D., Adjunct Professor, New York University Polytechnic School of Engineering; Vice President, Data Science, OSTHUS, Inc.

Allotrope Foundation is building a framework (a software toolkit) to embed a set of federated, public, non-proprietary standards for analytical data in software utilized throughout the entire analytical chemistry data lifecycle, and serves as a basis for providing controlled vocabularies and taxonomies for a variety of pharmaceutical and biotech R&D applications. This framework provides extended capabilities to build in business rules and other analytics on top of the standardized vocabularies allowing companies enhanced abilities to classify and manage their data. Legacy systems can be maintained more easily and new technologies including cloud databases, Big Data Analytics, or reasoning engines can be employed to allow researchers unprecedented access to important contextualized data, because the foundational class structure is common and highly extensible to new and expanding domains. We will briefly describe some of the current data integration and management challenges facing the industry, e.g., utilization of legacy data warehouses, the creation of new data lakes, integration of existing semantic models, cloud-scale applications and how the Allotrope Framework provides a semantic basis for improved metadata and master data management through the use of modularized semantic models that capture the most pertinent entities, attributes and relationships needed to capture the plethora of laboratory data. We will provide an update on the rapid progress of development and the release of the Allotrope Framework 1.0, including: the Allotrope Data Format (for data and semantically-described metadata), Allotrope Taxonomies, and the first release of APIs (application programming interfaces), and how Allotrope Member companies have begun to integrate these into their internal environments. We will then discuss some of the potential extensions of this framework, which in the future, could enable state-of-the-art data integration and analytics capabilities for various applications.

11:30 An Overview of the RightFind XML for Mining Platform

Haralambos Marmanis, Ph.D., CTO & Vice President, Engineering & Product, Copyright Clearance Center

In the pharmaceutical and biomedical industries, easy access to the complete scientific corpus can become a catalyst for new discoveries in drug and treatment research. We have created a single platform that provides access to full-text XML articles from the most sought after international, peer-reviewed, scientific journals. We will present the current platform capabilities, talk about the problems it solves, and future opportunities.

12:00 pm The Role of an Integrated Software Solution in Supporting Advanced Biologics Development

Sean McGee, Product Marketing Manager, BIOVIA

The shifting landscape of the life sciences industry has been continually tightening its focus on the utilization of biologics as the primary source of new therapies. To stay competitive, optimizing the biologics development workflow has taken a leading role in the strategic initiatives of many leading life science companies. With that comes a need for tools that better support integration across globally externalizing research teams while maintaining compliance with multiple regulatory organizations. The ONE Development Lab solution for biologics, developed by BIOVIA, now a member of Dassault Systèmes, serves as an integration hub for advanced research groups, providing an open foundation which allows streamlining and integrating the flow of information and tasks within and between teams, reducing development cycle times, increasing R&D output, and mitigating compliance risks for biologics development throughout the biotherapeutics lifecycle.

Core Informatics12:15 Strategies for Interoperability Using Modern API’s

John Stalker, Product Manager, Core Informatics

R&D organizations need to analyze and manage data across informatics systems. Historically, this interoperability has required coding complex, one-off integrations. Well-architected modern API’s can leverage a standardized platform to broker data exchange, mitigating the need for purpose-built code. This presentation will share strategies and examples of how modern API’s can help you achieve these interoperability goals.

12:30 Session Break

OpenEye NEW
12:40 Luncheon Presentation I: Instant 3D Molecular Search for Everyone: FastROCS on the Web

Brian Cole, Toolkit Product Manager & Lead Technology Strategist, OpenEye Scientific Software

FastROCS won the BioIT World 2011 Best of Show for its paradigm-shifting performance improvements using GPUs. Adoption continues, but is still restricted to molecular modeling platforms used by full-time modelers. To reach a broader audience of chemists OpenEye broke free from traditional monolithic modeling applications and created an interface in the universal language of the web. The web-platform is the future direction of OpenEye and a perfect place to showcase OpenEye’s other novel technology: Grapheme-TK.

1:10 Luncheon Presentation II (Sponsorship Opportunity Available) or Lunch on Your Own

1:40 Session Break


1:50 Chairperson’s Remarks
Brian Bissett, Senior Member, Baltimore Section, Institute of Electrical and Electronic Engineers (IEEE)

1:55 Enabling Cross-Group Collaboration on Cell Lines via Arxspan’s ArxLab

Bruce Kozuma, Systems Analyst & Project Manager, Broad Information Technology Services, The Broad Institute of MIT and Harvard

One of the key challenges in conducting research in a diverse and dynamic organization like the Broad Institute is connecting islands of related data. Since scientific groups have traditionally been separated from each other, relying on each other as internal suppliers and customers, their data has similarly been separated. It is not uncommon to have two groups working on the same cell line but have no means of finding out about each other's work, partially due to different means of tracking cell line data. The Broad Institute has collaborated with Arxspan to develop a configuration of ArxLab to share a common registry of parental cell lines, allowing different groups to have a common vocabulary about cell lines and opening collaboration possibilities for both new science and accelerated progress on existing science.

2:25 Regeneron Genetics Center’s Use of the DNAnexus Annex in the Amazon Cloud for Large-Scale NGS Downstream Compute

Christopher Sprangel, Director, IT, Human Genetics, Genome Informatics, Regeneron Genetics Center
Nathan Wallace, Founder & CEO, Turbot

The Regeneron Genetics Center (RGC) has worked with DNAnexus to build out a secure but highly flexible high performance compute (HPC) environment in the AWS cloud. This compute environment, providing high scalability and security, is managed by a high-reliability DNAnexus system that provides layered, software-defined compute instances, with continual monitoring and patching of the systems, available in VPCs for general compute use. This provides the ability to spin up a required number of instances to install genomics analysis packages to perform statistical analyses on case and control sets of Whole Exome genomic data reaching into the hundreds of thousands of samples. RGC is also using the environment to establish clinical query and combined phenotype/ genotype data systems at large scale, reaching to a proposed 40 billion records in time.

Caringo2:55 Combining Life Science Applications with the Economical Benefits of a Cloud-Based Archive

Tony Barbagallo, VP, Product Marketing, Caringo

Advancements in research instrumentation such as gene sequencers, and mass spectrometers combined with increases in image resolution are leading to a tremendous amount of data. Often the resulting data is stored in silos, limiting reuse and collaboration. We will describe how you can consolidate all data on one public/private or hybrid cloud storage solution and provide secure access and search across the consolidated data set while still using your existing applications.

Microsoft Way3:25 Refreshment Break in the Exhibit Hall with Poster Viewing


4:00 Computerized Clinical Decision Support for Laboratory Services: The Brigham and Women’s Hospital Experience

Milenko Tanasijevic, M.D., MBA, Vice Chair for Clinical Pathology, Department of Pathology & Director, Clinical Laboratories, Brigham and Women’s Hospital and Dana Farber Cancer Institute; Associate Professor of Pathology, Harvard Medical School

The talk will focus on our experience with development and deployment of various computerized, physician order-entry driven interventions to improve utilization of laboratory tests. These include lab charge displays, reminders for redundant tests, computerized alerting protocols, messaging about appropriate frequency and timing of therapeutic drug monitoring levels. Their impact on lab utilization will be discussed along with plans for future interventions using our newly implemented EPIC / eCare hospital information system.

4:30 From Bathroom to Healthroom: How Magical Technology Will Revolutionize Health

Juhan Sonin, Director, Design, Mechanical Engineering, GoInvo, MIT

As design harnesses digital, materials and networking technologies, a very new health experience is just over the horizon. Proactive, lifestyle design. Tracking real-time health data. Non-invasive tools. Custom “just for you” treatments based on your actual genome. These are all real technologies, being used by ordinary people. From Bathroom to Healthroom introduces participants to the macro factors shaping these realities, along with an in-depth exploration of the various impacts of and opportunities for design.

5:00 How Biogen Doubled Biologics Manufacturing Yield through Advanced Predictive Analytics
Matt Griffiths, Senior Vice President and CIO, Biogen 
This talk highlights Biogen’s Advanced Process Control (APC) technology platform, which enables optimization and control of a biological process of growing cells in a manner akin to a well-controlled chemical reaction resulting in high efficiency, high yield manufacturing. APC combines science, process development and data analytics to deliver previously unattainable yields and the ability to control biological product quality in real time at full manufacturing scale.

5:30 – 6:30 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing

Thursday, April 7

7:00 am Registration and Morning Coffee


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


10:30 Chairperson’s Opening Remarks

Dinesh Vandayar, Vice President, Personalized Medicine, SAP SE

10:40 Standardized Security Systems: How They Protect Pharmaceutical Data from Breaches

Mollie Shields-Uehling, President, SAFE-BioPharma Association

Information security breaches are a problem. Globalization and digitization of drug development relies on the Web to share information, exposing patient data and scientific intellectual property to hacks. The session reviews standardized security systems, and their use allowing the secure free flow of information across firewalls among collaborating parties. It includes best practices used by stakeholders such as Merck, GSK and Pfizer.

11:00 Possession is 9/10ths of the Law: Considerations and Evaluations for IT Security Policies

Brian Bissett, Senior Member, Baltimore Section, Institute of Electrical and Electronic Engineers (IEEE)

High-level IT security breaches have made the news numerous times over the past year. Despite the awareness of the risks security breaches pose to organizations, they are still occurring with alarming frequency across all enterprises in both the public and private sector. Is this to become the new norm or has it ushered in a catalyst for change?

11:20 Accessing and Utilizing Public Genomic Data: How Hard Can It Be?

Dianne Pacheco, Information Security Officer, The Jackson Laboratory

Gregg TeHennepe, IT Project Manager, The Jackson Laboratory

The world is awash in Big Data, including large public genomic data sets such as TCGA. Access to these data sets is cited as a high-priority need for research programs; however, the technical and administrative logistics can be daunting. In this talk we will cover the security policies and practices needed to satisfy the data use requirements associated with major public genomic data sets.

SAP11:40 Innovating, Reimaging, and Digitally Transforming Personalized Medicine

David Delaney, Ph.D., Chief Medical Officer, SAP SE

With a flexible platform and advanced analytics, new digital solutions from SAP are uniquely positioned to help advance personalized medicine. The SAP Foundation for Health and applications such as SAP Health Engagement support deeper insights and connect data silos. Bring together your mission-critical structured, unstructured, public private, and experimental health data to provide better patient outcomes.

12:10 pm Session Break

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

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


1:55 Chairperson’s Remarks

John M. Conley, J.D., Ph.D., William Rand Kenan, Jr. Professor of Law, University of North Carolina, Chapel Hill; Counsel, Robinson Bradshaw & Hinson

2:00 Featured Presentation: precisionFDA

Taha A. Kass-Hout, M.D., MS, Chief Health Informatics Officer & Director, Office of Health Informatics, FDA

precisionFDA is an informatics cloud-based platform for ensuring the accuracy of Next-Generation Sequencing (NGS) tests by crowdsourcing reference material and data. A key part of President Obama’s Precision Medicine Initiative, it serves as a collaborative research effort that will inform later regulatory pathways and decision making. During this talk, Dr. Taha Kass-Hout, FDA’s Chief Health Informatics Officer, describes the platform and its successes since the December 2015 beta release.

2:30 Featured Presentation: How the Plecosystem, Blockchain, and Federated Data Enclaves will Shape Genomics Innovation and Application: Emerging Initiatives from the Global Alliance for Genomics and Health

John E. Mattison, M.D., Chief Medical Information Officer, Assistant Medical Director, Southern California Medical Group, Kaiser Permanente; Co-Chair, eHealth Workgroup, Global Alliance for Genomics and Health GA4GH

How can we maximize genomic research for the good of all citizens without violating their privacy? We need powerful new approaches to ensure ethical research without unwarranted risk to citizens who consent to use of personal data. The Global Alliance for Genomics and Health includes worldwide institutions seeking consensus on policy frameworks supported by creative technical solutions to achieve these paired goals of higher value and lower risk. I discuss progress to date.

3:00 Featured Presentation: Large-Scale Data Commons for Genomic and Clinical Data and the Changing Landscape for Sharing Research Data

Robert Grossman, Ph.D., Director, Center for Data Intensive Science (CDIS); Core Faculty, Institute for Genomics & Systems Biology and Computation Institute, Professor of Medicine, Section of Genetic Medicine, University of Chicago

Open commons containing large amounts of public biomedical data from the research community can, potentially, dramatically speed up medical research. We describe our experiences developing large-scale open source data commons for genomic and associated clinical data. We also discuss options for integrating and interoperating in-house genomic and clinical data with public data commons and private data partnerships.

3:30 PANEL DISCUSSION: How Will Data Sharing Innovations Fare in the Regulatory Environment?

Moderator: John M. Conley, J.D., Ph.D., William Rand Kenan, Jr. Professor of Law, University of North Carolina, Chapel Hill; Counsel, Robinson Bradshaw & Hinson


Robert Grossman, Ph.D., University of Chicago

Taha A. Kass-Hout, M.D., MS, FDA

John E. Mattison, M.D., Kaiser Permanente

Andrew K. Porter, Merck & Co.

Mollie Shields-Uehling, SAFE-BioPharma Association

The growth in patient healthcare and life sciences innovations can be attributed to technology enhancements like cloud computing, big data analytics and mobile applications, but may conflict with increasing regulatory compliance demands to ensure protection of healthcare life and quality as well as patient data privacy and security. This panel of esteemed technology solution providers and regulators debates real-world challenges and how regulation must also innovate at technology’s pace.

4:00 Conference Adjourns

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