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.
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Tuesday, April 5
7:00 am Workshop Registration and
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
5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster
Wednesday, April 6
7:00 am Registration Open and
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.
12:15 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
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
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.
2:55 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.
3:25 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
4:30 From Bathroom to Healthroom: How Magical Technology Will
Juhan Sonin, Director, Design, Mechanical Engineering, GoInvo,
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
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
10:00 Coffee Break in the Exhibit Hall and Poster Competition
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
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.
11:40 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
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
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.
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
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.
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.
DISCUSSION: How Will Data Sharing Innovations Fare in the Regulatory
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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