Track 10 - April 21 – 23, 2015
Collaborations and Open Access Innovations
Using Collaborative Technologies and Methodologies to Accelerate Basic, Translational and Clinical Research
Track 10 presents case studies on collaborative technologies and methodologies used to aggregate and harmonize data from heterogeneous sources to accelerate basic, translational and clinical research. Speakers will show novel approaches of key drivers, technology innovations, collaboration platforms, open-source frameworks, and other factors that are managing data and empowering transformative changes through translation. Additional themes that will be covered include emerging security, analytic and semantic capabilities.
Tuesday, April 21
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7:00 am Workshop Registration and Morning Coffee
8:00 – 11:30 Recommended Morning Pre-Conference Workshops*
Gamification of Science
12:30 – 4:00 pm Recommended Afternoon Pre-Conference Workshops*
How Data-Driven Patient Networks are Transforming Biomedical Research
IT & Informatics in Support of Collaboration and Externalization
* Separate registration required
2:00 – 6:30 Main Conference Registration
5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing
Wednesday, April 22
7:00 am Registration Open and Morning Coffee
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
11:00 Imitation and Disruption: Impact on Open Source Software Success in the Life Sciences
Jay Bergeron, Director, Translational and Bioinformatics, Pfizer, Inc.
There are many successful examples of open source software (OSS) both within and outside of the life sciences community. However, investigators sponsoring software-based efforts need to consider many factors, including resourcing, architecture fragmentation, maintenance and their customer community when selecting between commercial and open license alternatives. This presentation will review such factors. Motivations that give rise to voluntary participation, by software developers, in OSS projects have been well analyzed. Socio-Psychological factors that include the potential for individual development and personal recognition, as well as the opportunity to contribute to self-selected high value efforts, have been promoted as drivers of OSS contribution. Substantial work has been conducted to relate architectural elements with the free-rider tolerance that is associated with successful OSS initiatives. However, empirical evidence to support the hypothesized relationship between architecture and OSS participation is limited. Moreover, the extent to which Socio-Psychological factors promote OSS participation is difficult to quantify given substantial OSS investments that are provided by government and commercial enterprises. Additionally, open source licensing models may not preclude commercial extension, packaging and consultancies. To extend the traditional dialog regarding OSS implementation, imitation of existing business patterns and discretionary pricing models that enable under-served customers, leading to market disruption, are considered as key drivers of OSS success.
11:30 OpenBEL: Collaborative Knowledge Base and Tools for Biomedical Research
Natalie Catlett, Ph.D., Senior Computational Scientist, Engineering, Selventa
Anthony Bargnesi, Application Architect, Engineering, Selventa
OpenBEL is an open source platform for managing biological knowledge, comprised of the Biological Expression Language (BEL) and a knowledgebase platform. BEL is a standard for qualitative representation of cause and effect relationships in molecular biology in a format that is both computable and human readable. The BEL knowledgebase platform compiles BEL knowledge from heterogeneous sources into cohesive networks that can be used for a broad range of biopharma, academic, or goverment research applications including the interpretation of large-scale 'omic data sets and modeling cellular responses. We will describe a next-generation Semantic Web RDF platform for harmonization, storage, and access of BEL knowledge; language expansion; and development of an exchange format for biological models derived from BEL knowledge networks.
12:15 An Integrated Informatics Solution to Optimize Collaborative Research
Robert Brown, Ph.D., Vice President, Global Informatics, Dotmatics
Conducting research projects across multiple organizations presents a number of challenges which must be overcome for them to be successful. Using case studies from pharma, biotech and CROs, this talk will discuss how dedicated hosted informatics systems designed to support collaborative research can help enhance the success of such projects.
12:30 Session Break
12:40 Luncheon Presentation I: Accelerators to Collaboration between Pharma and Providers
Dan Housman, CTO, ConvergeHEALTH by Deloitte, Deloitte Consulting LLP
Janak Joshi, Product Strategist, ConvergeHEALTH by Deloitte, Deloitte Consulting LLP
1:10 Luncheon Presentation II (Sponsorship Opportunity Available) or Lunch on Your Own
1:40 Session Break
1:50 Chairperson’s Remarks
1:55 Open Source National Network Facilitating Healthcare and Resource Data Sharing
Doug Macfadden, Chief Informatics Officer, Harvard Catalyst
Bhanu Bahl, Director of Informatics, Harvard Catalyst
In the era of personalized medicine there is an ever increasing need to match patients with clinical trials specific to their indications. In the absence of a common way to describe, organize and query the data, the information is silo-ed and fractured across healthcare providers and hospitals. Recognizing this gap, Accrual to Clinical trials (ACT) project supported by NCATS was launched with the goal of creating a network of 60 Clinical Translational Science Center Award (CTSA) sites. The network will facilitate investigators to query EHR data across all these sites for cohort exploration and subsequently engage and enroll identified patients into clinical trials. SHRINE (Shared Health Research Information Network) is a system developed by Harvard Catalyst for enabling clinical researchers to query across distributed hospital electronic medical record systems. SHRINE is built on top of i2b2 a widely used and robust platform for clinical research. In the immediate future for the ACT project the plan is to scale SHRINE functionality to establish a national network of CTSA sites, to facilitate more sophisticated querying and allow users to trigger detailed review of potential trial subjects at each site. Biomedical researchers spend lot of time and money finding necessary resources for their research. There is a need for a common way to describe and publish resource information which will allow search of all published resources. Some of the resources maybe created by small-labs in remote locations and thus hidden from the research community. The goal of eagle-i project is to make all aspects of research resources as transparent as possible, putting all information into the public domain and enabling scientists to easily find and obtain resources from the groups that make them. Launched as a consortium of 9 universities in 2010 funded by NIH grant, today eagle-i network spans 40 sites nationwide and publishes resources for reagents, antibodies, bio-specimens, stem cell lines, mice etc.
2:25 NeuroBANK™, Accelerated Research Environment as a Model for Collaboration and Cooperation in Clinical Research
Alex Sherman, Director, Strategic Development and Systems, Neurological Research Institute, Massachusetts General Hospital
NeuroBANK™, a patient-centric platform that allows clinicians and investigators to aggregate and cross-link clinical and research information from clinical visits, clinical studies, health records, and self-reported patient outcomes, and to connect it to biospecimen, images and genetic files. Will discuss how to find or create incentives for collaborations. The system is also utilized in two patient-centered research networks (PPRNs) of PCORnet. Utilization of the Global Unique Patient Identifier (GUID), first ever in ALS research, allows to link information in NeuroBANK™ to biospecimen, image banks and genetic material collections. Comparative effectiveness research and practice quality improvement become a standard and achievable objective.
2:55 Data Access Models for Genetic Data Sharing – GSK SHARE and the GA4GH Beacon
Karen King, Head, Genetic Data Sciences, GlaxoSmithKline
3:25 Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 CureAccelerator™: How a New Global Platform Will Help Propel Cures for the World’s Unsolved Diseases
Bruce Bloom, D.D.S., J.D., President and Chief Science Officer, Cures Within Reach
More than 7,000 diseases have no fully effective treatment, affecting more than 500 million people worldwide. Conceived by Cures Within Reach, CureAccelerator™ is the world’s first open-access, online platform dedicated to repurposing research – the quest to create new medical treatments from existing therapies, to drive more cures more quickly to more patients. Learn how this innovative IT tool will enable researchers, funders, the biomedical industry and patient groups to collaborate far more efficiently, to propel the pace of repurposing research. Platform features include: Global access. Various levels of transparency, from fully open forums to invitation-only, to facilitate the free flow of ideas while protecting privacy and intellectual property. Highly customizable dashboard, filters, searches and other features to prevent information overload and speed “matchmaking” among researchers, funders and others who are focused on the same disease state or target treatment.
4:30 Delivering on a Promise: Achieving a Patient-Centric Open Information Ecosystem
Walter Capone, President and CEO, The Multiple Myeloma Research Foundation
Patient-centric, open access research models are widely acknowledged catalysts of scientific and medical progress. Yet despite the benefits, in practice these models are rarely achieved. From misaligned incentives among stakeholders to inadequate technologies, there are a myriad of challenges that must be overcome to turn these noble ambitions into reality. Here we present a first-in-kind model for combining an observational clinical study with a participatory, community driven research program for Multiple Myeloma, and in doing so, providing a powerful example that can lead the way forward in other disease areas.
5:00 Presentation to be Announced
5:30 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing
6:30 Close of Day
Thursday, April 23
7:00 am Registration and Morning Coffee
10:00 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced
10:30 Chairperson’s Remarks
10:40 PANEL DISCUSSION: Multiple Sclerosis Conquered by the Data Science Revolution: Patients Win
Ken Buetow, Ph.D., Director, Computational Sciences and Informatics, Arizona State University
Robert McBurney, CEO, Office of the Chief Executive, Accelerated Cure Project
Marcia Kean, Chairman, Strategic Initiatives, Feinstein Kean Healthcare
Joseph LaFerrera, J.D., Partner, Gesmer Updegrove LLP
Funded by a grant from PCORI (Patient-Centered Outcomes Research Institute), the Accelerated Cure Project for MS is collaborating with all the key organizations in the MS community, gathering patient-reported and EHRs from 20,000 patients. It’s a best-practice model for data-enabled research; patient-centricity; and public-private partnerships. The key players from life sciences, data sciences, medicine patient advocacy and communications will describe the winning formulas that are making it successful. Attendees will learn how to design and fund such an initiative; how to collect standards-based data including the horrendous challenges around EHRs; best tools for analytics and data visualization; handling research queries; and overcoming the traditional silos that prevent seamless data exchange and global big data-enable basic, clinical and comparative effectiveness research.
CONSORTIA EFFORTS: UPDATES, OPPORTUNITIES AND DISCUSSION
11:40 The Open PHACTS Foundation - Semantic Data Integration for Life Sciences
Bryn Williams-Jones, Founder & Chief Operating Officer, Open PHACTS, Connected Discovery
Building on the success of the Open PHACTS IMI project, the Open PHACTS Foundation is a not-for-profit membership organisation, supporting the Open PHACTS Discovery Platform: A sustainable, open, vibrant and interoperable information infrastructure for applied life science research and development. To reduce the barriers to drug discovery in industry, academia and for SMEs, the Open PHACTS Discovery Platform provides tools and services to interact with multiple integrated and publicly available data sources. To integrate this data, extensive cross-referencing of scientific concepts is needed across all databases – a task currently involving 18 million links. Building on the success of the IMI public private partnership model, The Open PHACTS Foundation is leveraging the community of users to bring new data sources, tools and analysis to key drug discovery and development business questions. We will describe some of the capabilities of The Open PHACTS Discovery Platform, as well as show how commitment to pre-competitive and open innovation remains at the heart of The Open PHACTS Foundation with opportunities for all to get involved.
12:10 pm Session Break
12:20 Luncheon Presentation I: Accelerating Cancer Informatics at Foundation Medicine using SciDB
Eric Neumann, Ph.D., Neurobiology and Developmental Genetics, Vice President, Knowledge Informatics, Foundation Medicine
Marilyn Matz, CEO, Paradigm4
Alex Poliakov, Solutions Architect, Paradigm4
Much can be learned from the proper analysis of large sets of genomic data. We will describe a few examples of scalable analytics applied to cancer genomics, and how SciDB enables this kind of analytics. Combining statistical analysis with other knowledge discovery tools can help accelerate this transformation of large data sets into biological insights.
12:50 Luncheon Presentation II (Sponsorship Opportunity Available)
1:20 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing
1:55 Chairperson’s Remarks
Rudy Potenzone, Ph.D., Vice President, Marketing, tranSMART Foundation
2:00 Incubating Open Innovation - the IMI2 Case Study
Anthony Rowe, Ph.D., Principal Research Scientist, External Innovation R&D IT, Janssen R&D, LLC
After a set of successful Innovative Medicine Initiative (IMI) public-private consortia has been launched the learnings from the first 6 years now informing how the processes in the follow on IMI2 could be refined. One particular area of interest is how to improve the incubation of new project ideas which eventually lead to pre-competitive open innovation projects. In this presentation we will describe the mechanism how the European Federation of Pharmaceutical Industry and Associations is handling this opportunity as well as the initial experiences of a particular group.
2:30 Allotrope Foundation: A Collaboration Making Real Progress Addressing the Data Management Problems Facing the Analytical Laboratory
Dana Vanderwall, Ph.D., Associate Director, Cheminformatics, Research Information Technology and Automation, Bristol-Myers Squibb
Allotrope Foundation is building a framework (a software toolkit) to embed a set of public, non-proprietary standards for analytical data in software utilized throughout the entire analytical chemistry data lifecycle. We will discuss why embedding standards addresses the fundamental, root causes of our data challenges, rather than merely treating symptoms of the problem. This standards-based, community-driven approach, where people who make devices (laboratory instruments) are collaborating with those who create and depend on analytical data (the industry) to transform how we create, use, disseminate and manage scientific data through the creation of innovative products. We will provide an update on the rapid progress in the first year of development, which has demonstrated that the core concepts of the Allotrope Framework are technically feasible through the creation and delivery of proof of concept framework components and applications. The project has moved from concepts to reality, with tangible capabilities and software that have begun delivering the vision of Allotrope Foundation. The next phase of work will be discussed including finalization the Allotrope data and metadata format, the first release of APIs (application programming interface) and collaborations with the vendor community as well as the long term plans for deployment. The audience will learn about Allotrope Foundation and the substantive progress in the development of the Framework including:
• The completed architecture and implementation of a basic framework that handles the standard data format, contextual metadata and workflow concepts
• The metadata repository, related services and APIs
• The completed proof-of-concept applications (PoCs) the use using the initial Framework and enabled the evaluation and testing of standards for document format, metadata and implementation. This enabled the demonstration of capabilities that use a standard document format and metadata.
• The standard interfaces (APIs) created using established software development standards for all Framework capabilities built and which were used in PoCs and between Framework components
• The novel data archiving concept demonstrated with enriched with standard metadata definitions acquired in workflow or added post-hoc in the archiving step and using a vendor-independent data format.
• The design and implementation of the Allotrope standard file format for data and metadata, which leverages many existing standards in analytical, as well as general scientific, and big data domains.
• The roadmap to build out that Framework to the level of functionality and robustness required for use in production by pharma/biopharma companies and vendors. This will enable solutions for managing analytical data that are fundamentally different than what is available today, and for Allotrope Foundation members to realize the far reaching benefits and return on investment that define our vision.
• Finally, we will explain how stakeholders in the analytical community can work with us through collaboration, expert advice, and active membership.
3:00 Creating an Open Innovation Platform for the Promotion of Precompetitive Collaboration – The Pistoia Alliance’s Interactive Project Portfolio Platform (IP3)
Carmen Nitsche, Executive Director Business Development North America, Pistoia Alliance
In order to promote the free exchange of ideas and increase the transparency of the portfolio development process, the Pistoia Alliance recently launched its Interactive Project Portfolio Platform (IP3). Members and non-members alike can review and contribute to the pool of ideas and assist in their evaluation. The membership then prioritizes and funds the top projects that address immediate and universal pain points within the precompetitive arena of Life Sciences R&D. In this talk we will review the development and application of the platform as a key tool to advance the Pistoia Alliance’s mission.
3:30 The New tranSMART Platform v1.2 Provides Unparalleled Functionality for Translational Medicine
Rudy Potenzone, Ph.D., Vice President, Marketing, tranSMART Foundation
The tranSMART Platform is in active use by over 50 organizations worldwide and the basis for a growing number of large data integration and analysis projects. It is becoming the premier platform for translational studies as the Community continues to expand this Open Source platform by their contributions. Learn about the Platform, see a large number of user examples and see the breadth of the user community contributing to the Platform.
4:00 Conference Adjourns
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