Bio IT World Expo 2016  
Bio IT World Expo 2016
Archived Content

Open Source Solutions 

Final Agenda


7:00 am Workshop Registration and Morning Coffee

8:00 am - 4:00 pm Pre-Conference Workshops*

  • Planning and Structuring Collaborative Innovation and Open Source Deals: Techniques and Lessons from the Leaders
  • Cloud Computing

*Separate Registration Required

2:00 - 7:00 pm Main Conference Registration

4:00 Event Chairperson's Opening Remarks

Cindy Crowninshield, RD, LDN, Conference Director, Cambridge Healthtech Institute

4:05 Keynote Introduction

Sanjay Joshi, Solutions Architect, Life Sciences, EMC Isilon Storage Division



Martin LeachMartin Leach, Ph.D., CIO, Broad Institute of MIT and Harvard

Jill MesirovJill P. Mesirov, Ph.D., Associate Director and Chief Informatics Officer; Director, Computational Biology and Bioinformatics, Broad Institute of MIT and Harvard

Hitachi Data Systems5:00 - 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Drop off a business card at the CHI Sales booth for a chance to win 1 of 2 iPod touches® or 1 of 2 Xbox 360s®*!

*Apple® is not a sponsor or participant in this program



7:00 am Registration and Morning Coffee

7:55 Chairperson's Opening Remarks

Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute

8:00 Keynote Introduction

Bas Burger, President, Global Commerce, BT Global Services



Eric PerakslisEric D. Perakslis, Ph.D., CIO and Chief Scientist of Informatics, U.S. Food and Drug Administration

8:45 Benjamin Franklin Award & Laureate Presentation

9:10 Best Practices Award Program

Cycle Computing small9:45 Coffee Break in the Exhibit Hall with Poster Viewing


Open Access Models & Tools for Data Management,
Research Communications, and Computing Resources

10:50 Chairperson's Remarks

Anil Srivastava, Director, Cancer Collaboratory, Open Health Systems Laboratory

11:00 Panel Discussion: Global Shared Cyberinfrastructure for Medical Research

Moderator: Anil Srivastava, Director, Cancer Collaboratory, Open Health Systems Laboratory

Ken Buetow, Ph.D., Director, Computational Sciences and Informatics, Arizona State University

Marcia Kean, Chairman, Strategic Initiatives, Feinstein Kean

George A. Komatsoulis, Ph.D., Deputy Director/Chief Operating Officer (acting)/Chief, Informatics Operations Branch (acting), Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Department of Health and Human Services

H. Kim Lyerly, M.D., George Barth Geller Professor of Cancer Research, Duke University; Director, Duke Comprehensive Cancer Center

James G. Williams, Director, International Networking, Indiana University

Physical sciences have created the basic infrastructure of advanced networks and high performance computing for research, however, the life sciences have been lagging behind in spite of the growing need for computational and systems biology; translational and personalized medicine; and the fact that data intensity of medical and life sciences may be many times more than physical sciences. The panel will bring together experts from across the world with use cases and a practical vision to put together a Global Shared Cyberinfrastructure for Medical Research. Hear ideas for a practical roadmap that integrates networks and computing resources in accordance with the best of breed knowledge of interoperable, standard based, open source biomedical informatics into an open system and creating an 'ever widening, never ascending' collaboratory framework.

12:00 pm Sponsored Presentation (Opportunity Available)

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:40 Chairperson's Remarks

Chris Southan, Ph.D., B.Sc.Hons, M.Sc., Consultant, Knowledge Engineering, ChrisDS Consulting

1:45 Mining Drug Targets, Structures and Activity Data Using Public Full-Text Patent Sources and Open Web Tools

Chris Southan, Ph.D., B.Sc.Hons, M.Sc., Consultant, Knowledge Engineering, ChrisDS Consulting

Historically, the estimated 70% of drug discovery data published in patents has been brokered to the academic community and pharmaceutical companies via subscription databases. Recently this monopoly has been broken by a combination of several factors. This presentation will show how these can be combined to extract targets, key compounds and assay results not only from patents but also from papers.

2:15 The New Frontier of Open Access Research and Tools: Accelerating the Process and Exchange of Medical Research

Jennifer Lin, Ph.D., Product Manager, Public Library of Science

This presentation will share PLoS's innovations in catalyzing the rapid dissemination of medical research communications. It will also discuss how novel tools for navigating, filtering, aggregating, and assessing research content are integral to the advancement of medicine. It will close with a description of PLoS's efforts to this end (article level metrics, PLoS Currents and PloS Hubs), which focus on post-publication organization and content assessment.

NVIDIA2:45 Bioinformatics Algorithms on Emerging Parallel Architectures

Jonathan Cohen, Manager, Emerging Applications, NVIDIA Corporation

NVIDIA graphic processor units (GPUs) are high-performance processors designed for intense computational and high-throughput workloads.  I'll review open source bioinformatics algorithms and codes that take advantage of NVIDIA GPUs and applications where GPUs may provide benefit.  I will share results from NVIDIA's Emerging Applications group to develop efficient computational building blocks for a variety of genomic processing tasks.

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing


Open Access and Cloud Computing 

3:45 Balancing and Augmenting Local Resources with Remote Clouds

Angel Pizarro, Director, ITMAT Bioinformatics Facility, University of Pennsylvania

4:15 Transparent and Public Genomics

Alexander Wait Zaranek, Ph.D., Director, Informatics, Harvard Personal Genome Project, Genetics, Harvard Medical School

At the Personal Genome Project, we are building a transparent and public resource consisting of genomes, detailed phenotypes, as well as cell-lines and other tissue samples for more than 100,000 individuals. With inspiration from the open source and free knowledge movements, we will discuss new ways to benefit from the breathtaking improvements in genomic technologies.

Illumnia logo4:45 BaseSpace: A Scalable Cloud Platform for Research and Clinical Sequencing InformaticsAlex Dickinson, Senior Vice President, Cloud Genomics, Illumina, Inc.The rapid migration of sequencing from the core lab, to the researcher desktop, to the clinical lab has major implications for bioinformatics. In particular, these new users are looking for solutions that provide ease of use, require no investment in IT infrastructure, and are compliant with the appropriate regulations. Illumina has developed BaseSpace, a cloud computing platform that meets these needs by seamlessly linking on-instrument, local cloud, and public cloud bioinformatics.

5:15 Best of Show Awards Reception in the Exhibit Hall

6:15 Exhibit Hall Closes




Open Source Platforms and Collaborative Technologies 

8:40 Chairperson's Opening RemarksEric Neumann, Ph.D., CTO, PanGenX 

8:45 A Fully Automated, Open Platform for Molecular Differential Diagnoses

Jian Han, Ph.D., President and CSO, iCubate

We ( have developed a patented mPCR (multiplex PCR) technology; a fully integrated molecular diagnostic system, the iCubate system, that can perform extraction, amplification, and detection steps, multiplexed, automatically, and in a closed cassette; and established an open business model, iCubate 2.0 (

9:15 Clinical Diagnostics Testing with NGS: Challenges and Opportunities

Eric W. Klee, Ph.D., Assistant Professor of Medical Informatics, Division of Biomedical Informatics and Statistics, Mayo Clinic Rochester

The emergence of next generation sequencing has opened numerous opportunities to the field of clinical diagnostic testing, but with it also comes the formidable challenge of managing, processing, and interpreting the data. This deluge of data has resulted in the need for bioinformatics expertise to assist in interpretation of NGS results, and innovative systems to aggregate and integrate disparate data sources for the purpose of the resulting variants.  This presentation will discuss the challenges and opportunities we have faced in implementing an NGS based clinical diagnostic test at the Mayo Clinic.

9:45 Linking Together Pharmacogenomics Knowledge: Enabling Diagnostic to be ActionableEric Neumann, Ph.D., CTO, PanGenX 

10:15 Coffee Break in the Exhibit Hall and Poster Competition

10:45 Plenary Keynote Panel Chairperson's Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

10:50 Plenary Keynote Panel Introduction

Geoffrey Noer, Senior Director, Product Marketing, Panasas

11:00 Plenary Keynote Panel:
A special plenary session featuring trends and challenges in cancer research:

Julian Adams, Ph.D., President, Research and Development, Infinity Pharmaceuticals, Inc.

Jose Baselga, M.D., Ph.D., Chief and Bruce A. Chabner Chair, Division of Hematology/Oncology, Massachusetts General Hospital; Associate Director, Massachusetts General Hospital Cancer Center; Professor of Medicine, Harvard Medical School

Sir John Burn, MD, FMedSci, Professor of Clinical Genetics, Institute of Genetic Medicine, Newcastle University, UK; Genetics Lead, National Institute of Health Research, UK; Medical Director, QuantuMDx Ltd

John Quackenbush, Ph.D., Professor, Biostatistics and Computational Biology, Cancer Biology Center for Cancer Computational Biology, Dana-Farber Cancer Institute

12:15 Luncheon in the Exhibit Hall with Poster Viewing

Open Source Platforms and Collaborative Technologies 

1:55 Chairperson's Remarks

2:00 User Gateway: A System to Accelerate Molecular Epidemiology

Christopher Farah, Ph.D., Bioinformatics Systems and GIS Specialist, Maine Institute for Human Genetics and Health, Eastern Maine Healthcare Systems
Co-authored with Janet Hock, B.D.S., Ph.D., Senior Investigator, Maine Institute for Human Genetics and Health, Eastern Maine Healthcare Systems

User Gateway is web-based, open source software developed to bridge cancer diagnosis, annotations from banked specimens, and clinical data to outcomes and environmental history. By incorporating GIS technology, existing biobanking functionality is extended through two key functions: advanced specimen requisition and spatiotemporal analysis of patient data. Learn about the core functionality of the software, followed by a software demonstration. Novel use cases will be highlighted.

2:30 A Scientific Spreadsheet for Big Data Analysis, Reporting, and Real-time Collaboration 

Mario Morales, Statistician, Simulmedia, Inc.; Programmer, Stanford University School of Medicine 

We will present new tools and services that have been designed in collaboration with BD to improve the productivity of biostatisticians, to allow them to work with large volumes of data on a private cloud and on EC2 and to collaborate easily. We have combined the highly popular interaction model of Spreadsheets with capabilities de manipulate very large data sets and to use any scientific computing environment’s libraries in formula cells. We have made the spreadsheets fully programmable in R and in Python, we have added layers to which Bio-statisticians can drag and drop widgets for data manipulation and visualisation of any complexity and  we have enabled real-time collaboration in all the usage scenarios. We have made the produced spreadsheets, reports and dashborads easy to save with all the software stacks and data they depend on and also easy to publish with simple URLs.


3:00 Development and Implementation of Distributed Health Data Networks: Lessons from Medical Product Safety, Public Heath Surveillance, and Comparative Effectiveness Research 

Jeffrey Brown, Ph.D., Assistant Professor, Population Medicine, Harvard Pilgrim Health Care Institute/ Harvard Medical School

This presentation describes the development, implementation and selected uses of an open-source software platform (PopMedNetTM) for the creation of distributed health data networks. A distributed health data network advances the secondary use of electronic health information by creating standardized and re-usable data sources in multiple sites, as well as tools to use it. Understand the barriers in creating a distributed health network and approaches for overcoming them.

3:30 Closing Featured Speaker

Pistoia Alliance: Progress in Pre-Competitive Collaboration

Ramesh Durvasula, Ph.D., Director, Molecular Sciences & Candidate Optimization Informatics, Bristol-Myers Squibb

Since 2009, the Pistoia Alliance has drawn significant interest from across the industry. We are focused on the highest-value, most-challenging opportunities for developing technology standards and new capabilities. The industry as a whole benefits from the efforts of Pistoia, not just any single segment. Learn the latest updates and current priorities of the Pistoia Alliance projects and how to become engaged in the Pistoia efforts.

4:00 Conference Adjourns


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DDN Storage  

Elsevier R&D Solutions


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Precision for Medicine


 Seven Bridges Genomics

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Conference CD

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View white papers, listen to podcasts, and more!

  • Making the World's Knowledge Computable
  • Bioinformatics in the Cloud
  • The Application of Text Analytics to Drug Safety Surveillance

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