2016 Presentations and Webcasts

Presentations and Webcasts from the
2016 All Hands Meeting and
Open Data Science Symposium

All Hands Meeting Agenda
Open Data Science Symposium Agenda
Session Descriptions

November 29, 2016
All Hands Meeting, Day 1

Jennie Larkin Welcome View Video  
Robert Califf Keynote Address View Video View Slides
Philip Bourne BD2K @ NIH – A Vision Through 2020 View Video View Slides


Research Highlights

Soojin Park Predicting Vasospasm After Subarachnoid Hemorrhage Using High-Frequency Physiological Data View Video View Slides
Anders Dohlman Predicting Adverse Cardiovascular Events for Tyrosine Kinase Inhibitors From Molecular Features View Video View Slides
Alexander Tropsha Hypothesis Fusion to Improve the Odds of Successful Drug Repurposing View Video View Slides
David Haussler BD2K and Global Genomic Data Sharing View Video View Slides
Vikas Singh Multi-resolution Analysis of Brain Connectivity: Associations With PET-Based Alzheimer's Pathology View Video View Slides
Paul Avillach Identification of Genotype-Phenotype Associations in Phelan-McDermid Syndrome Using Patient-Sourced Data View Video View Slides


Data Commons Session

Vivien Bonazzi NIH Data Commons Overview View Video View Slides


Standards Development

Susanna-Assunta Sansone An Informative and Educational Service for Community-Developed Standards (Biosharing) View Video View Slides
Mark Musen Use of Standard Common Data Elements (CDEs) in CEDAR View Video View Slides
Sherri de Coronado and Cindy Lawler Emerging Topics in Data Related Standards View Video View Slides
Julie McMurry An Urban Dictionary of Identifier Syntax for the Data Integration Jungle (Prefix Commons) View Video View Slides
Melissa Haendel Making Phenotypic Data FAIR++ for Disease Diagnosis and Discovery (Phenotype Exchange Format) View Video View Slides


Training & Workforce Development

Michelle Dunn Education, Training, and Workforce Development Session View Video View Slides
Jack Van Horn Training Coordination Center's Efforts to Foster New Collaborations Through the ROAD-Trip Program, Innovation Labs, and the BD2K Guide to the Fundamentals in Data Science Lecture Series View Video View Slides
Jose-Luis Ambite ERuDIte, the Educational Resource Discovery Index View Video View Slides
Vivek Shetty An example of One Center's (MD2K's) Training Efforts View Video NA
Kevin Read Curricula to Prepare Medical Librarians to Understand and Teach Data Management View Video View Slides
Patricia Ordonez Efforts at the University of Puerto Rico, Rio Pedras That Increase Didactic and Research Opportunities for Undergraduates and Their Instructors View Video View Slides
Daniela Witten University of Washington's R25 Short Course View Video View Slides
Rafael Irizarry A BD2K-Funded MOOC and How It Influenced Classroom Instruction View Video View Slides
Jonathan Chen Decaying Relevance of Clinical Data when Predicting Future Decisions View Video View Slides
Vivek Shetty Training, Education and Development of a Transdisciplinary mHealth Workforce View Video View Slides


BioCADDIE & Resource Indexing

Lucila Ohno-Machado bioCADDIE: Progress and Next Steps View Video View Slides
Henning Hermjakob Omics Discovery Index – Discovering and Linking Public 'Omics' Datasets View Video View Slides
Denis Torre Datasets2Tools: Enriching DataMed With Canned Analyses View Video View Slides
Susanna-Assunta Sansone The DataMed DATS Model, Annotated With Schema.org View Video View Slides
Tim Clark The bioCADDIE Data Citation Implementation Pilot View Video View Slides


Software, Analysis & Methods Development

Peter Rose Compressive Structural Bioinformatics: Large-Scale Analysis and Visualization of the PDB Archive View Video View Slides
Olgica Milenkovic New Algorithms for RNA-Seq and ChiP-Seq Data Compression View Video View Slides
Joseph Picone EEG Event Detection Using Deep Learning View Video View Slides
Chunlei Wu BioThings APIs: Linked High-Performance APIs for Biological Entities View Video View Slides
Jun Zhu Curate Patient-Centric Multi-Omics Data for Precision Medicine View Video View Slides
Satya Sahoo Scientific Reproducibility Using the Provenance for Clinical and Healthcare Research Framework View Video View Slides
Haixu Tang Enabling Privacy-Preserving Biomedical Data Analytics in the Cloud and Across Institutions View Video View Slides
Griffin Weber Visualizing Healthcare System Dynamics in Biomedical Big Data View Video View Slides
T.M. Murali Using Crowds to Design Biological Network Visualizations View Video View Slides
Avi Ma'ayan GEN3VA: Aggregation and Analysis of Gene Expression Signatures From Related Studies View Video View Slides
Gregory Cooper Fast, Accurate Causal Search Algorithms From the Center for Causal Discovery (CCD) View Video View Slides
David Page Computational Drug Repositioning by Machine Learning from EHR Data View Video 1
View Video 2
View Slides
Charles Blatti KnowEnG: Cloud-Based Environment for Scalable Analyses of Genomic Signatures View Video View Slides
Martin O'Connor A Standards-Based Model for Metadata Exchange View Video View Slides


November 30, 2016
All Hands Meeting, Day 2

Jennie Larkin Roundup of Day 1 & Day 2 Activities View Video NA

Warren Kibbe, John J McGowan,
Mike Huerta, James McClain,
Greg Farber, Matthew Gillman

Moderator: Philip Bourne

Panel: Unmet Opportunities & Challenges Afforded by Big Data View Video View Warren Kibbe's Slides
View John J McGowan's Slides
View Mike Huerta's Slides
View Greg Farber's Slides
View Matthew Gillman's Slides


Research Highlights

Chris Wiggins Data Science @ The New York Times View Video View Slides
Clark Glymour From Brain Images to Causal Connections Center for Causal Discovery (CCD) View Video View Slides
Wilbert Van Panhuis Integrating Data With Epidemic Simulators to Improve Pandemic Preparedness: Chikungunya in Colombia View Video View Slides
Amin Emad Knowledge-Guided Prioritization of Genes Determinant of Drug Resistance Using ProGENI View Video NA
Eni Halilaj Predicting Phenotypes of Osteoarthritis Progression View Video View Slides
Quynh Nguyen Geotagged Tweets as Predictors of County-Level Health Outcomes View Video View Slides
Peipei Ping Understanding Cardiovascular Health and Revealing Pathogenic Insights via Text-Mining Approaches View Video View Slides


Initial Implementation of the Commons Session

Owen White & Ian Foster A Roadmap for the Commons View Video View Slides
Neil McKenna & Michel Dumontier Development of FAIR-ness Metrics View Video View Slides
Michel Dumontier API Interoperability View Video View Slides
Umberto Ravaioli & Brian O’Connor Workflow Sharing & Docker Registry View Video View Slides
Lucila Ohno-Machado, Wei Wang, & Michel Dumontier Data-Object Registry View Video View Slides
George Komatsoulis Cloud Credits Model View Video View Slides


Collaborative Presentations

Pablo Roman-Garcia ELIXIR; A European Distributed Infrastructure for Life-Science Information View Video View Slides
Tim Clark PREFIX: ACCESSION Compact Identifier Resolution: An EBI/CDL Collaboration View Video View Slides
Mark Musen When the World Beats a Path to Your Door: Collaboration in the Era of Big Data View Video View Slides
Paul Thompson Worldwide Big Data Collaborations: Examples from ENIGMA, spanning 35 Countries View Video NA
Ida Sim Count Everything: Secure Count Query Framework Across Big Data Centers View Video View Slides
Ben Heavner Annual California BD2K Centers Regional Meetings – Building Connections Across Centers View Video View Slides
Elvira Mitraka Revisions to the Disease Ontology to Support the Alliance of Genome Resources View Video View Slides



Allen Dearry Introduction View Video NA
Izumi Hinkson RFI - Metrics to Assess the Value of Biomedical Digital Repositories View Video View Slides
David Giaretta The Role of Trustworthy Digital Repositories in Sustainability View Video View Slides
George Alter The Stewardship Gap View Video View Slides
Melissa Landrum Archiving Interpretations of Variants in ClinVar View Video View Slides
Cathy Wu Interoperability, Sustainability, and Impact: A UniProt Case Study View Video View Slides


December 1, 2016
Open Data Science Symposium

Elizabeth Kittrie and Philip Bourne Welcome and Meeting Objectives View Video NA
John Wilbanks Vannevar Bush in the 21st Century View Video View Slides
Robert Kiley and Philip Bourne Vision and Overview of Open Science Prize View Video View Slides

Open Science Prize Finalists

Emma Beer, Stephen Abbott Pugh, Ben Goldacre, Erick Turner, and Paul Walsh OpenTrialsFDA: Making Unbiased Clinical Trial Data Accessible View Video View Slides
Trevor Bedford and Richard Neher Real-Time Evolutionary Tracking for Pathogen Surveillance and Epidemiological Investigation View Video View Slides
Aurel A. Lazar, Ann-Shyn Chiang, Daniel Coca, Lev Givon, Dorian Florescu, Chung-Chuan Lo, Luna Carlos, Paul Richmond, Adam Tomkins, Nikul Ukani, Chung-Heng Yeh, and Yiyin Zhou The Fruit Fly Brain Observatory View Video View Slides
Mike Bamshad, Jessica Chong, Tudor Groza, Craig McNamara, and Edwin Zhang MyGene2: Accelerating Gene Discovery via Radically Open Data Sharing View Video View Slides
Christa Hasenkopf OpenAQ: A Global Community Building the First Open, Real-Time Air Quality Data Hub for the World View Video View Slides
Roberto Toro, Sastrajit Ghosh, Katja Heuer, and Amy Robinson Open Neuroimaging Laboratory View Video View Slides

Francis Collins and Harold Varmus

Moderator: Chris Wiggins

Open Science: An NIH Perspective View Video NA

New Models Team:
Niklas Blomberg
Peter Goodhand
Robert Kiley
Tanja Davidsen

Moderator: Philip Bourne

Elixer; Global Alliance for Genomics and Health; New Models for Open Science Emerging Around the Globe; NCI's Genomics Data Commons (GDC) & Cloud Pilots; View Video View Slides:

Heather Joseph, Mike Huerta, Jim Anderson

Moderator: Jerry Sheehan

Viewpoints on Open Science and Open Data in Biomedical Research View Video NA
Elizabeth Kittrie and Philip Bourne Closing View Video NA

This page last reviewed on September 5, 2018