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Track 8: Data Visualization and Exploration Tools 

Data visualization goes far beyond the generation of (interactive) images based on some large data sets. There is a growing body of knowledge about how to design, implement and evaluate visualization techniques and tools that offer real value to the user. Track 8 presents carefully chosen talks that showcase novel visualization approaches that address important challenges in genomic data, networks, microscopy, imaging and the support of discovery, clinical and translational research.

Final Agenda


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TUESDAY, APRIL 9

7:00 am Workshop Registration and Morning Coffee

8:00 Pre-Conference Workshops*


*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

Kevin Brode, Senior Director, Health & Life Sciences, Americas Hitachi Data Systems


» 4:15 PLENARY KEYNOTE 

Do Network Pharmacologists Need Robot Chemists?

Andrew HopkinsAndrew L. Hopkins, DPhil, FRSC, FSB, Division of Biological Chemistry and Drug Design, College of Life Sciences, University of Dundee





 

OKTA10 Minute Welcome to the Reception!

Mike Nolte, Regional Sales Manager – East, Okta


Cycle Computing logo
OKTA
5:00 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 iPads® or 1 of 2 Kindle Fires®!*

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



WEDNESDAY, APRIL 10

7:00 am Registration and Morning Coffee

8:00 Chairperson’s Opening Remarks

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

8:05 Keynote Introduction

Sanjay Joshi, CTO, Life Sciences, EMC Isilon


» 8:15 PLENARY KEYNOTE 

Atul ButteAtul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children's Hospital; Co-founder, Personalis and Numedii





 


8:55 Benjamin Franklin Award & Laureate Presentation

9:15 Best Practices Award Program

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


Visualization Tools in Development to Support Discovery and Translational Research 

Chairperson’s Remarks

Nils Gehlenborg, Ph.D., Research Associate, Center for Biomedical Informatics, Harvard Medical School

10:50 Understanding Biomedical Complexity through Visualization

Lawrence Hunter, Ph.D., Director, Center for Computational Pharmacology, Professor, Computer Science, University of Colorado

The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain; however, effective design and implementation of computational tools that genuinely facilitate the generation of novel and significant scientific insights remains poorly understood. In this talk, I will discuss visual approaches to knowledge-based analysis of biomedical data, and present some new ideas about Degree of Interest functions that might be used to guide visual explorations.

11:10 Seeing the Forest through the Trees: Integrating in silico, in vitro and in vivo Data for Small Molecule Knowledge Discovery

Jeffrey Sutherland, Prinicipal Research Scientist and Group Leader, IT Informatics, Eli Lilly and Co.

Knowledge discovery around a list of targets or a series of molecules can be a daunting task in drug discovery efforts.  In silico, in vitro and in vivo data are distributed across many internal databases and effectively querying and visualizing the data requires an integration framework coupled with an advanced visualization platform.  Rapidly improving public resources offer additional opportunities for knowledge discovery, and increasing their utilization alongside internal data is a longstanding challenge. This presentation will demonstrate data integration and visualization platforms used within discovery research at Lilly, including applications for target identification, compound design and lead optimization.

11:35 Data Visualization in Discovery and Clinical Research: Art, Science, and Intuition

Dimitris K. Agrafiotis, Vice President, Informatics & Enterprise Architecture, Covance

CambridgeSemantics12:00 pm Whence the Data? The Importance of Feeding the Right Data to Your Visualizations

Lee Feigenbaum, Vice President, Marketing & Technology, Cambridge Semantics

Visualizations are only as good as the data that drives them. And frequently, the right data comes from many & diverse sources. This talk presents the case for Unified Information Access, a paradigm that lets you easily combine structured and unstructured data from inside and outside your organization in support of ever-evolving data exploration & visualization. We'll look at examples from competitive intelligence, safety, & assay data management. 

IBM small logo12:30 Luncheon Presentation: Visual Analytics in Healthcare

David Gotz, Ph.D., Research Staff Member, Healthcare Analytics Research Group, IBM T.J. Watson Research Center  

As the adoption rates grow for electronic medical systems, clinical institutions are amassing ever-larger collections of patient-centered data. Visual analysis techniques, designed to mine and interactively visualize this data in the context of individual patients, are enabling new opportunities for personalized data-driven clinical insights.  This talk will provide an overview of our emerging work in this area and include demonstrations of some prototype visualizations. 

1:40 Chairperson’s Remarks

Jeffrey Sutherland, Prinicipal Research Scientist and Group Leader, IT Informatics, Eli Lilly and Co.

1:45 Visualizing and Interpreting Pathway Analysis Results to Aid Drug Repurposing

Gary Bader, Ph.D., Associate Professor, The Donnelly Centre, University of Toronto

Enrichment maps organize the results of gene set enrichment analysis as a network to provide a quick visual summary of gene function enrichment. Users can explore the map to zoom in to functions of interest for deeper exploration. I will also briefly present the application of pathway analysis for drug repurposing in cancer.

2:15 Visual Analytics Case Study: Making Data Translatable

Luiz Miguel Camargo, Associate Principle Scientist, Translational & Health Informatics, Informatics IT, Merck & Co.

Deriving and prioritizing actionable hypotheses to guide drug discovery requires transformation of multidimensional data and ‘known’ biology into frameworks for intuitive exploration and interpretation. Combining aggregated phenotypic/pathway information with visual analytics generates comprehensive, interactive biological landscapes toward this end.

Ayasdi2:45 The Shape of Data Can Impact Cancer Outcomes

Pek Lum, Ph.D., Vice President, Solutions, Ayasdi

Using the entire Cancer Genome Atlas (TCGA) dataset, Dr. Lum will present how a new approach called Topological Data Analysis (TDA) reveals novel DNA variations of tumors, discovers new cancer sub-populations and provides evidence on how cancer diseases are similar across different genetic populations automatically without asking any questions.

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

3:45 Organizing and Mining Data for Biologics Research

Hugo O. Villar, Ph.D., President, Altoris, Inc.

Therapeutics research is undergoing a transformation with the more extensive use of biologics. The amount of information being generated by researchers in the field has exposed some limitations in the informatics tools available. Particularly lacking are tools to analyze the experimental results generated for hundreds of biopolymers, including peptides and other biotherapeutics. SARvision|Biologics is a desktop application to fill in the gap that exists in research informatics to deal with data on biologics. The software can be used to mine and visualize trends in data generated for biologics. At the same time, it illustrates how some concepts from small molecule SAR can be effectively be adapted to guide biologics research.

4:05 Data Visualization Case Study: Integration of a Spotfire Web Player Mashup into a Discovery Search Application

Jason Gratt, Ph.D., Lead Software Engineer, Research and Development Systems, Information Technology Group, Millennium Pharmaceuticals

An overview of Millennium’s Discovery Data Viewer (a custom search tool used by ~100 Medicinal Chemists), and how the Spotfire Web Player was integrated into it to provide users with advanced, interactive visualization features for hypothesis generation and confirmation.

4:25 Caleydo enRoute: Visualizing Large Quantities of Experimental Data in the Context of Pathways

Alexander Lex, Ph.D., Research Scientist, Visual Computing Group, Harvard School of Engineering and Applied Sciences

Caleydo enRoute takes a new approach to visualizing experimental data in the context of pathways. By dynamically extracting paths out of well known pathway maps enRoute can show hundreds of experimental values for every node. Consequently enRoute is the ideal tool to analyze the effects of experimental data for both individual samples or groups of samples on pathways, enabling analysts to work with large datasets as, for example, generated by The Cancer Genome Atlas (TCGA).

4:45 Q&A with Session Speakers

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

6:15 Exhibit Hall Closes


Thursday, April 11

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Technology Demo

Presenters from the Data Visualization track will be demoing their visualization and exploration tools in an informal setting just prior to the session continuing for the day. If you want to see the tools in action or learn more about a specific tool, come along and enjoy morning coffee with us!


Visualization of Genomic Data 

8:45 Chairperson’s Opening Remarks

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

8:50 Visualizing and Analyzing Chromatin Accessibility from Clinical Samples of Renal Cell Carcinoma

Michael J. Buck, Ph.D., Assistant Professor, Biochemistry, SUNY Buffalo; NY State Center of Excellence in Bioinformatics and Life Sciences, Cancer Genetics Roswell Park Cancer Institute; Co-Director, Next-Gen Sequencing and Expression Analysis Core; Director WNYSTEM Stem Cell Sequencing/Epigenomics Facility

Using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) combined with next-generation sequencing (FAIRE-seq) we identify changes in chromatin accessibility in human solid tumors. To examine this and other chromatin datasets we have developed a suite of chromatin architecture tools (ArchAligh, ArchTex, and ArchBlast) and will present exciting findings from these tool when applied to renal cell carcinoma.

9:20 The Integrative Genomics Viewer (IGV)

James T. Robinson, Ph.D., Principle Software Engineer, Cancer Informatics, The Broad Institute of MIT and Harvard

We describe the Integrative Genomics Viewer (IGV), a flexible, high-performance viewer that enables intuitive real-time exploration of genomic datasets. IGV is developed with a focus on the integrative nature of cancer genomic studies and the need to visualize and flexibly integrate a wide range of data types. A particular strength of IGV is its ability to visualize very large datasets, for example deep-coverage sequence data from whole genome scans, or high-resolution copy number data from thousands of samples, on standard desktop computers.  IGV permits the user to move seamlessly across the data at any level of detail, and quickly zoom in and out, from the whole genome down to base-pair resolution. Data can be annotated, filtered, grouped, and sorted, based on clinical and phenotypic attributes. This ability to dynamically and flexibly integrate multiple different datasets and view them at any scale allows investigators to elucidate complex biological relationships that are otherwise not readily apparent.

Thomson Reuters logo 9:50 Disease Maps & Evaluating New Opportunities: How the Children’s Tumor Foundation and Thomson Reuters are Collaborating for a Better Future

Annette Bakker, Ph.D., CSO, Children’s Tumor Foundation

Elona Hart, Research Scientist, Biologist, Thomson Reuters

The Children’s Tumor Foundation is the leading nonprofit funding source of Neurofibromatosis (NF) research in the world aimed at accelerating the transition from bench to bedside. Learn how their collaboration with Thomson Reuters is helping to develop new approaches to investing and show future research opportunities.

10:20 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

10:45 Plenary Keynote Panel Chairperson’s Remarks

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

10:50 Plenary Keynote Panel Introduction

Yury Rozenman, Head of BT for Life Sciences, BT Global Services

Niven R. Narain, President & CTO, Berg Pharma


» PLENARY KEYNOTE PANEL 

11:05 The Life Sciences CIO Panel

Panelists:
Remy Evard, CIO, Novartis Institutes for BioMedical Research
Martin Leach, Ph.D., Vice President, R&D IT, Biogen Idec
Andrea T. Norris, Director, Center for Information Technology (CIT) and Chief Information Officer, NIH
Gunaretnam (Guna) Rajagopal, Ph.D., VP & CIO - R&D IT, Research, Bioinformatics & External Innovation, Janssen Pharmaceuticals
Cris Ross, Chief Information Officer, Mayo Clinic
Matthew Trunnell, CIO, Broad Institute of MIT and Harvard


12:15 pm Luncheon in the Exhibit Hall with Poster Viewing

1:55 Chairperson’s Remarks

Anne E. Carpenter, Ph.D., Director, Imaging Platform, Broad Institute of Harvard and MIT

2:00 New Insights from Dynamic Exploration of Genomics Data

Carl Meinhof, Ph.D., Manager, Research Informatics, Ceres, Inc.

Exploration of large genomic data sets requires the ability to navigate through the genome and dynamically zoom in and out of regions of interest without delay. The ability to visualize genomic data in real-time yields new insights and also brings to light new questions. The Persephone genome explorer application has been developed and optimized using algorithms from game development. It enables dynamic exploration of large, diverse genomic data sets - comparable to how Google Earth has changed how we explore and use geographic data.

2:20 Visual Exploration of Cancer Genomics Data for Identification and Characterization of Tumor Subtypes

Nils Gehlenborg, Ph.D., Research Associate, Center for Biomedical Informatics, Harvard Medical School

Caleydo StratomeX is a visual exploration system developed to support the identification and characterization of tumor subtypes in large patient populations such as those studied by The Cancer Genome Atlas (TCGA) project. The system integrates multiple genomic data types (e.g. mRNA, DNA methylation, copy number, mutations) with clinical data, enabling analysts to efficiently generate and confirm hypotheses about tumor subtypes and to evaluate their functional properties and clinical effects.

2:40 JBrowse: A Next-Generation Genome Browser

Robert Buels, JBrowse Lead Developer, University of California Berkeley

JBrowse is a next-generation web-based genome browser built from the ground up with JavaScript and HTML5. JBrowse offers advanced integration, fluid interactivity, and native support for very large datasets (such as deep-coverage resequencing alignments) that were once possible only for desktop-based genome viewers, while at the same time enabling the reproducible deployments and seamless data interchange that are possible in a cloud-based application.


Microscopy/Imaging 

3:00 Visualizing High-Throughput Microscopy Imaging Data

Anne E. Carpenter, Ph.D., Director, Imaging Platform, Broad Institute of Harvard and MIT

High-throughput screening using fluorescence microscopy generates hundreds of thousands of images, showing the response of trillions of cells to chemical or genetic perturbations being tested. Assistive computational tools are needed to identify samples of interest and patterns in this data.

3:30 Integrating High Content Imaging of 3D Organotypic Tumor Cultures into Basic and Preclinical Cancer Research

Andrew J. Ewald, Ph.D., Assistant Professor, Departments of Cell Biology and Oncology, Johns Hopkins Medical Institutions

We developed innovative primary tumor isolation, 3D culture, and high-content imaging strategies to analyze the relative contributions of tumor cell populations to invasion, dissemination, and therapeutic resistance in real-time. We will discuss medium throughput imaging and analysis techniques to integrate these results into preclinical research.

4:00 Conference Adjourns



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