Bio IT World Expo 2016  
Bio IT World Expo 2016
2014 Archived Content

Data Visualization and Exploration Tools 

The Data Visualization and Exploration Tools Track will showcase how to design, implement and evaluate visualization techniques and tools that offer real value to the user both in support of genomics and sequencing research, as well as in drug discovery and development. We will present case studies that showcase approaches to data visualization and analysis that address important challenges in genomics, pathway analysis, oncology and drug discovery.

Final Agenda

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7:00 am Workshop Registration and Morning Coffee

8:00 - 11:30 Recommended Morning Pre-Conference Workshops*

Data Visualization in Biology: From the Basics to Big Data - View Detailed Agenda 

12:30 - 4:00 pm Recommended Afternoon Pre-Conference Workshops*

UCSC Genome Browser Interactive Workshop - View Detailed Agenda 

*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


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5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing




7:00 am Registration Open and Morning Coffee

8:00 Chairperson's Opening Remarks

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


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9:00 Benjamin Franklin Award & Laureate Presentation

9:30 Best Practices Awards Program

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

Visualization and Analysis of Genomic Data 

10:50 Chairperson's Remarks

Jeremy Goecks, Ph.D., Computational Biology Institute, George Washington University

11:00 Featured Presentation

Variant View: Visualizing Sequence Variants in their Gene Context

Tamara Munzner, Ph.D., Professor, Computer Science, University of British Columbia

The Variant View visualization tool supports variant impact assessment with an information-dense visual encoding that provides maximal information at the overview level, in contrast to the extensive navigation required by currently-prevalent genome browsers. We discuss design considerations, and show how the tool simplified and accelerated workflows through four case studies.

11:30 Featured Presentation

A Compendium of Next-Generation Clustered Heat Maps for Interactive Exploration of TCGA Data

John N. Weinstein, M.D., Ph.D., Professor & Chair, Bioinformatics & Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center

The Cancer Genome Atlas (TCGA) program is generating comprehensive molecular profiles of more than 25 clinical tumor types, the first 12 of which have been incorporated into a Pan-Cancer project. One challenge is statistical analysis of the resulting profiles; a second is the visual detective work necessary to explore individual genes, pathways and patterns in the data. For the latter purpose, we have developed “next-generation” clustered heat maps (NG-CHMs), which use a Google-maps-like tiling technology for extreme zooming and navigation without loss of resolution. NG-CHMs provide pathway and gene ontology information, re-coloring on the fly, high-resolution graphics output and link-outs to public sources of information on genes, proteins, pathways and drugs. The result is a visually rich, dynamic environment for exploration of the masses of data produced by TCGA. The Compendium of TCGA Pan-Cancer NG-CHMs currently includes 667 maps as an initial set, but the numbers will soon rise into the thousands as more data types, tumor types, and algorithms are incorporated (at

12:00 pm Choose the Right: The Right Information to the Right Person in the Right Way to Support Clinical Research Decision Making

Aaron Kamauu, M.D., M.S., M.P.H., CEO, Anolinx LLC

Use of healthcare data as real world evidence has become a forefront for clinical research. However, this “big data” is very complex and difficult to interpret. This presentation will describe the representation of analysis results conducted on big patient-level electronic health records data to support drug development and clinical research.

12:15 pm Sponsored Presentation (Opportunity Available)

12:40 Luncheon Presentation I: Big Data & Little Data in the Pharma Industry

Andreas Matern, Vice President, Disruptive Innovation, Thomson Reuters

Big Data is quickly becoming an overused, and poorly understood, term in technology. This talk will focus on Big Data for the life sciences. What role does visualization have in Big Data? How do we resolve gaps in life sciences data? How can we spot trends, and effectively ask questions and monitor the amount of structured and unstructured content?

1:10 Luncheon Presentation II (Sponsorship Opportunity Available)

1:50 Chairperson's Remarks

John N. Weinstein, M.D., Ph.D., Professor & Chair, Bioinformatics & Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center

1:55 Making the UCSC Genome Browser Work for You

Robert Kuhn, Ph.D., Associate Director, UCSC Genome Browser, Center for Biomolecular Science and Engineering University of California, Santa Cruz

The UCSC Genome Browser provides visualization tools for a large genomic database spanning more than 100 animals. New features include a tool to analyze sequence variant data and hosting organisms not part of the UCSC infrastructure. Browser views of user data may be saved and shared with colleagues.

2:25 Visualizing the Broad Institute’s Connectivity Map

Bang Wong, Creative Director, Broad Institute of MIT & Harvard; Adjunct Assistant Professor, Art as Applied to Medicine, Johns Hopkins University School of Medicine

The CMap is a catalog of a gene-expression data generated by exposing cells to chemical and genetic modifiers. Depicting findings from this 26 trillion point dataset requires thoughtful decisions about data presentation. I will describe how we apply design principles to develop user-friendly tools to explore the data.   

Novel Visualizations in Pharma & Life Science Companies 

2:55 Visualization of Heterogeneous, Multidimensional Data to Support Lead Discovery

Anne Mai Wassermann, Ph.D., Researcher, Novartis Institutes for BioMedical Research, Inc.

In the course of a lead discovery project, the biological action of small molecules is investigated from many different angles. Orthogonal experiments such as biochemical, high-content screening, or gene expression assays yield a rich source of information to generate hypotheses about the mechanisms-of-action of small molecules. Integrating and providing easy access to complex, multidimensional data is crucial for success. Therefore, many different visualization tools have been developed to facilitate data analysis at the early stages of drug discovery. In this presentation, an overview is given about different visual analysis approaches to lead discovery at Novartis.

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing

4:00 GWAVA: Genome-Wide Association Visual Analyzer

Peter Henstock, Ph.D., Senior Principal Scientist, Research Business Technology Group, Pfizer, Inc.

GWAVA serves as our new corporate standard tool for the visual analysis of genome-wide association studies (GWAS) data loaded into the tranSMART platform. GWAVA provides an interactive visualization of the study-SNP data extracted both from queries using tranSMART’s native interface, or through GWAVA’s own query interface. By managing multiple gene queries and studies, it facilitates an understanding of the SNP p-values across both studies and chromosome regions using different views of the data. GWAVA has been recently been made available as open source software.

4:30 Navigating to the Needle in the Haystack – Interactive SAR Analysis Tools

Lisa Sach-Peltason, Ph.D., Cheminformatics and Statistics, Pharma Research & Early Development Informatics, F. Hoffmann-La Roche Ltd.

The major goal in early drug discovery is to identify compounds that have the most favorable property profiles and the potential to be developed towards a promising drug candidate. With hundreds of thousands of biological assay results that scientists need to analyze in just one small-molecule drug discovery project, it is clear that computational tools are very much needed to help navigating large and complex data landscapes. At Roche, we have created an innovative application for chemical data visualization and analysis of structure-activity relationships (SAR). Built on top of our small-molecule assay data warehouse, cutting-edge visualization approaches have been implemented and enhanced with interactive drill-down capabilities. Offering a quick overview of compound data sets as well as ways to focus in on regions of interest in more detail, the tool provides complementary views on a data landscape and helps to address questions relevant in different stages of a medicinal chemistry research project.

5:00 Select Poster Presentation: GenCloud: A Modular Genomics Data Organization, Analytics and Visualization Platform

Nejc Skoberne, Ph.D., Faculty of Computer and Information Science, University of Ljubljana

Various methods and scripting tools for analysis, visualization and interpretation of NGS data are available. In order to have the data ready for further analysis, a secure system for data storage, sharing and organization is required. GenCloud is a web platform with intuitive interface for securely storing, sharing and organizing NGS data. It is also a development platform for web applications that enable interactive analysis and visualization of NGS data.

5:30 - 6:30 Best of Show Awards Reception in the Exhibit Hall


7:00 am Registration Open

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

8:00 Chairperson’s Opening Remarks

Kevin Davies, Ph.D., Vice President Business Development & Publisher C&EN, American Chemical Society; Founding Editor, Bio-IT World


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10:00 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

Novel Visualizations in Pharma & Life Science Companies (cont'd) 

10:30 Chairperson's Opening Remarks

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

10:35 Merck's Information Landscape Knowledgebase

Kelly Clark, Lead Analyst, Scientific Information Architecture, Merck & Co., Inc.

Merck’s Informatics IT team has developed the Information Landscape Knowledgebase, a semantically rich, intuitively accessible repository of information sources across Merck. In this talk, we will discuss how the solution takes advantage of underlying semantic models and novel visualizations to address the needs of both scientists and data stewards while providing valuable insights for IT resourcing.

11:05 Persephone: Enabling Real-Time Exploration across Genomes

Stanislav Freidin, Senior Software Engineer, Persephone, Ceres, Inc.

As the volume of genomic analysis results increases, navigating the data becomes more difficult. Our tool allows the user to quickly navigate between different genomes, as well as between different areas of a single genome, in real time. It allows a user to explore a genome even when the user has no particular destination in mind, to view different genomes side by side, and to zoom in and out of regions of interest very quickly. Persephone's exploratory visualization enables users to generate new insights and potentially devise new avenues of analysis.

11:35 Cross-Organizational Data Visualization and Correlation to Design Drug and Process in the Pharmaceutical Industry

Jean-Etienne Fortier, Knowledge Management Specialist, GPS, UCB PHARMA

At UCB, the Knowledge Management department recently implemented a system to provide scientists and managers an easy access to scientific data and visualization tools, to support decisions during drug and process development. This platform uses a very simple architecture and allows mixing any type of data, associated with any metadata.

12:15 pm Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

1:15 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing

Visualization and Analysis of Genomic Data 

1:55 Chairperson's Remarks

Alexander Lex, Ph.D., Researcher, Harvard School of Engineering & Applied Sciences

2:00 Integrated Analysis and Visualization of Large-Scale Biological Data with the Refinery Platform

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

Data sets with dozens or hundreds of samples are now common in molecular biology and the development of visualization tools for such large and complex data sets requires extensive software infrastructure. To address these challenges, we have developed the Refinery Platform (, a web-based data visualization and analysis system powered by an ISA-Tab-compatible data repository for public and private data sets. Analyses are implemented as Galaxy workflows and executed through the Galaxy API.

2:30 Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy

Jeremy Goecks, Ph.D., Computational Biology Institute, George Washington University

Learn about how to use the popular, web-based Galaxy platform to analyze and visualize your high-throughput genomics data. Galaxy visualizations require only a web browser to use and no software or data downloads. Galaxy visualizations include a genome browser, Circos plot, phylogenetic tree, and a parameter sweeping application.

Pathway Analysis & Cancer Data Visualization 

3:00 NetGestalt: Integrating Multidimensional Omics Data over Biological Networks

Bing Zhang, Ph.D., Associate Professor, Biomedical Informatics, Vanderbilt University School of Medicine

Node-link diagram-based network visualization becomes inadequate as network size and data complexity increase. NetGestalt exploits the inherent hierarchical modular architecture of biological networks to achieve high scalability. It allows simultaneous presentation of large-scale experimental and annotation data from various sources in the context of biological networks to facilitate data visualization, analysis, interpretation and hypothesis generation.

3:30 Caleydo Entourage: Visualizing Relationships between Biological Pathways

Alexander Lex, Ph.D., Researcher, Harvard School of Engineering & Applied Sciences

This talk will introduce Entourage, a visualization technique for analyzing interrelationships between multiple related biological pathways. We use a novel technique - contextual subsets - to determine and present parts of other pathways that are relevant in the context of a focus pathway. Entourage supports dynamic querying of pathway based on node occurrence, overall similarity of pathways, or over-representation of pathways in experimental data. I will demonstrated three case studies showing how Entourage can be used to judge potential side-effects of compounds, to find potential targets for drug-repositioning and how it can be combined with visualization of experimental data to reason about varying effects of compounds on samples. Entourage is part of Caleydo, an open-source visualization framework.

4:00 Conference Adjourns


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

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