2014 Archived Content

Cambridge Healthtech Institute’s Third Annual

Bioinformatics for Big Data

How Applications of Big Data will Drive Research Forward

February 10-12, 2014 | Moscone North Convention Center | San Francisco, CA

 

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Wednesday, February 12

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


8:00 Plenary Keynote Session (Click Here For More Details) 


9:45 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall


DATA INTEGRATION & SHARING: TOOLS AND POLICIES FOR VISUALIZATION AND ANALYSIS 

10:35 Chairperson’s Remarks

Larry Hunter, Ph.D., Director, Center for Computational Pharmacology & Computational Bioscience Program, Professor, Pharmacology, University of Colorado

10:40 Knowledge-Based Analysis at Genomic Scale

Larry Hunter, Ph.D., Director, Center for Computational Pharmacology & Computational Bioscience Program, Professor, Pharmacology, University of Colorado

High-throughput instruments and the explosion of new results in the scientific literature is both a blessing and a curse to the bench researcher. Effective design and implementation of computational tools that genuinely facilitate the generation of novel and significant scientific insights remains poorly understood. This talk presents efforts that combine natural language processing for information extraction, graphical network models for semantic data integration, and some novel user interface approaches into a system that has facilitated several significant discoveries.

11:10 Combining Visual Analytics and Parallel Computing for Data-Driven Analysis Pipeline Selection and Optimization to Support the Big Data to Knowledge Transformation

Richard Scheuermann, Director, Informatics, J. Craig Venter Institute

This presentation describes our efforts at the J. Craig Venter Institute (JCVI) in collaboration with the Texas Advanced Computing Center (TACC) in the development of a high performance cyber-infrastructure that combines visual analytics and parallel computing for data-driven selection and optimization of analytical pipelines based on objective performance metrics. We demonstrate the application of these principles and infrastructure for the analysis of genome-wide gene expression and high-throughput, high dimensional flow cytometry data in clinical and translational research settings.

11:40 Co-Presentation: Spotfire Templates for Analysis & Visualization of Project Data 

Sandhya Sreepathy, PMP, Head of Operations, Global Discovery Chemistry, Novartis

Heather Hogg, Ph.D., Business Analyst, Novartis Institutes for Biomedical Research

There has been a significant increase in the usage of Spotfire by project teams in Emeryville for visualization and analysis of data. To help streamline development activity and support the needs of project teams with data analysis and visualization, NIBR-IT in collaboration with computational chemistry group in Emeryville developed project based Spotfire templates. Templates were built leveraging existing technologies for retrieval/import of data and incorporated common elements of analysis and visualization(scaffold assignment, ligand, lipophilic efficiency, activity ratios, r-group decomposition etc). Predefined visualizations and filters helped accelerate project team decision making.

12:10 pm Session Break

12:20 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:00 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing


HOW BIG DATA WILL DRIVE RESEARCH FORWARD 

1:40 Chairperson’s Remarks

Michael H. Elliott, CEO, Atrium Research & Consulting LLC

1:45 Harnessing Big Data to Accelerate Drug Development

Vinod Kumar, Ph.D., Senior Investigator, Computational Biology, GlaxoSmithKline Pharmaceuticals

With the rapid development of high-throughput technologies and ever-increasing accumulation of whole genome-level datasets, an increasing number of diseases and drugs can be comprehensively characterized by the changes they induce in gene expression, protein, metabolites and phenotypes. Integrating and querying such large volumes of data, often spanning domains and residing in diverse sources, constitutes a significant obstacle. This talk presents two distinct approaches that utilize these data types to systematically evaluate and suggest new disease indications for new and existing drugs.

2:15 Drug Process Design Improvement based on Data Management and Analysis

Valérie Vermylen, Knowledge Management, Director, GPS, UCB

Most of the scientific process data generated are not free to access, even if managed in databases. At UCB, data was recently made available including its context. It allows process developers to draw easily designed space and define critical parameters. To support investigation studies as impact analysis, manufacturing dashboards and trends are automatically published. An example of correlation between process data and patients’ clinical responses will be presented as an illustration of advanced data analysis.

2:45 The Library of Integrated Network-based Cellular Signatures (LINCS) Information FramEwork (LIFE)

Stephan C. Schürer, Ph.D., Associate Professor, Pharmacology, Center for Computational Science at Miller School of Medicine, University of Miami

The NIH-funded LINCS consortium is producing an extensive dataset of cellular response signatures to a variety of small molecule and genetic perturbations. We have been developing the LINCS Information FramEwork (LIFE) – a specialized knowledge-driven search system for LINCS data.

3:15 An Enhanced Molecular Design Platform That Fosters Ideation, Knowledge Transfer, and Collaboration

Leah Frye, Ph.D., Vice President, Drug Discovery Applications Group, Schrödinger

Drug discovery is the ultimate team sport. Schrödinger is developing a collaborative and knowledge engineered platform—LiveDesign—to help scientists not only capture their ideas and best practices, but to exploit and share these with select team members. Above and beyond the aggregation of 2D data, this platform will allow users to bring together 3D data with its associated annotations. LiveDesign will ultimately lead to better patient outcomes, promoting better scientific communication by exposing data, ideas, and colleague feedback during the design and redesign phases of molecular discovery.

3:45 Refreshment Break


BIG DATA DRIVING PERSONALIZED MEDICINE 

4:00 Chairperson’s Remarks

Dalia Cohen, Ph.D., Founder & President, ALN Associates

4:05 Big Data's Big Role in Understanding Complex Diseases

Andreas Kogelnik, M.D., Ph.D. Founder and Director, Open Medicine Institute

The Open Medicine Institute (OMI) is effectively applying a collaborative, "big data" approach to understand and address complex diseases including: Autism, Lyme, Chronic Fatigue Syndrome, Parkinson's, and various cancers. This presentation will discuss the creation of a patient-centric infrastructure that handles and analyzes genomic sequencing information, bio-sampling data, physiology tests, basic research, patient experiences and physician evaluations to deliver needed information about a range of diseases.

4:35 Progress on Aggregating all the World’s Genetic Tests into a Single Assay

Randy Scott, Ph.D., CEO and Co-Founder, InVitae

Technology is moving rapidly to enable massively parallel genetic testing. The ability to sequence DNA, however, is only the first step in building the infrastructure to analyze, store, manage, and interpret medical genetic information for patients. InVitae is focused on building the infrastructure to bring more comprehensive genetic testing into routine medical practice throughout the world.

5:05 It’s Not Just About Big Data...Big Analytics for Identifying What Works and for Whom in Healthcare

Iya Khalil, Ph.D., Executive Vice President and Co-Founder, GNS Healthcare

We are living in the era of big data in healthcare, with unprecedented ability to collect data at multiple levels (genomic/'omic', phenotypic, health records, mobile health, etc.) and at scale. The key will be leveraging advanced analytics and appropriate feedback loops to identify what works on an individual patient level. 

5:35 Close of Conference Program



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2015 MMTC Final Agenda 

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