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Track 4: Bioinformatics

 

Final Agenda:

Track 4 explores bioinformatics and cancer, next-gen sequencing and novel bioinformatics and data integration approaches, data modeling and computational integrative tools, and bioinformatics in the cloud.

 

TUESDAY, APRIL 12

7:00 am Workshop Registration and Morning Coffee

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

*Separate Registration Required.

2:00 - 6:00 Main Conference Registration

4:00 Event Chairperson’s Opening Remarks

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

Sponsored by
Isilon Systems
4:05 Keynote Introduction

Chris Blessington, Life Sciences Solutions Architect, Isilon





Plenary Keynote
4:15 Making the World’s Knowledge Computable

StephenWolframStephen Wolfram, Ph.D., CEO, Wolfram Research; Creator of Wolfram|Alpha

 

 

 

Sponsored by
BlueARC-125px
5:00 Welcome Reception in the Exhibit Hall and Poster Viewing


 

 


WEDNESDAY, APRIL 13

7:00 am Registration and Morning Coffee

8:00 Event Chairperson’s Opening Remarks

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

Sponsored by
TessellaNEW 
8:10 Keynote Introduction
 
Grant Stephen, CEO, Tessella, Inc.



Plenary Keynote
8:15 Interacting with Complex Information Landscapes: Integration and Next Generation User Interfaces

Bryn RobertsBryn Roberts, Ph.D., Global Head, Informatics, Pharma Research and Early Development, F. Hoffmann-La Roche Ltd.

 

 

 

 

8:45 Benjamin Franklin Award/Presentation: Jonathan Eisen, Ph.D., Professor, Genome Center, University of California, Davis

9:10 Best Practices Awards Program

Sponsored by
Scynexis
9:45 Coffee Break in the Exhibit Hall and Poster Viewing




Bioinformatics & Cancer

10:50 Chairperson’s Remarks

Eitan Gross, Ph.D., Assistant Professor, Physics, University of Arkansas

11:00 Web Portal for Integrated Analysis of Radiation Responsive Cancer Gene Expression Profiles

Uma Shankavaram, Ph.D., Staff Scientist, National Cancer Institute/National Institutes of Health

The abundance of cancer research is evident from a PubMed search. However, studies focusing strictly on Radiation effects on cancer are rare and, to our knowledge, there are no web portals dedicated to this topic. This presentation will describe a web portal called MAQuery we have created that would house cancer related microarray expression data focusing primarily on radiation oncology data. Attendees will learn how MAQuery will help in the search for genes with particular expression profiles in cancers.

11:30 Lung Genomics Research Consortium: Building a Translational Research Portal to Improve the Molecular Understanding of Lung Disease

Mick Correll, Associate Director, Center for Cancer Computational Biology, Dana-Farber Cancer Institute

The LGRC portal represents a revolutionary new way to support collaborative research in the genetics of chronic lung disease. The portal addresses many needs, from supporting uploading of large experimental data seta, assessment of available samples and their characteristics, sample and data tracking capabilities across a distributed consortium, and the availability of sophisticated, automated analytical tools. Learn about the project requirements, solution design, and commercial and open source tools that were utilized to construct the system.

12:00 Enhancing Cancer Biobanks through Novel IT: The BioGeoBank
Janet M. Hock, B.D.S., Ph.D., Senior Investigator & Founding Director, Maine Institute of Human Genetics and Health; Professor, Tufts University School of Dental Medicine


Sponsored by
Biofortis smaller 
12:30 Luncheon Presentation
Data Exploration as an Integral Component of Data Cleaning and Standardization in Translational Informatics  
Mark Brocato, Director, Software Engineering, BioFortis, Inc. 
Traditionally, data cleaning and standardization must happen first before meaningful queries and reports can be generated in clinical and translational research. In this presentation, we will describe a new paradigm that allows data cleaning and standardization to be an iterative process enabling scientific value to be derived every step of the way.

 

Next-Generation Sequencing
And Novel Bioinformatic And
Data Integration Approaches

1:40 Chairperson’s Remarks
Eitan Gross, Ph.D., Assistant Professor, Physics, University of Arkansas

Sponsored by
caBIG logo
1:45 Leveraging caBIG®: New Collaborative Models in Science and Business

Brent Gendleman, President and CEO, 5AM Solutions

Joel Saltz, M.D., Ph.D., Director, Center for Comprehensive Informatics, Emory University

Vast amounts of data generated by sophisticated research techniques and millions of clinical interactions represent an un-mined opportunity for advancing collaborative research and discovery at a 21st century pace. Realization of this potential is predicated upon an interoperable IT environment to facilitate data integration and exchange in support of a wide variety of basic, clinical and translational research efforts. The caBIG® principles of open access, open source, open development, and federation drive unique opportunities for business, academic, and research enterprises to solve research challenges that translate into viable results.

2:15 Broad-Scale Next-Generation Sequencingin Marine Metagenomics - Novel Applications and Future Prospects

Hanno Teeling, Ph.D., Scientist, Department of Molecular Ecology/Microbial Genomics & Bioinformatics Group, Max Planck Institute for Marine Microbiology

This talk will demonstrate by means of the German research project MIMAS (Microbial Interactions in Marine Systems) and the European project MAMBA (Marine Metagenomics for New Biotechnological Applications) how next-generation sequencing in combination with novel bioinformatic and data integration approaches can be used to link biodiversity and functional information, and thus turn the data deluge from broad-scale environmental sequencing into meaningful biological knowledge.

Sponsored by
Nextbio
2:45 Democratizing Large-Scale Genomic Data for Basic and Clinical Researchers

Ilya Kupershmidt, Co-Founder and Vice President, Products, NextBio

Evolution of array and next-generation sequencing technologies is driving exponential growth of data in the public domain, as well as private data generated by individual labs and organizations. In order to truly make use of this information, data-driven understanding of disease by different types of researchers is required. In this talk I will describe how NextBio platform is enabling scientific groups with diverse backgrounds to utilize massive quantities of genomic information across basic and clinical research initiatives.

Sponsored by
Teradata sm
3:00 Drug Discovery Optimization in the Teradata Agile Analytics Cloud
Ed Acker, Senior Consultant, Life Sciences Industry, Teradata
Scientists can optimize discovery/replication analyses of gene to protein experiment data using Teradata's Agile Analytics Cloud to quickly create/combine/share and analyze customizied private virtual data marts without IT participation.  

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

Data Mining and Modeling

3:45 Data Mining & Synthetic Biology: A Tool for Knowledge Discovery

Merridee Wouters, Ph.D., Group Leader, Structural & Computational Biology, Victor Chang Cardiac Research Institute

As a relatively new field, bioinformatics is still in the process of defining itself and demonstrating its usefulness to biological and medical research. The large amount of publicly available data is a rich source of biological systems knowledge which is currently underutilized. Effective data mining programs can maximize the potential of acquired data and are a cost effective solution for knowledge discovery. Learn the importance of data mining and its relationship to other areas of bioinformatics.

4:15 A Data Warehouse for Translational Research

Hai Hu, Ph.D., Deputy CSO, Senior Director, Biomedical Informatics, Windber Research Institute

We have developed an extensible data warehouse, the Data Warehouse for Translational Research (DW4TR), based on a novel patient-centric modularly-structured clinical data model and a specimen-centric molecular data model. Learn how we conceived and developed the model, how temporal relationships are modeled and incorporated, how the DW4TR is used as a research environment for clinicopathologic risk factor analysis and for virtual experiments, and how the DW4TR can be used as the basis for the development of a physician decision-support system.

4:45 Clustering Algorithms in Gene Expression Analysis 

Eitan Gross, Ph.D., Assistant Professor, Physics, University of Arkansas

The exponential growth in gene expression data in recent years, due to the introduction of fast sequencing technologies, calls for fast, reliable and automatic clustering algorithms that can assist in analyzing and extracting valuable information that is potentially embedded in the ever growing gene expression data banks.  This talk will discuss the various methods and approaches (parametric, non-parametric, etc.) used to cluster gene expression data.

6:15 Exhibit Hall Closes

 

THURSDAY, APRIL 14

8:45 am Event Chairperson’s Opening Remarks

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

Sponsored by
BT small
8:50 KEYNOTE PANEL: Keynote Introduction
A special plenary session featuring a series of succinct, forward-looking presentations by:

Ken Buetow, Ph.D., Associate Director, Bioinformatics and Information Technology, National Cancer Institute

Debra Goldfarb, Senior Director, Strategy, Microsoft

Martin D. Leach, Ph.D., Executive Director, MRL IT for Discovery & Pre-Clinical Sciences, Merck & Co.

Mark Boguski, M.D., Ph.D., Founder, Resounding Health Incorporated

Jamie Heywood, Co-founder and Chairman, PatientsLikeMe
Yury Rozenman, Global Head of Marketing, Pharmaceutical and Life Sciences Sector, BT Global Services

 

10:30 Coffee Break in the Exhibit Hall with Poster Competition

 

Data Modeling & Computational
Integrative Tools

10:55 Chairperson’s Remarks
Rong Chen, Ph.D., Bioinformatics Scientist, Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine

11:00 Affordable Departmental Supercomputer Facilitates the Conformational Modeling and Simulation of Protein Dynamics

Nurit Haspel, Ph.D., Assistant Professor, Computer Science, University of Massachusetts, Boston

Through academic and industry research collaborations, we have developed a computational, theoretical and experimental framework to rationally design nano- and micro-structures made of amphiphilic hybrid materials which combine peptides used in the formation of amyloids with polyesters. This work was made possible through the use of a NAMD molecular dynamics software installed on a supercomputer. This presentation will describe our work and how the supercomputer helps us to perform research more efficiently than any other locally or nationally available resource.

11:30 Using Public Molecular Measurements to Drive Discovery of Biomarkers and Therapeutics

Rong Chen, Ph.D., Bioinformatics Scientist, Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine

The measurement of most molecular states is now a commoditized service on well established platforms. Funding agency and journal mandates have led to the deposition of billions of data elements into international repositories, while the lay public and press have demanded more clinical translation from these data. This presentation will describe how computational integrative tools can be used to convert more than 15 billion points of molecular, clinical, and epidemiological data measured by researchers and clinicians over the past decade into novel diagnostics, therapeutics, and insights into disease. The presentation will end with six important lessons learned from using public molecular measurements.

12:00 pm Inspire: Novartis Translational Science Data Warehouse  

Philippe Marc, Ph.D., Safety Knowledge Management Expert, Translational Science, Novartis Institute for Biomedical Research

The Novartis Institutes for Biomedical Research (NIBR) are composed of approximately 6 000 scientists and physicians located in various locations worldwide. We are known for our robust pipeline and our track record of innovation. One of the keys to such success is to have a proper flow of ideas and information across the organization. This talk will illustrate a successful project – the creation and use of Inspire, our translational data warehouse. Inspire is aggregating data from fifty internal and external sources in a single place, including data from clinical trials, preclinical studies, drugs and targets. We will discuss agile programming, business and IT communication, ETL, service orientation, use of master data, and ontologies.

 

12:30 Luncheon in the Exhibit Hall and Poster Viewing

2:00 Exhibit Hall Closes

Bioinformatics in the Cloud:
An Affordable Alternative

1:55 Chairperson’s Remarks
Bill Frezza, Venture Partner, Adams Capital Management

2:00 Bioinformatics in the Cloud

Giles Day, Managing Director, Distributed Bio, LLC

This talk will describe how to implement a complete sequence annotation pipeline on Amazon, including maintaing databases, using queuing systems and interacting with relational databases.

2:30 Translational Bioinformatics: A Multidisciplinary Approach to Biomedical Research

Yate-Ching Yuan, Ph.D., Director, Bioinformatics Core Facility, Molecular Medicine, Beckman Research Institute, City of Hope

This presentation will describe our use of cloud computing to help streamline our data analysis pipelines. We have been able to provide cost-effective translational bioinformatics platforms using an integrated cyber-infrastructure to support high-throughput data analysis, management, and integration in order to advance research on predictive, preventive, personalized and participatory medicine.

3:00 Bioinformatics on Cloud Cyberinfrastructure

Geoffrey Fox, Ph.D., Professor, Informatics and Computing; Director, Community Grids Laboratory, School of Informatics and Computing, Indiana University, Bloomington

Clouds offer computing on demand plus important platforms capabilities including MapReduce and Data Parallel File systems. This talk will look at public and private clouds for large scale sequence processing characterizing performance and usability, as well as FutureGrid, an NSF facility supporting such studies.

3:30 The Atlas Cloud Computing Infrastructure for Organizing and Querying Multiomics Data (Joint with Tracks 1-5)

Misha Kapushesky, Ph.D., Functional Genomics Team Leader, EBI, Cambridge UK

The Expression Atlas is a cloud computing based distributed infrastructure for organizing and querying multiomics data. Built upon the open-source Expression Atlas project at the EBI in partnership with the pharmaceutical industry, the Atlas provides a scalable solution that can be easily deployed on in-house servers or accessed remotely in the cloud. Learn how the Atlas deals with secure processing and combined analysis and integration of public/private transcriptomic and proteomic data, with an emphasis on our novel pipeline for next-generation sequencing data processing and reporting.

4:00 Conference Adjourns



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  • Making the World's Knowledge Computable
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