Track 5 is dedicated to advances in analysis and intepretation of next-gen data. Topics to be covered include analysis of sequence variants related to cancer research from NGS data, instruments facilitate a cloud approach for NGS, analysis tools and workflows, and network biology/network medicine.
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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 L. Hopkins, DPhil, FRSC, FSB, Division of Biological Chemistry and Drug Design, College of Life Sciences, University of Dundee
10 Minute Welcome to the Reception!
Mike Nolte, Regional Sales Manager – East, 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 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
10:50 Chairperson’s Remarks
Steve Dickman, Founder & CEO, CBT Advisors, Inc.
11:00 CLARITY Challenge
Shamil Sunyaev, Ph.D., Associate Professor, Division of Genetics, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School
11:30 HLA and KIR Typing from NGS Reads with Omixon Target
Attila Berces, Ph.D., CEO, Omixon
HLA is the most polymorphic region of the human genome with several segmental duplications and its analysis is a computational challenge. In this presentation I will show examples including validation studies of HLA typing from various sources of genomic data: whole genome, whole exome, targeted amplicon sequencing with Illumina, Ion Torrent and Roche sequencer.
11:45 Comparison of Genome Analysis Tools
Jason Wang, Co-founder & CTO, Arpeggi, Inc.
A major impediment to clinical sequencing is the paucity of analysis standards and comparison metrics. We present our progress towards developing analysis standards, as well an open-access collaborative tool that enables anyone to define comparison metrics and compare tool performance. We hope that in making available this resource we can help fuel a community-driven solution for standardizing genome analysis pipelines.
12:00 Case Study: Sequencing Informatics System to Profile Genetic Changes in Tumors
Long Phi Le, M.D., Ph.D., Department of Pathology, Massachusetts General Hospital
This presentation will discuss the development of a sequencing informatics system to profile genetic changes in tumors that is in collaboration between PerkinElmer with Massachusetts General Hospital. This system, based on PerkinElmer’s Geospiza platforms, will allow genotype analysis to define key targets.
12:30 Luncheon Presentation: Ion Torrent Informatics Enables Semiconductor Sequencing
Darryl León , Ph.D., Associate Director, Product Management, Ion Torrent, Life Technologies
Data generated by the Ion Torrent Personal Genome Machine Sequencer or the Ion Torrent Proton Sequencer are analyzed by Torrent Suite Software. An overview of the data analysis steps will be provided. Torrent Suite offers a flexible plug-in system allowing software developers the ability to deliver custom analysis solutions using the compute resources associated with the local Torrent Server. For researchers with need for either rich annotations or controlled data analysis, the Ion Reporter Software offers a streamlined data analysis and decision engine for use with amplicons, exomes, or genomes.
1:40 Chairperson’s Remarks
Jeffrey Rosenfeld, Ph.D., Assistant Professor of Medicine, IST/High Performance & Research Computing, New Jersey Medical School (UMDNJ)
1:45 Data Intensive Academic Grid (DIAG): A Free Computational Cloud Infrastructure Designed for Bioinformatics Analysis
Anup Mahurkar, Executive Director, Software Engineering and IT, Institute for Genome Sciences, University of Maryland School of Medicine
We have deployed the NSF funded Data Intensive Academic Grid (DIAG), a free computational cloud designed to meet the analytical needs of the bioinformatics community. DIAG has 200+ registered users from 130 institutions worldwide who conduct large-scale genomics, transcriptomics, and metagenomics data analysis. Learn about the grid’s architecture, how to access this free resource, and success stories.
2:15 Performance Comparison of Variant Detection Tools for Next Generation Sequencing (NGS) Data: An Assessment Using a Pedigree-Based NGS Dataset and SNP Array
Ming Yi, Ph.D. IT Manager, Functional Genomic Group, Advanced Biomedical Computing Center, SAIC-Frederick at Frederick National Laboratory for Cancer Research (formerly National Cancer Institute)
There is an urgent need for the NGS community to be able to make the right choice out of a large collection of available SNP detection tools. Our methodology offers a great example of comparing SNP discovery tools and paving a way to expand such methods in more global scope for comparison.
2:45 Informatics in the Cloud
Karan Bhatia, Ph.D., Solutions Architect, Amazon Web Services
Learn about how to easily create sophisticated, scalable, secure pipelines to accelerate life science research with Amazon Web Services. In this presentation, you will learn how to drive scale out, tightly coupled and Hadoop based workflows on Amazon EC2, a utility computing platform that provides a perfect fit for data management and collaboration.
3:15 Refreshment Break in the Exhibit Hall with Poster Viewing
3:45 InSilico DB Genomic Datasets Hub: An Efficient Starting Point for Managing and Analyzing Genomewide Studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor
David Weiss, Ph.D., CEO, InSilico Genomics
Alain Coletta, Ph.D., Co-Founder and CTO, InSilico Genomics
The InSilico DB platform is a powerful collaborative environment, with advanced capabilities for biocuration, datasets subsetting and combination, and datasets sharing. InSIlico DB solution architecture will be presented along with a live demo of the InSilico DB online platform. Learn how more than 1000 users from top academic and research institutions are using InSilico DB in their daily research.
4:15 Constructing a Comprehensive Map for Molecules Implicated in Obesity and Its Induced Disorders
Kamal Rawal, Ph.D., Faculty, Biotechnology and Bioinformatics, Jaypee Institute of Information Technology
We have constructed a comprehensive map of all the molecules (genes, proteins, and metabolites) reported to be implicated in obesity. This map paves the way to understanding the pathophysiology of obesity and identify drug targets and off-targets for existing drugs. This talk discusses the integrated approach we used in combining public resources, abstracts, and research articles to construct this map.
4:45 Quality Assurance: An Essential Step for Gene Expression Analysis Using Deep Sequencing
Dan Kearns, Director, Software Development, Maverix Biomics, Inc.
Dave Mandelkern, CEO & Co-Founder, Maverix Biomics, Inc.
With the advancement of deep sequencing technologies, researchers expect to obtain high quality results from their studies. However, this cannot be obtained solely by successful sequencing runs. Multiple data checks and pre-processing must be performed before downstream analysis. In this case study, we will present an automated quality assurance pipeline that helps improve gene expression analysis results.
5:00 DDN LS Appliance - Simple Platform for NGS Analysis, Data Distribution and Collaboration
Jose L. Alvarez, WW Director Life Sciences, DataDirect Networks
With this unique approach the DDN LS appliance can deliver flexible data ingest options, optimized data analysis resources, a policy based data tiering/archive solution and a geo-distributed secure collaboration platform. The appliance delivers 1.46X better performance on popular LS applications like Bowtie when compared to NFS based solutions.
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
8:45 Chairperson’s Opening Remarks
Mathukumalli Vidyasagar, Ph.D., Cecil & Ida Green Chair in Systems Biology Science; Head, Bioengineering Department, University of Texas at Dallas
8:50 Network Biology and Personalized Medicine in Multiple Sclerosis
Mark Chance, Ph.D., Vice Dean for Research, Proteomics, Case Western Reserve University
Almost nothing is known about biological factors underlying the remarkable disease heterogeneity observed across multiple sclerosis (MS) patients, and there are no accurate biological predictors of disease severity that can be used for guiding clinical treatment options. Learn about the network biology methods we are using to analyze blood cell gene expression and understand good and poor responders to therapy.
9:20 GeneSeer: A Flexible, Easy-to-Use Tool to Aid Drug Discovery by Exploring Evolutionary Relationships between Genes across Genomes
Philip Cheung, Bioinformatics Group Leader, Scientific Computing, Dart Neuroscience
GeneSeer is a publicly available tool that leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as human. This talk describes GeneSeer’s underlying methods and the user-friendly interface.
9:50 Cloud Computing For Smart People
Dave Maples, Senior Vice President, Bright Computing
Smart people are turning to the cloud as a powerful option for pharmaceutical and life sciences computing. This presentation is about how to make the most of cloud computing without becoming IT experts or reallocating research time to manage cloud resources. Two scenarios will be offered: creating cloud-based servers on the fly, and extending on-premise servers into Amazon EC2.
10:05 Sponsored Presentation (Opportunity Available)
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
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 Luncheon in the Exhibit Hall with Poster Viewing
2:00 Closing Featured Panel Session Introduction
Wanmei Ou, Senior Product Strategist, Oracle Health Sciences
2:10 Panel Session: Building the IT Architecture of the New York Genome Center
Moderator: Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World
Chris Dwan, Acting Senior Vice President, Information Technology and Research Computing, New York Genome Center
Jim Harding, CTO, Sabey Corporation
Sanjay Joshi, CTO, Life Sciences, EMC Isilon Storage Division
Robert B. Darnell, M.D., Ph.D., President & Scientific Director, New York Genome Center
George Gosselin, CTO, Computer Design & Integration LLC
In 2011, a consortium of 11 major academic and medical organizations in and around New York announced the creation of the New York Genome Center (NYGC). Under the direction of Robert B. Darnell, the NYGC aspires to be a world-class genomics and medical research center, and is currently undergoing construction in the heart of Manhattan. NYGC management has the opportunity to design and create a state-of-the-art IT and data management infrastructure to handle, store and share the output from what will rapidly become one of the world’s foremost genome sequencing facilities. This series of talks will describe the thinking that went into the design, creation and construction of the NYGC’s IT infrastructure and entire data management strategy.
4:00 Conference Adjourns
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