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IT Infrastructure - Hardware 

Final Agenda

TUESDAY, APRIL 24


7:00 am Workshop Registration and Morning Coffee

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

  • Planning and Structuring Collaborative Innovation and Open Source Deals: Techniques and Lessons from the Leaders
  • Data Visualization in Biology: From the Basics to Big Data

*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

Sanjay Joshi, Solutions Architect, Life Sciences, EMC Isilon Storage Division


4:15 PLENARY KEYNOTES 

Martin LeachMartin Leach, Ph.D., CIO, Broad Institute of MIT and Harvard

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


Hitachi Data Systems5:00 - 7:00 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 iPod touches® or 1 of 2 Xbox 360s®*!

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



WEDNESDAY, APRIL 25

7:00 am Registration and Morning Coffee

7:55 Chairperson’s Opening Remarks

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

8:00 Keynote Introduction

Bas Burger, President, Global Commerce, BT Global Services


8:15 PLENARY KEYNOTE 

Eric PerakslisEric D. Perakslis, Ph.D., CIO and Chief Scientist of Informatics, U.S. Food and Drug Administration


8:45 Benjamin Franklin Award & Laureate Presentation

9:10 Best Practices Award Program

Cycle Computing small9:45 Coffee Break in the Exhibit Hall with Poster Viewing

 

Technologies and Infrastructure for Acquiring, Storing, and Sharing Data 

10:50 Chairperson’s RemarksKevin Brode, Head, Health Sales, Hitachi Data Systems 

11:00 A Nation-Wide Area Networked File System for Very Large Scientific Data

William K. Barnett, Ph.D., Director, Science Community Tools, Research Technologies, Indiana University

The explosion of next generation sequencing data is a key example of the stress the rapidly expanding scientific data are placing on the ability to undertake science. The National Center for Genome Analysis Support (NCGAS) at Indiana University is part of an institutional intiative to develop advanced cyberinfrastructures to address these challenges. This presentation will describe a nationally accessible high performance filesystem based on Lustre to enable remote execution of sequence assembly and other genomics analyses. This sytem, The Data Capacitor WAN, has been in production for several years supporting a centralized data model with remote computational and visualization capabilities. With upgrades to national and international research networks planned for 2012, this architecture can help address the needs to deliver large scientific data sets to computational assets without the delays of shipping hard drives or slow file transfers.  

11:30 IT at Yale's Center for Genome Analysis: Two Years in the Trenches at a High-throughput Sequencing Center

Robert Bjornson, Ph.D., Research Scientist, Yale University

Yale's Center for Genome Analysis provides DNA sequencing and bioinformatics support to the Yale community.  The Center's hardware infrastructure includes the largest disk storage facility at the University as well as a substantial compute cluster.  This presentation will discuss some of the challenges encountered and experiences gained while managing data and computing for a large-scale high-throughput DNA sequencing facility serving academic and research users.

Hitachi Data Systems12:00 pm Be Prepared for the Unexpected - Architect Your Storage Infrastructure to Enable New Science

Jeff Kenkel, Specialist, Solution Consultant, Health & Life Sciences, Hitachi Data Systems

Genomic sequencing and imaging instruments continue to generate vast amounts of data to be analyzed by multiple applications and used in collaborative research. Data needs to be stored, managed and shared. Storage infrastructures need to be designed from the start to handle rapidly changing workflows. BlueArc is a leader in file storage solutions at scale for mixed and unpredictable workflows.

HP Small Logo 

12:30 Luncheon Presentation
Let’s be Sensible: Maximizing Productivity and Research through Scientific Computing

John M. Cho, Senior Technologist and Futurist, FDA, HP Enterprise Services
Sustainable growth of any health & life sciences organization depends on continual refinement and innovation of existing processes and technology. That ability to innovate is directly tied to enabling collaboration between key stakeholders while providing them the ability to aggregate and analyze vast amounts of structured and unstructured scientific data.  Furthermore, misalignment of critical IT infrastructure often leads to resource contention, silos of compute-intensive applications and fragmented data sources that sometimes results in duplication of effort, cost overruns and inefficient execution. In this presentation, HP will provide some high-level guidance in applying IT services, resources and technology to address complex problems, whether it be driving scientific research, reducing IT infrastructure costs within scientific computing, or enabling secure and efficient discovery of new therapies from bench to bedside.

1:40 Chairperson’s Remarks

Zheng Yang, Ph.D., Associate Director, IS Business Partnering Research, Boehringer Ingelheim Pharmaceuticals, Inc.


SGI small logo1:45 Conquering Computational Complexities in Cancer Research
Large Shared Memory and Big Dynamic Range Computing - Essential Drivers in Global Modeling of Cancer Cells

Rune Linding, Ph.D., Professor, Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU)

The size and complexity of cell-imaging, mass-spectrometry and deep-sequencing systems biology data is exploding. We perform global, non-linear algorithmic integration of these to model cancer progression. While in scale corresponding to models of climate/weather systems the underlying data is vastly more complex creating formidable computational challenges. I will discuss how computational dynamic range and large-shared memory are two critical technologies in systems biology, translational cancer research and personalized medicine.

Cambridge Computer Logo Small2:15 Bio-IT: Reigning in Research Data: Adding Intelligence to Conventional File Systems

Jacob Farmer, CTO, Cambridge Computer

There is a growing need to put structure on unstructured research data, being driven by a number of different factors:
- Granting agencies are requiring investigators to specify and conform to data management plans that preserve and make data available to other researchers.
- Research institution are seeking to charge storage consumption back to individual grants and projects.
- Data storage administrators need better content classification in order to manage data protection and life cycle management.
- As capacity grows and time progresses, it becomes futile to rely on any given individual's memory as the only means for content classification.

Unfortunately, research scientists are fundamentally resistant to traditional efforts to put structure on their instructured data. Commercial content management systems are seen as cumbersome to operate, not to mention that they might add latency to high-performance processing jobs. As such, many scientists have no tools other than directory names to identify their data. Others rely on spreadsheets and home-grown software applications to track their files, but often these links break as files are moved and renamed. Cambridge Computer has embarked on a project to define the best practices for content classification of research data. We are collaborating with a number of leading institutions and have completed development of a working prototype. The purpose of this talk is to share the highlights of our work, stimulate discussion, and make contact with potential collaborators.

2:45 Content Classification of Research Data at Harvard Medical School

Christopher Botka, Director of Research Computing, Research Information Technology Group, Harvard Medical School

Harvard Medical School has been exploring novel ways of overlaying metadata onto conventional file systems to solve a variety of problems. First, we wanted to get a better idea on how our various users are consuming storage. We want to visualize capacity consumption trends, better understand our data retention requirements, and identify data that can be deleted or moved to a lower cost tier. Next, we want to match up data sets on disk with specific grants and projects to enable charbe-back. Finally, we hope to classify data data collections with discipline-specific ontologies to enable data mining. In this talk, we will outline our experiences and observations thus far and describe the next phase of the project for the coming months.

IBM small logo3:00 Building a Scalable IT Architecture for Next Generation Sequencing and Genomic Analysis -
A Comprehensive Approach

Janis E. Landry-Lane, Program Director, World Wide Deep Computing, Life Sciences/Higher Education Segments, IBM

Institutions are taking on the task of designing IT systems for NGS. Solutions that are scalable, both in terms of processing and storage, will better serve the institution long-term. There is a life-cycle management of data, and making it usable for downstream analyses and applications is an important aspect in system design. We will also discuss techniques for application acceleration without additional hardware.

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


Technologies and Infrastructure for Acquiring, Storing, and Sharing Data (cont’d)
 

3:45 Emergency Medical Services and the Bio-IT World

Joe Acciavatti, Director, Operations and Communications, MONOC

Tim Harren, IT Director, Pro EMS

This presentation will describe the data and technology challenges that New Jersey’s largest provider of EMS services face. The world of EMS and IT work hand in hand on a daily basis with the acquisition of electronic patient care reports, cardiac electrocardiograms, physician-to-field consultations, medication monitoring, and big data management. Learn about the software and technical aspects utilized to address these challenges.

4:15 The Department of Veterans Affairs Million Veteran Program and the Information Infrastructure Making it Possible

Leonard D’Avolio, Ph.D., Associate Center Director, Biomedical Informatics, Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC)

Saiju Pyarajan, IT Manager, Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC)

The Department of Veterans Affairs launched an initiative to recruit and enroll 1 million Veteran volunteers to contribute blood, survey data, and access to their EMRs to discover relationships between biology and health. Learn about the information infrastructure that was designed to manage the logistics of recruiting and enrolling Veterans as well as to facilitate analysis of combined phenotype and genotype data.

Panasas small logo4:45 Parallel Storage: Addressing the Bio and Life Sciences Big Data Challenge

Geoffrey Noer, Senior Director, Product Marketing, Panasas

The exponentially growing volumes of data generated by Bio IT applications (especially next-gen sequencing) compound the challenge of selecting a storage infrastructure capable of linearly scaling capacity and performance. Panasas will discuss how to address this big data storage challenge with high-performance parallel storage and how the emerging open standard parallel NFS (pNFS) protocol will further enable performance at scale.

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

6:15 Exhibit Hall Closes



THURSDAY, APRIL 26

Intel7:00 am Breakfast Presentation
The Growth of Personalized Medicine: Big Data in the Era of the Impossibly Small

Kristina M. Kermanshahche, Chief Architect of Healthcare, Intel Corporation
Alan Louie, Ph.D., Research Analyst, IDC Health Insights

As we arrive at the $1000 genome, we find the fundamental problems have shifted… it is no longer about shrinking the cost of sequencing but the explosive growth of big data:  the downstream analytics with rapidly evolving parameters, data sources and formats; the storage, movement and management of massive datasets and workloads; and perhaps most paradoxical of all, the challenge of articulating the results and translating the latest findings directly into improving patient outcomes.  Indeed, as we approach the scale of “impossibly small” for both technology and disease management, the complexity of problems grows by orders of magnitude.  IDC will present “Trends and Challenges in Genomics Research and Personalized Medicine”, followed by Intel presentation on how they collaborate with researchers and the technology ecosystem to develop innovative solutions to seemingly intractable problems emerging in  life sciences today. We look forward to learning about the specific challenges you face and optimizing our technologies to help you to accelerate discoveries.

8:00 am Featured Speaker Introduction

David A. Medina, Director, Product Management, Healthcare Analytics & Life Sciences, Business Solutions, Hewlett-Packard

8:10 Featured Speaker
HPC Trends from the Trenches

Chris Dagdigian, Founding Partner and Director of Technology, BioTeam, Inc.

HPC Trends from the Trenches is one of the most popular presentations of the Expo! This talk will present how common HPC problems in life science informatics have been approached by organizations of varying type and size. We will discuss observed trends in computing, workflows and data movement, along with details on particularly clever solutions observed in production environments around the world.

8:40 Chairperson’s Opening Remarks

Mollie Shields Uehling, CEO, SAFE-BioPharma Association


Security Informatics & Cloud Computing 

8:45 The Role of a Standard-Based Interoperable Digital Identity in Unlocking the Cloud

Mollie Shields Uehling, CEO, SAFE-BioPharma Association

9:15 Security and Compliance for Pharma Cloud Computing

Zheng Yang, Ph.D., Associate Director, IS Business Partnering Research, Boehringer Ingelheim Pharmaceuticals, Inc.

Co-Author: Erhard Wais, Architect, IS Business Partnering Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG.

EMC9:45 Implementing Sequencing Services in the Cloud

Sanjay Joshi, Solutions Architect, Life Sciences, EMC Isilon Storage Division

As genome sequencing services on the cloud mature, the implementation technologies need to move from ‘research-ready’ to ‘clinic-ready’. This means working within a standards, performance and monitoring sandbox and their interaction with high performance computing (HPC) and data life-cycle management. We will present a Cloud Standards and Trust Framework for public and private clouds and its various hybrid models.

10:15 Coffee Break in the Exhibit Hall and Poster Competition

10:45 Plenary Keynote Panel Chairperson’s Remarks

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

10:50 Plenary Keynote Panel Introduction

Geoffrey Noer, Senior Director, Product Marketing, Panasas


11:00 Plenary Keynote Panel:
A special plenary session featuring trends and challenges in cancer research:
 

  • Julian Adams, Ph.D., President, Research and Development, Infinity Pharmaceuticals, Inc.
  • Jose Baselga, M.D., Ph.D., Chief and Bruce A. Chabner Chair, Division of Hematology/Oncology, Massachusetts General Hospital; Associate Director, Massachusetts General Hospital Cancer Center; Professor of Medicine, Harvard Medical School
  • Sir John Burn, MD, FMedSci, Professor of Clinical Genetics, Institute of Genetic Medicine, Newcastle University, UK; Genetics Lead, National Institute of Health Research, UK; Medical Director, QuantuMDx Ltd
  • John Quackenbush, Ph.D., Professor, Biostatistics and Computational Biology, Cancer Biology Center for Cancer Computational Biology, Dana-Farber Cancer Institute
 

12:15 Luncheon in the Exhibit Hall with Poster Viewing


HPC on the Cloud – Implementation Issues and Hardware 

1:55 Chairperson’s Remarks

Arista2:00 Scaling Biosciences Research with Petabytes of Data and Ultra Fast Computing

Chris Bellmare, Director, Arista Networks

The increased use of common database sources with petabytes of stored data is driving new computing cluster architectures. Research needs have grown, R&D budgets have shrunk. Can your network keep up with increased CPU density bursts to 10Gbps, or can Latency sensitive data movement? Do you have fast access to petabytes of processed data, Parallelization of the data, storage, and analysis algorithms? Arista is the leader in Life Sciences Data Center design, and attendees will learn about intelligent placement of compute to storage, as well as how to scale to meet the research needs while keeping the performance up and costs down.

Data Direct Networks2:30 NGS Data Storage and Management - From Data Ingestion to Archive Simplified

Jose L. Alvarez, WW Director, Life Sciences, DataDirect Networks, Inc.

DDN is partnering with NGS industry leaders to deliver an array of flexible; highly scalable and easy to manage unified data storage solutions that are helping research groups around the world accelerate their time to discovery. Instruments data ingestion, sequencing pipeline performance, intelligent archive and sharing of research data in a geo-distributed modelwill be discussed.

3:00 Biopharma Case Study 

Speaker to be Announced 


3:30 Closing Featured Speaker: Platform for Clinical Research Networks: Novel Approach towards Discovers in Rare Diseases

Alex Sherman, Director, Systems, Department of Neurology, Massachusetts General Hospital


4:00 Conference Adjourns

 

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