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IT Infrastructure - Software 

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 Applications for Acquiring,
Managing, Sharing, and Presenting Data
 

10:50 Chairperson's Remarks
Irene Polikoff, CEO, TopQuadrant 

11:00 Radical Quality and ROI Gains Using Model Driven and DSL (Domain Specific Language) Software Development

Anthony Leotta, Bioinformatics Manager, Cold Spring Harbor Laboratory

This presentation describes a software engineering process that features model driven design. We created a framework to support the process along with implementing a Laboratory Information Management System for the CSHL Core Next Gen Sequencing facility using it. Learn how we build software with less implementation and maintenance time, allowing us to focus more on end-user needs. 

 

11:30 Data-Rich SharePoint for Drug Discovery

James Ewen, Business Analyst, Research Informatics & Automation, Bristol-Myers Squibb Company

Jared Shockcor, Domain Architect, Research Informatics & Automation, Bristol-Myers Squibb Company

We describe a novel technology for managing Discovery operations, tracking team decisions, and communicating and sharing data. By leveraging RESTful Services, existing databases, and un-altered SharePoint, we created a Data-Rich SharePoint experience for our scientists. Learn the nature of the challenges our scientists faced and how we addressed them and the creation and implementation of the technical foundations of the technology project.

Tessella12:00 pm Maximizing the Return on your Data Assets

Mark Evans, Digital Archiving Practice Manager, Tessella 
Even as the Era of “Big Data” engulfs life sciences and researchers rush to wring immediate value from the data deluge, the long-term archiving of this valuable asset is unfortunately, widely neglected. Few industries face a more daunting data management challenge. The size of datasets is numbing, the diversity of data types is bewildering, and technologies used to produce and analyze the data are advancing at an ever increasing rate. Coping with obsolescence is becoming a real challenge.

Platform Computing 12:15 A Shared Services Platform for Bio-informatics and Hadoop Applications
Jeremy Chambers, Solution Architect, Platform Computing, an IBM Company
This session looks at the benefits of adopting a multi-tenant big data cluster platform for bio-informatics applications. In this session, we introduce a shared services platform capable of running multiple bio-informatics applications  including MapReduce applications on the same shared grid,  while delivering guaranteed SLAs to different lines of business. With such a shared services platform, IT organizations can achieve higher resource utilization and cost savings as well as improved application performance.

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:40 Chairperson's Remarks
Paul Lappas, Director, Products, Piston Cloud Computing, Inc. 

1:45 Insilico DB: An Efficient Web-Based Collaborative Platform for Managing and Sharing Genomic Datasets that Are Tightly Integrated with Analysis Platforms Genepattern and R/Bioconductor

David Y. Weiss Solís, Ph.D., Project Lead, InSilico Project, U.L.B. - Université Libre de Bruxelles

Alain Coletta, Ph.D., Development Leader, InSilico Project, U.L.B. - Université Libre de Bruxelles

InSilico DB (http://insilico.ulb.ac.be) allows to manage and share large collections of genomic data. Advanced search, meta-data editing, and data normalization capabilities allow for efficient use of stored data. Proprietary, as well as 99,349 expert-verified, re-normalized assays pre-installed can be immediately analysed in GenePattern (GUI) and R/Bioconductor (Command-line). Ongoing integration with GenomeSpace will further enhance the analysis options available through InSilico DB.

2:15 Having a Mobile App Presence: Necessary or Nice to Have?Steven Muskal, Ph.D., CEO, Eidogen-Sertanty, Inc. 

Cambridge Semantics small2:45 Semantic Web for Flexible Competitive Intelligence

Rob Gonzalez, Senior Product Manager, Cambridge Semantics & Editor-in-Chief, Semantic University

Semantic Web technologies are the only technologies that are powerful, flexible, and mature enough to handle the diverse and ever-changing information needs of the pharmaceutical industry. Come learn how 5 of the top 10 pharma companies are using Cambridge Semantics' Anzo platform to deliver key competitive intelligence insights to stakeholders in R&D, business development, sourcing, and marketing.

Revelytix small logo
Spry small logo
3:00 Using Ontologies to Enhance Analytic Capabilities

Todd Jones, Senior Information Architect, Spry, Inc.
Paul Bradley, Senior Vice President, Account Management, Revelytix

Ontologies allow many different artifacts to be described using a common, executable language. Through these precise descriptions, information can be federated from different sources at run time, providing a single, holistic, traceable view. Using ontologies and semantic technologies as the underlying information management environment can greatly enhance the quality and accuracy of analytic capabilities.

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

 

Technologies and Applications for Acquiring,
Managing, Sharing, and Presenting Data
 

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 next-generation sequencers and other BioIT applications tends to compound storage consolidation and scalability challenges. In this presentation, Panasas will discuss how building a private cloud backed by scalable, high-performance parallel storage is the best solution for the unique challenges presented by bio and life sciences applications.

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

6:15 Exhibit Hall Closes

 

 

THURSDAY, APRIL 26

HP Small Logo8:00 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 RemarksDavid A. Medina, Director, Product Management, Healthcare Analytics & Life Sciences, Business Solutions, Hewlett-Packard 

8:45 Neuroimaging Informatics: From Cancer to Connectomes

Daniel Marcus, Ph.D., Director, Neuroinformatics Research Group, Washington University School of Medicine; President, Radiologics, Inc.

Diseases and disorders of the brain remain among the most intractable in medicine.  For reasons both known (traumatic brain injury, Alzheimer’s disease) and unknown (autism), their prevalence continues to increase.  Neuroimaging, with its ability to portray the architecture and function of the brain in both health and disease, promises to play a major role in developing a better understanding of and better treatments for these conditions.  Dr. Marcus will discuss informatics technologies being developed in his lab and elsewhere that are enabling neuroimaging reach this potential.  Examples will be drawn from the Human Connectome Project, the Comprehensive Neuro-Oncology Data Repository, and the Central Neuroimaging Data Archive.

9:15 Pathway to Global Product Safety and Quality, Mobility and Big DataMichael Coene, Chief Technology Officer, FDA 


Aspera9:45 High-Speed Data Movement for Effective Global Collaboration in Genomic ResearchMichelle Munson, President & Co-founder, Aspera, Inc.To collaborate effectively, scientific organizations need to implement large-scale computing and networking infrastructure, select storage systems and integrate high-speed transport technologies to power the collection and distribution of terabytes of sequencing data to researchers globally. Learn about best practices, requirements and challenges of IT infrastructure designs and how Aspera powers data movement in support of global research. 

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

 

Open Source Platforms and Collaborative Technologies 

1:55 Chairperson's Remarks

2:00 User Gateway: A System to Accelerate Molecular Epidemiology

Christopher Farah, Ph.D., Bioinformatics and GIS Specialist, Maine Institute for Human Genetics and Health, Eastern Maine Healthcare Systems

Co-authored with Janet Hock, B.D.S., Ph.D., Senior Investigator, Maine Institute for Human Genetics and Health, Eastern Maine Healthcare Systems

User Gateway is web-based, open source software developed to bridge cancer diagnosis, annotations from banked specimens, and clinical data to outcomes and environmental history. By incorporating GIS technology, existing biobanking functionality is extended through two key functions: advanced specimen requisition and spatiotemporal analysis of patient data. Learn about the core functionality of the software, followed by a software demonstration. Novel use cases will be highlighted.

2:30 A Scientific Spreadsheet for Big Data Analysis, Reporting, and Real-time Collaboration

Mario Morales, Statistician, Simulmedia, Inc.; Programmer, Stanford University School of Medicine

We will present new tools and services that have been designed in collaboration with BD to improve the productivity of biostatisticians, to allow them to work with large volumes of data on a private cloud and on EC2 and to collaborate easily. We have combined the highly popular interaction model of Spreadsheets with capabilities de manipulate very large data sets and to use any scientific computing environment’s libraries in formula cells. We have made the spreadsheets fully programmable in R and in Python, we have added layers to which Bio-statisticians can drag and drop widgets for data manipulation and visualisation of any complexity and we have enabled real-time collaboration in all the usage scenarios. We have made the produced spreadsheets, reports and dashborads easy to save with all the software stacks and data they depend on and also easy to publish with simple URLs.

 

3:00 Development and Implementation of Distributed Health Data Networks: Lessons from Medical Product Safety, Public Heath Surveillance, and Comparative Effectiveness Research

Jeffrey Brown, Ph.D., Assistant Professor, Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School

This presentation describes the development, implementation and selected uses of an open-source software platform (PopMedNetTM) for the creation of distributed health data networks. A distributed health data network advances the secondary use of electronic health information by creating standardized and re-usable data sources in multiple sites, as well as tools to use it. Understand the barriers in creating a distributed health network and approaches for overcoming them.

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

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

This presentation describes a TREAT ALS™ software platform that is currently deployed to support a clinical research network in Lou Gehrig's disease and allows investigators from 100+ academic institutions around the world to collaborate, share data, and biological specimen. This is a unique solution and approach in managing disease-specific research networks and may serve as a model for academic and industry collaboration in finding cures for rare diseases.

4:00 Conference Adjourns

 

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