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Next-Generation Sequencing Data Analysis - Day 3

Conference Proceeding CD Now Available
  • Speaker Presentations
  • Poster Abstracts
  • and More!



8:00 Java and Jive Discussion Groups
Time has been designated for facilitated discussion groups with specific themes. This unique opportunity allows conference participants to focus on a topic and exchange ideas, information, experiences, and develop future collaborations.

Data Management: Storage Strategies “To Store or Not to Store, that is the Question”

9:00 Chairperson’s Remarks
Stan Gloss, Managing Director, BioTeam Inc.

9:05 Data Storage Strategies in a Multi-Laboratory Environment
Robert Stephens, Ph.D., NIH/NCI
With the advent of next-generation sequencing, and its integration with mass-spectroscopy driven proteomics, microarray analysis, pathology and imaging, successful data management is often the limiting factor for scientific success. Issues that impact data analysis, integration, accessibility, and collaboration must be addressed from an IT and Bioinformatics point of view since most individual laboratories are only concerned with their locally generated data and analysis. We will share our experiences in creating an infrastructure conducive to achieving the goal of an integrated view of cancer biology from multiplexed data sources.

9:35 An Industry Perspective on Storage and Data Management
Reece Hart, Ph.D., Scientific Manager, Research Computing & Informatics, Genentech, Inc.
The rate and cost of data acquisition for new and upcoming technologies will change the way we think about the value of data. Presented in this session, will be some of the considerations in choosing high-performance storage for general computing and discuss our desires for future storage platforms in a biotechnology/pharmaceutical research environment.

10:05 Selected Poster Presentation

10:20 Morning Coffee, Poster and Exhibit Viewing

11:00 Managing Massive Data Storage Volumes
Jacob Farmer, CTO, Cambridge Computer
In the world of enterprise computing, data storage capacities tend to double on the order of once every 18 months.  In BioInformatics, the expansion of storage capacity can be much more dramatic, often exceeding the capabilities of traditional enterprise storage devices and best practices.  This session describes a number of technologies and approaches to managing massive data storage volumes.  Topics include:  leveraging low-cost storage devices; high-capacity / high-performance file systems, back-up and replication, as well as tape-based file systems. 

11:30 Data Standards for Next-Generation Sequencing
Asim Siddiqui, Ph.D., Senior Consultant, Strategic Incite Inc.
This presentation outlines the current state of data standards for next generation sequencing providing an overview of SRF (sequence read format) and support for the standard in the commercial and academic communities. I will describe the roadmap for new standards that are building on SRF to describe higher level features such as alignments and assemblies.

12:00 pm Close of Session
12:15 Luncheon Technology Workshop Sponsored By Isilon Systems 
Storage for Science -- Managing Large and Rapidly Growing Data Stores in Life Science Research Environments
Chris Dwan, Director of Products & Principle Investigator, BioTeam
Large and rapidly growing stores of file-based and other data are a hallmark of life science research and bioinformatics. Determining how best to manage those data stores has become a significant challenge for Researchers and IT Pros alike. This session is intended to: provide guidance on the many storage requirements common to Life Science research; explain the evolution of modern storage architectures; summarize the major data storage architectures currently in use and present Isilon IQ clustered storage as a strong and flexible solution to those needs.


Shared with Exploring Next-Generation Sequencing

2:00 Chairperson's Remarks
Kevin Davies, Ph.D., Editor-in-Chief, BioIT World 

2:05   AppliedBiosystems 

The SOLiD System - Setting New Standards in Genomic Analysis
Michael Rhodes, Ph.D., Product Applications Senior Manager, Genetic Analysis, High Throughput Discovery, Applied Biosystems
The SOLiD™ System generates in excess of 6Gb of mate paired sequence data from a single run and recent throughput in the range of 12-17Gb has been demonstrated in Applied Biosystems R&D labs as well as customer sites. This enables the rapid sequencing of entire human genomes. As a result of this data availability, Applied Biosystems has sequenced a single Yoruban and analyzed the data for SNPs, insertions and deletions and structural variations. This presentation will review some of the challenges of analyzing such data sets. The advantages di base encoding will be discussed, especially in context of SNP calling. In addition, the use of Mate pairs and the latest tools for utilizing SOLiD™ System data will be presented.

2:35 Helicos
True Single Molecule Sequencing™: The Continuing Path to the $1000 Genome
Patrice M. Milos, Ph.D., Vice President and Chief Scientific Officer, Helicos BioSciences Corporation
The Heliscope™ Single Molecule Sequencer, an advanced technology platform capable of directly measuring single DNA molecules without the cost and complexity of amplification, provides the opportunity for high throughput genomic studies to address important biological questions. This presentation will provide an update on the platform as well as describe scientific applications that are being developed for the platform including recent studies on genomic sequencing, SNP detection, expression studies, and paired reads.

3:20 Refreshment Break, Poster and Exhibit Viewing

Length Really Matters: 400 Base Pair Sequencing Reads Using the 454 Genome Sequencer FLX
Jason Affourtit, Director of Advanced Technologies, 454 Life Sciences
With over 250 publications, the Genome Sequencer FLX system has been demonstrated to support an increasing number of applications from whole genome shotgun sequencing to the detection of somatic mutations. Recent advancements in the technology allow for the generation of over 1 million sequencing reads that are between 400 to 500 base pairs in length, allowing for the displacement of traditional Sanger sequencing technologies. The addition of paired end sequencing with spacing of 20kb between the sequencing tags has enabled whole genome sequencing of complex genomes. Data will be presented showing the de novo assembly of Arabidopsis and drosophila. Additional examples of cDNA, metagenomics, and amplicon studies will be shown.

4:30 Illumina
Enabling Genome Biology with the Illumina Genome Analyzer
Gary P. Schroth, Ph.D., Senior Director, Applications R&D, Illumina Inc.
The Illumina Genome Analyzer is an ultrs-high throughput DNA sequencing platform that routinely generates billions of bases of very high quality sequence information from each short run. We will show examples of how the instrument is being used for a large variety of applications in genome biology including human genome sequencing, SNP discovery, gene expression analysis, protein-DNA interactions (ChIP-seq), genome-wide DNA methylation analysis, and small RNA discovery and profiling. We will discuss the development of software and analysis tools that can help users glean biological meaning from the massive amounts of data produced by the system.

5:00 Interactive Panel Discussion
Moderator, Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
It’s been three years since the debut of the first commercial next-generation sequencing platform. Since then, remarkable advances have been made in the quality, reliability, and throughput of all of the major commercial platforms. This session features presentations from some of the most established next-gen platform providers, showcasing advances in technology, affordability, and applications.

6:00 Close of Tech Expo/Short Course Registration

6:30-8:30 Recommended Short Courses III or IV*

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