Starting first in the Boston area and expanding elsewhere if demand allows we are offering the following Grid Engine training workshops:

1-Day Grid Engine User/Usage Workshop Dates

• April 15, 2008
• June 17, 2008

2-Day Grid Engine Administration Workshop Dates

• April 16-17, 2008
• June 18-19, 2008

Registration & Enrollment Deadlines

To register, contact info@bioteam.net

• Registration ends for the April workshops on April 7th, 2008
• Registration ends for the June workshops on June 9th, 2008

Workshop Location:

Residence Inn by Marriott (link)
6 Cambridge Center
Cambridge, MA, 02142 USA

SGE User Workshop Description

BioTeam is the first organization to offer open-enrollment training focused on making people more comfortable and more productive. Our goal is to help users, application integrators and developers understand Grid Engine features and capabilities in a way that allows them to become more productive at home. New SGE cluster operators or systems administrators may also benefit from the user and usage-centric perspective.

SGE Admin Workshop Description

Intended to provide comprehensive coverage of Grid Engine administration in a small-group, highly interactive setting. This workshop covers more in-depth technical material than other “Advanced” SGE training offerings. However, we do not use the word “Advanced” to describe this workshop, as Grid Engine sourcecode details, internal data structures, JGDI, ARCo queries and the DRMAA API are not typically addressed.

Workshop Brochure (click to download)

SGE User Workshop Details

Duration

1 Day

Cost

$375 USD (special pricing through June 2008). List price: $475 USD.

Intended Audience

Anyone interested in a user-centric view of distributed computing with Grid Engine. Note: this is not an advanced operator/admin course.

Our goal is to help users, application integrators and developers understand Grid Engine features and capabilities in a way that allows them to become more productive at home. New SGE cluster operators or administrators also may benefit from the user and usage-centric perspective.

Scope

Our materials use the open source Sun Grid Engine 6 product from http://gridengine.sunsource.net. Lab systems may run version 6.0 although 6.1 specific features can be addressed. Upon request, SGE 5.x behavior and features can also be covered.

Difficulty

No Grid Engine experience necessary but attendees should be comfortable with Linux and a bit of shell/perl scripting in order to work with demo code and examples presented in the longer seminar format. The seminar is targeted towards new or moderately experienced Grid Engine users. Individuals with advanced Grid Engine skills will not gain much from this 1-day seminar - we are considering offering future sessions targeted specifically at advanced end-user audiences.

Prerequisites

Attendees must bring wireless-capable laptops. A SSH client is required in order to connect to the classroom and lab systems.

Workshop Content Outline

I. Clustering Overview
II. Grid Problem Types
III. Distributed Resource Management
- Overview
- What it provides
IV. How Grid Engine Works
- Job Types
- Resource Allocation
- Policies
- Tickets
- Architecture
- Scheduling
V. Basic Usage
- Running Jobs
- Checking Status
- Troubleshooting
VI. Advanced Usage
- Resource requests
- Job Arrays
- Job Dependencies
- Simple Workflows
- Parallel Environments
- Loose vs Tight parallel environment integration
- Understanding resources & the SGE complex
VII. Policy Based Resource Allocation
- Overview
- How it works
- Effect on end-users
- Commonly seen implementations
VIII. Grid Engine Application Integration
- Standalone applications & web front-ends
- Parallel applications
- Licensed applications

SGE Administration Workshop Details

Duration

2 Days

Cost

$1,100 USD (special pricing through June 2008). List price: $1,400 USD.

Intended Audience

New or existing Grid Engine administrators or cluster operators.

Intended to provide comprehensive coverage of Grid Engine administration in a small-group, highly interactive setting.

Advanced Course?

This workshop covers more in-depth technical material than other “Advanced” SGE training offerings. However, we do not use the word “Advanced” to describe this workshop, as Grid Engine sourcecode issues, internal data structures, JGDI, ARCo queries and the DRMAA API are not typically addressed.

Scope

Our materials use the open source Sun Grid Engine 6 product from http://gridengine.sunsource.net. Lab systems may run version 6.0 although 6.1 specific features can be addressed. Differences between Grid Engine versions 5.x through 6.2 will be addressed.

Difficulty

Prior Grid Engine experience is highly desirable but not strictly required. We’ve run this workshop successfully with audiences of Linux and cluster system administrators having no previous SGE exposure.

Attendees should be comfortable and capable with Linux, command line operating envirinments and shell/perl scripting in order to work with demo code and classroom exercises.

Prerequisites

Attendees must bring wireless-capable laptops. A SSH client is required in order to connect to the classroom and lab systems.

Workshop Content Outline

I. Overview
- Grid Problem Types / High-throughput vs. High-performance
- Distributed Resource Management
-- DRM Benefits for Users & Workgroups
-- DRM Benefits for operators & organizations
- How Grid Engine Works
- Grid Engine Architecture
- Grid Engine Job Lifecycle
II. Installation & Deployment
- Pre-installation decisions
- Spooling & High Availability issues / decision points
- Template driven autoinstallation
- CSP mode installation
III. CLI Configuration
- Command line operation
- Host and hostgroup configuration
- Cluster configuration
- Queue configuration
- Parallel Environments
- Resources & the SGE Complex
- Load Sensors
- Access Control
- Aliases & Default requests
IV. SGE 5.x vs. 6.x vs. 6.1x
- Feature & behavior differences between major SGE release milestones
V. SGE Usage for Admins
- Brief review of SGE usage with focus on User-centric needs
VI. Monitoring & Reporting
- System Monitoring
- SGE Accounting
- SGE Reporting
- Accounting & Reporting tools
- 3rd party tools & utilities
VII. Policies & Resource Allocation
- Ticket-based Policies
-- Share Tree
-- Functional
- Urgency & Override Policies
- Resource Reservations & Backfilling
- Resource Quotas
IX. Application & Workflow Integration
X. Troubleshooting
- Cluster, job and general-purpose troubleshooting & diagnostics


From the AGBT website:

“The Advances in Genome Biology and Technology (AGBT) meeting will be held again in Marco Island, Florida, from February 6-9, 2008. The AGBT meeting has become the premiere scientific forum for capturing the latest advances in new DNA sequencing technologies and an outstanding venue for presentations on the applications of genomics to diverse areas in biology and biomedicine. The meeting will have daytime plenary sessions that feature keynote speakers, additional invited speakers, and abstract-selected talks. These sessions will highlight cutting-edge research in areas such as next-generation DNA sequencing technologies, metagenomics, medical sequencing, complex genetic diseases, application of genomic approaches to cancer research, and population genomics. Technical approaches being developed and utilized in contemporary genomics research will be presented during evening concurrent sessions. Our annual pre-meeting ‘training’ workshop will feature overviews on emerging DNA sequencing technologies and talks on the practical implementation of various next-generation instruments from experienced early users. Please plan to join us in Marco Island, where the relaxed atmosphere and outstanding science at the 2008 AGBT meeting will provide an exceptional opportunity to meet and interact with scientific leaders from the many disciplines being advanced by genomics.

The organizing committee for the 2008 AGBT meeting includes Eric Green (NHGRI/NIH), Elaine Mardis (Washington University School of Medicine), Deanna Church (NIH/NCBI), Colin Collins (UCSF), George Grills (Cornell University), Tim Harkins (Roche Applied Science), Steven Jones (BC Cancer Agency), Andre Marziali (University of British Columbia), Michael Metzker (Baylor College of Medicine), Chad Nusbaum (Broad Institute of MIT and Harvard), Michael Rhodes (Applied Biosystems), Lisa Stubbs (Lawrence Livermore National Laboratories), and Mike Zody (Broad Institute of MIT and Harvard).”

Drop us a line if you’d like to arrange a meeting or conversation while at Marco Island.

We will also be at this social event:

Genome Technology Party at Cathy O’Clarke’s Bar
9:30 p.m. – 12:00 a.m.
(Sponsored by Illumina)
On Collier Bvld

On April 22nd, as part of a “pre-conference technical workshop”, BioTeam’s own Michael Cariaso will be demonstrating WikiLIMS to interested attendees. From the workshop details:

“…In this 3-hour course, Michael Cariaso will guide you through the functionality of a WikiLIMS and the real-world experiences of researchers using the system. Attendees will explore a unified interface for tracking samples and their analyses across next-generation (Roche FLX, Solexa) and traditional platforms.“

The official conference site is online at http://www.healthtech.com/2008/seq/index.asp.

This talk will review some of the BioTeam’s recent work with biotech, pharmaceutical, government and enterprise clients. As an independent consulting firm, the BioTeam is able to see how HPC problems in life science infor-matics have been approached by organizations of varying type and size. We will address common problems and observed trends in computing, workflows and data movement, along with details on particularly clever solutions observed in production environments around the world.

BioTeam has been on the frontlines of next-generation sequencing integration, having helped several organizations with the unique next-gen IT, storage, and data management challenges. This workshop will present real-world customer experiences straight from the trenches.

You’ll get practical information about the analysis, assessment, design, implementation, testing, and support needed to bring a research organization from technology adoption to publication in the next-gen world.

This informative session will feature special guest speakers from Cold Spring Harbor Laboratory, Broad Institute, Cornell University Biotechnology Resource Center, Harvard-Lipper Center for Computational Genetics, Naval Medical Research Center, and Intel, as well company representatives from Applied Biosystems, Helicos, Illumina, and Roche.

Event Information:

April 28, 2008

8am - 4pm

Boston, Massachusetts USA

http://www.bio-itworldexpo.com/workshops.asp

[Download Agenda in PDF format here]

PRELIMINARY AGENDA

7:00-8:00am Pre-Conference Workshop Registration and Morning Coffee

8:00 Workshop Chairperson’s Remarks

William Van Etten, Ph.D., Founding Partner and Director of Consulting Services, BioTeam, Inc.

8:15 Advancing Personal Genetics with Second Generation Sequencing

Second generation DNA sequencing has arrived and along with it, affordable personal genomics in which anyone will be able to access their own genetic information.

George Church, Ph.D., Professor of Genetics at Harvard Medical School and Director of the Center for Computational Genetics

8:45 Managing the Data Flood in Next-Generation Sequencing

The staggering amount of data a next-generation sequencers produce is a boon and a challenge. Fortunately, there are new tools that can help.

W. Richard McCombie, Ph.D., Professor, Cold Spring Harbor Laboratory

9:15 Bringing Next-Gen Sequencing Technologies into Large-Scale Production

Matthew Trunnell will discuss the computational and data management architecture of the Broad Institute’s environment and will share some of the operational lessons learned in the past 18 months as they have scaled up their next-gen sequencing infrastructure.

Matthew Trunnell, Group Leader, APSG, Broad Institute of MIT and Harvard

9:45 Refreshment Break

10:00 Implementing Next-Gen Sequencing in the Small Research Lab

Being a small facility doesn’t mean you don’t have big data management problems. It just means your resources are limited. However, a new interface gave the Naval Medical Research Lab the support it needed.

Timothy Read, Ph.D., Principle Investigator, Naval Medical Research Center

10:30 Meeting the Challenges of Data Management and Analysis for New Sequencing Technologies in an Academic Core Facility

Using next generation sequencing platforms as shared resources with robust IT and informatics support enables cost effective and broad based use of these emerging technologies.

George Grills, Director of Operations of Core Facilities, Cornell University Life Sciences Core Laboratories Center

11:00 Lunch on Your Own

1:30 Next-Generation Computing Strategies for Next-Generation Sequencing

The data challenges posed by the new generation of high throughput sequencers require advanced compute and storage solutions. Intel is working on new strategies to make analysis easier, faster, and more cost effective.

Wilfred Pinfold, Ph.D., General Manager, Integrated Analytic Solutions, Intel Corporation

2:00 Commercial Next-Generation Sequencing Technology Update

Are you in the market for a commercial solution? This technology showcase will highlight the most advanced systems to help you make an informed decision.

• Kevin McKernan, Senior Director, Scientific Operations, Applied Biosystems
• Avak Kahvejian, Product Manager Heliicos BioScience Corporation
• Abizar Lakdawalla, Ph.D., Senior Product Manager, Illumina, Inc.
• Timothy Harkins, Marketing Manager, Roche Diagnostic Corporation

3:00 Panel Discussion: Industry Overview
3:45 Workshop Chairperson’s Closing Remarks

William Van Etten, Ph.D., Founding Partner and Director of Consulting Services, BioTeam, Inc.