Etzard Stolte and Ralph Schlapbach introduce the proof of concept provided by Hewlett-Packard Life Sciences for Phase 2 of the Pistoia Alliance Sequence Services project.

1. HP Sequence Services
Pistoia Alliance Annual Conference
24th April 2012
Etzard Stolte, PhD, Hewlett-Packard
Ralph Schlapbach, PhD, ETH Zurich
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2. HP Sequence Services
High scientific quality with maximal IT flexibility
Technical & scientific QC
Technical / Scientific Support Professional life cycle management of
bioinformatics tools and scientific
quality control of analysis results
HP Cloud / Data Center Secure & scalable
infrastructure
HP’s consolidated IT infrastructure
Functional provides a flexible storage and compute
both as services as well as public service
Platform
Mature functional
platform
Complete coverage of NGS
workflows within proven data
management and analysis system
© Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted

3. HP is the world's largest
provider of IT infrastructure,
software, services, and
solutions to individuals and
organizations of all sizes.
• Fortune 1 – U.S.
1
• Fortune 28 – Global
• Doing business in
approximately170 countries
• Over 320,000 employees
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4. Functional Genomics Center Zurich
Life science data management, analysis, and integration
• Joint Swiss research and technology center of University Zurich & ETH Zurich
21 Nobel Laureates since beginning last century, 215 spin-offs since late nineties
• Comprehensive coverage of systems-oriented life science research areas
Genomics, Transcriptomics, Proteomics, Metabolomics
• Full project support in User Lab concept
Scientific consulting, project consulting, researcher training, project collaboration, data analysis QC
• 10 Years of operational experience
> 2000 Users, > 1000 Projects, > 240 Institutes, > 30 Companies
• Full coverage of state-of-the-art analytical technologies
> 30 platforms, e.g. PacBio RS, Illumina HiSeq2000, LifeTech SOLiD5500xl, IonTorrent PGM, Roche/454 GS FLX+
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5. HP Sequence Services
Functionality overview
• Easy-to-use
• Cost-effective
• Increased scientific quality
• Comprehensive administration
• Powerful HP Cloud
• Industry leading security
• Open standards based
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6. HP Converged Infrastructure – Private or Public
World-class, open standards based, secure cloud infrastructure
• Adapt to changing needs
• Scale up dynamically
• Access your data globally
• Pay only what you use
• No lock-in through open standards
• Hybrid approach (private/public)
© Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted

7. HP Sequence Services
Sequencing in personalized medicine and resulting challenges
Disease Characterization
Genetic of disease agent Understanding
cause
characterization of disease mechanism
of indvidual Disease
mechanism
Diagnostic
characterization
of disease
Healthy Therapy Disease
Personalized Development
application of Therapeutic of therapy
therapeutic agent measure
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8. HP Sequence Services
Technical & scientific support
• NGS analysis challenges at all levels
• Experimental (specimen, molecular biology)
• Data management (terabytes per experiment)
• Data processing (large memory needs, large computational needs)
• Data processing and interpretation (algorithms, statistics, visualization)
• Technical and administrative support
• Project setup and management, application support, scalability, special hardware requirement
• Scientific support
• Essential at all levels of a successful project (beginning with experimental design)
• Feedback loops between bioinformatics and lab necessary to assess and enhance quality of output
8 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted

9. HP Sequence Services
Functional platform offering complete coverage of NGS workflows
Sequence Map Identify Associate Validate
read the genetic place the reads on find SNPs, Indels and link genetic changes visualize results in
code reference genome structural variations to diseases Genome Browser
(c) Nature & ETH/UNI
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9

10. HP Sequence Services
Running the GATK for the first time - GSA http://www.broadinstitute.org/gsa/wiki/index.php/Running_the...
Running the GATK for the first time
From GSA
Data analysis from single experiments to data integration
Once you've installed the GATK toolkit, whether from the source distribution or from a binary
distribution, you can run the various analyses that the GATK supports.
Test Your Installation
The first step is to test that the GATK is correctly installed, and that the supporting tools like Java are in
your path. Type the following command:
replacing the path to GenomeAnalysisTK.jar with the path you have setup.
You should see usage output similar to the following:
usage: java -jar GenomeAnalysisTK.jar -T <analysis_type> [-I <input_file>] [-L <inter vals>] [-R
<reference_sequence>] [-B <rodBind>] [-D <DBSNP>] [-H <hapmap>] [-hc <hapmap_c hip>] [-o <out>] [-e
<err>] [-oe <outerr>] [-A] [-M <maximum_reads>] [-sort <sort_on_the_fly>] [-co mpress
<bam_compression>] [-fmq0] [-dfrac <downsample_to_fraction>] [-dcov <downsampl e_to_coverage>] [-S
<validation_strictness>] [-U] [-P] [-dt] [-tblw] [-nt <numthreads>] [-l <loggi ng_level>] [-log
<log_to_file>] [-quiet] [-debug] [-h]
-T,--analysis_type <analysis_type> Type of analysis to run
-I,--input_file <input_file> SAM or BAM file(s)
-L,--intervals <intervals> A list of genomic interva ls over which
to operate. Can be explic itly specified
on the command line or in a file.
-R,--reference_sequence <reference_sequence> Reference sequence file
-B,--rodBind <rodBind> Bindings for reference-or dered data, in
the form <name>,<type>,<f ile>
-D,--DBSNP <DBSNP> DBSNP file
-H,--hapmap <hapmap> Hapmap file
-hc,--hapmap_chip <hapmap_chip> Hapmap chip file
-o,--out <out> An output file presented to the walker.
Will overwrite contents if file exists.
-e,--err <err> An error output file pres ented to the
walker. Will overwrite c ontents if file
exists.
-oe,--outerr <outerr> A joint file for 'normal' and error
output presented to the w alker. Will
overwrite contents if fil e exists.
...
Troubleshooting install
If you don't see this message, and instead get an error message there are a couple of things that you
should check. First, make sure that your Java version is at least 1.6, by typing the following command:
You should see something similar to the following text:
1 of 3 4/23/12 6:20 PM
Read processing Read mapping Functional association Validation
• De-multiplexing • Alignment • Element identification • Result visualization
• Trimming • Combination • Element association • Scientific validation
• Quality control • Statistics
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11. HP Sequence Services
Data analysis from single experiments to data integration
Q12860 Contactin-1 OS=Homo sapiens GN=CNTN1 PE=1 SV=1 sp|Q12860|CNTN1_HUMAN
Q99435 Protein kinase C-binding protein NELL2 OS=Homo sapiens GN=NELL2 PE=1 SV=1
sp|Q99435|NELL2_HUMAN
Data combination Data integration Collaboration Hypothesis
• Long / short reads • Other molecular levels • Technical discussion generation / validation
• Bias / error rates • Other technologies • Scientific exchange
Illumina, SOLiD, 454, Proteomics, Communication, Data and knowledge
IonTorrent, PacBio Metabolomics member management export and linking
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12. HP Sequence Services
Roadmap
2012 2013
development commercial
today
Pilot Release Production
• Transform platform • Extend platform • Commercialize platform
• In-house data center • HP Cloud 10th May • Region specific data center
• Minimal app set • LCM core apps • Integrate extended app set
• Develop Web GUI • Email based • Billing, pay-as-you-go
• User acceptance tests admin workflows • Technical & scientific support
• Demo data (35 GB) • Service ramp-up • Concept-based search
• Partner program
April July Dec
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13. HP Sequence Services
Three models starting 2013 – HP Cloud, in-house, or both
HP Cloud Subscription Pay-by-use/project In-house HP data center
• Project setup • Storage/Compute • Run functional platform in-house
• System training • Consultancy • HP platform support
• Public data sources • Custom applications • Burst-out to HP Cloud (opt.)
13 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted

14. HP Sequence Services
High scientific quality with maximal IT flexibility
• Easy-to-use • Complete administration
• Easy & fast web-based data access • Automated administration tasks • John Wise
• Standard & ad-hoc analysis workflows • Simplified IT admin, scientists, • Michael Braxenthaler
• Industry leading security secretarial work • Nick Lynch
• Increased scientific quality • Ashley George
• Role-based user authorization
• Deborah Ausman
• Regular security and quality reviews • Reproducibility of research results
• -------
• Cost-effective • Application life-cycle-management
• Scientific quality control & support A true catalyst for the
• Transparent subscription & pay-by-use
• Meaning based search Pharma- and IT industries
• Public data life-cycle-management
• Open standards based
• Powerful Search & HP Cloud
• Community application approach
• Dynamic storage & compute power on
the HP Cloud • Easily extensible with new applications
• Hybrid Cloud models • No vendor lock-in with OpenStack
© Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted

15. THANK YOU
© Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice.