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Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
Sequence Services Phase 2--Hewlett-Packard
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Sequence Services Phase 2--Hewlett-Packard

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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.

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.

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  • 1. HP Sequence ServicesPistoia Alliance Annual Conference24th April 2012Etzard Stolte, PhD, Hewlett-PackardRalph Schlapbach, PhD, ETH Zurich © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice.
  • 2. HP Sequence ServicesHigh 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 worlds 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 employees3 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice.
  • 4. Functional Genomics Center ZurichLife 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+4 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted
  • 5. HP Sequence ServicesFunctionality overview • Easy-to-use • Cost-effective • Increased scientific quality • Comprehensive administration • Powerful HP Cloud • Industry leading security • Open standards based5 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted
  • 6. HP Converged Infrastructure – Private or PublicWorld-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 ServicesSequencing 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 measure7 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted
  • 8. HP Sequence ServicesTechnical & 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 output8 © 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 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice.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 GSAData analysis from single experiments to data integration Once youve 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 dont 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 PMRead processing Read mapping Functional association Validation• De-multiplexing • Alignment • Element identification • Result visualization• Trimming • Combination • Element association • Scientific validation• Quality control • Statistics10 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted
  • 11. HP Sequence ServicesData 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_HUMANData 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 linking11 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted
  • 12. HP Sequence ServicesRoadmap 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 Dec12 © Copyright 2011 Hewlett-Packard Development Company, L.P. The information contained herein is subject to change without notice. HP Restricted
  • 13. HP Sequence ServicesThree 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 ServicesHigh 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.

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