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Closing the Gap in Time: From Raw Data to Real Science


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Closing the Gap in Time: From Raw Data to Real Science: Science as a Service (ScaaS)

Closing the Gap in Time: From Raw Data to Real Science: Science as a Service (ScaaS)

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  • Won’t bore you with the entire history of Edge Bio. Its been around 20 …I am sure there are several of you in this room that found yourself doing something you didn’t expect because NGS has provided new challenges to typical thinking and infrastructure.
  • I am sure you all have seen some sort of variation of this. You, like us, see the value in exploring the next gen landscape, but with such an infection – something has to give.Figure 1 The number of publications with keywords for nucleic acid detection and sequencing technologies. PubMed (http://www. was searched in two-year increments for key words and the number of hits plotted over time. For 2007–2008, results from January 1–March 31, 2008 were multiplied by four and added to those for 2007. Key words used were those listed in the legend except for new sequencing technologies (‘next-generation sequencing’ or ‘high-throughput sequencing’), ChIP (‘chromatin immunoprecipitation’ or ‘ChIP-Chip’ or ‘ChIPPCR’ or ‘ChIP-Seq’), qPCR (TaqMan or qPCR or ‘real-time PCR’) and SNP analysis (SNPs or ‘single-nucleotide polymorphisms’ and not nitroprusside (nitroprusside is excluded because sodium nitroprusside is sometimes abbreviated as ‘SNP’ but is generally unrelated to genetics)).
  • From the base of the inflection (or tipping point) in 06 - innovation and technology have been in a constant state of flux. Costs per base have plummeted.Still remains as significant capital expenditure in many areas
  • Lets hone in on a couple of those areas.- These are the players in the sequencing field as it is, and as it is emerging. - Where do you start – each are provide data at lower costs,- Each have their strengths and weaknesses, - How do you make sure you choose the right platform for your application.
  • Now, you have a platform – with the high throughout comes an immense range of applications – how do you become proficient?
  • Now you have an application, how do you design your project? And what many here are talking about today – how do you effectively analyze the data?To illustrate the complexity – this is a partial list of read mapping software from SeqAnswersSo testing, comparing, and honing in on an app is important. Then each one can be run in a multitude of ways. How many errors, colorspace, base, space, etc, Daunting,
  • Then there is the execution and operations of the projects, - We all wish we had a bag of money to do the science “in the right way”compromises are made to suit funders, timelines, quality standards, etc.How do we balance those limited resources – lets touch on that later.
  • I tend to start with the inherent challenges of the next gen landscape to lay the ground work for possible solutions.
  • I was lucky to grow up in genomics. 16 was high throughput. Infrastructureas we know it was rendered obsoletesheer scalechemistries (flows and colorspace data) error models.– significant issue lie ahead for next next gen in these areas.
  • Distributing the Problem- lower barrier to entry than before- it has somewhat democratized sequencing,
  • - Service based models becoming common in IT- They allow abstractions, so you don’t have to care about the hardware, or the software, or the platform that is built to accomplish the goals of the research organization or company.
  • Edge abstracts it to the most basic of levels. Our aim is to help researchers with all these considerations, to come out with optimal results. DNA/RNA in  answers out.
  • Though leaders in fields of genomics and bioinformatics.
  • Lets focus a bit more. Bioinformatics is a piece of the puzzle.
  • More recently, it just so happens to be a larger piece.
  • With limited time and so many cool things to talk about – I am going to touch on several. I would love to continue any one of these in a hallway or over coffee. My group’s goal is to leverage many technologies – commercial, academic, and internal to help our clients. Some of the areas we are focusing on are on this slide.
  • SO the first, and probability hottest topic out there is cloud.
  • ScalablePay as you GoRedundant data storageUbiquitous accessLower upfront and capital costs
  • Access resources in non-traditional ways.Paradigm shift needs to happen with funding agencies,think in traditional ways of funding capital infrastructure. We need to continue to educate.
  • - Oneneeds to be nimble in their ability to leverage computes from many pools. - With the ESG, we have built a flexible and scalable infrastructure
  • ESG is built around This plug and play architecture- continue to explore tools - Chef and other virtualization mechanism that ease the burden of infrastructure maintenance.
  • Note how each is a node which we can hotswap tools as needed.
  • This isn’t Panaceathough. There are are costs, whether front or back loaded. SO how do we minimize them? Spend time making things better, not just building pipelinesI’ll touch a bit more on each of these in the upcoming slides.
  • - Best of Breed. - Changing so rapidly. SOwhether we, or someone else figures out a way to do something better we can take advantage.- With software, make it better or run it less
  • How many times have you tried to install software that was sent to you or you downloaded from SourceForge that wouldn’t build or run as planned?We quickly learned with a community based AMI is very serial in its adoption and addition. Chef allows for developers to construct infrastructure much like SW
  • So, lets wind this down by looking at some examples. I guess if you take one term away – I would like it to be Science as a Service. This is a concept, an abstraction for a method of building infrastructure and transparency. So – does it work?
  • Note how each is a node which we can plug in tools as needed.
  • Balance between cost and coverage – this provides a talking point for a slide coming up in a few.
  • What is the best way to do this with what you have?If money not an object, get high coverage and 100% accuracyIn reality, What is the best way to do it with what you have?PlaftormBfx
  • What is the best way to do this with what you have?If money not an object, get high coverage and 100% accuracyIn reality, What is the best way to do it with what you have?PlaftormBfx
  • Transcript

    • 1. Closing the Gap in Time: From Raw Data to Real Science
      Science as a Service (ScaaS)
      Justin H. Johnson
      Director of Bioinformatics
      Gaithersburg, MD
    • 2. Edge Bio & Me
      Sequencing and Bioinformatics Shop
      I am a
      IT Professional
      The lines are blurred…
    • 3. NGS Exponential Growth
      Nature Biotechnology Volume 26 Number10 October2008
    • 4. Sequencing is Free?
      Machines and Vendors
      Lab Staffing, Integrations and LIMS
      Project Design
      Data Management and QC
      Bioinformatics and Data Analysis
      Data Computes and Storage
      Data Sharing
    • 5. Machines and Vendors
    • 6. Ultra High Throughput + Lower Cost = Broader Applications
    • 7. Bioinformatics Tools
      * BFAST - Blat-like Fast Accurate Search Tool. Written by Nils Homer, Stanley F. Nelson and Barry Merriman at UCLA.* Bowtie - Ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Transformed (BWT) index. Link to discussion thread here. Written by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X.* BWA - Heng Lee's BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence. C++ source.* ELAND - Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.* Exonerate - Various forms of pairwise alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.* GenomeMapper - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. A tool created by the 1001 Genomes project. Source for POSIX.* GMAP - GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences. Developed by Thomas Wu and Colin Watanabe at Genentec. C/Perl for Unix.* gnumap - The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. It seeks to align reads from nonunique repeats using statistics. From authors at Brigham Young University. C source/Unix.* MAQ - Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina with preliminary functions to handle ABI SOLiD data. Written by Heng Li from the Sanger Centre. Features extensive supporting tools for DIP/SNP detection, etc. C++ source* MOSAIK - MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Features a number of support tools. Support for Roche FLX, Illumina, SOLiD, and Helicos. Written by Michael Strömberg at Boston College. Win/Linux/MacOSX* MrFAST and MrsFAST - mrFAST & mrsFAST are designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. Robust to INDELs and MrsFAST has a bisulphite mode. Authors are from the University of Washington. C as source.* MUMmer - MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Released as a package providing an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. Version 3.0 was developed by Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, CorinaAntonescu and Steven L Salzberg - most of whom are at The Institute for Genomic Research in Maryland, USA. POSIX OS required.* Novocraft - Tools for reference alignment of paired-end and single-end Illumina reads. Uses a Needleman-Wunsch algorithm. Can support Bis-Seq. Commercial. Available free for evaluation, educational use and for use on open not-for-profit projects. Requires Linux or Mac OS X.* PASS - It supports Illumina, SOLiD and Roche-FLX data formats and allows the user to modulate very finely the sensitivity of the alignments. Spaced seed intial filter, then NW dynamic algorithm to a SW(like) local alignment. Authors are from CRIBI in Italy. Win/Linux.* RMAP - Assembles 20 - 64 bpIllumina reads to a FASTA reference genome. By Andrew D. Smith and ZhenyuXuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.* SeqMap - Supports up to 5 or more bp mismatches/INDELs. Highly tunable. Written by Hui Jiang from the Wong lab at Stanford. Builds available for most OS's.* SHRiMP - Assembles to a reference sequence. Developed with Applied Biosystem'scolourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. POSIX.* Slider- An application for the Illumina Sequence Analyzer output that uses the probability files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Authors are from BCGSC. Paper is here.* SOAP - SOAP (Short Oligonucleotide Alignment Program). A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The updated version uses a BWT. Can call SNPs and INDELs. Author is Ruiqiang Li at the Beijing Genomics Institute. C++, POSIX.* SSAHA - SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a tool for rapidly finding near exact matches in DNA or protein databases using a hash table. Developed at the Sanger Centre by ZeminNing, Anthony Cox and James Mullikin. C++ for Linux/Alpha.* SOCS - Aligns SOLiD data. SOCS is built on an iterative variation of the Rabin-Karp string search algorithm, which uses hashing to reduce the set of possible matches, drastically increasing search speed. Authors are Ondov B, Varadarajan A, Passalacqua KD and Bergman NH.* SWIFT - The SWIFT suit is a software collection for fast index-based sequence comparison. It contains: SWIFT — fast local alignment search, guaranteeing to find epsilon-matches between two sequences. SWIFT BALSAM — a very fast program to find semiglobal non-gapped alignments based on k-mer seeds. Authors are Kim Rasmussen (SWIFT) and Wolfgang Gerlach (SWIFT BALSAM)* SXOligoSearch - SXOligoSearch is a commercial platform offered by the Malaysian based Synamatix. Will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Web Portal. OS independent.* Vmatch - A versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements. Essentially a large string matching toolbox. POSIX.* Zoom - ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority. Commercial. Supports Illumina and SOLiD data.
      Courtesy of
    • 8. Experimental Design Considerations
      • Sequencing Platform in Use
      • 9. Choice of Library Construction
      • 10. Depth of coverage
      • 11. Re$ources
      • 12. Number of Replicates
      • 13. Number of Samples and Control
      • 14. Etc…
    • The Sky Isn’t Falling
    • 15. Its Building…
    • 16. …and distributing
      Distributing the Problem
      Exchanging Data
      Refreshing Data
    • 17. How do we avoid the Perfect Storm?
    • 18. Life Vests?
    • 19. Edge Bio
    • 20. You can’t do this alone, neither can we.
      Elaine Mardis, Ph.D.
      Co-Director, Genome Sequencing Center
      Washington University School of Medicine
      Sam Levy, Ph.D.
      Director of Genomic Sciences
      Professor of Translational Genomics & Human Genomic Medicine
      Scripps Translational Science Institute
      Scripps Health
      Scripps Research Institute
      Michael Zody, Ph.D.
      Chief Technologist
      Broad Institute of MIT
      Ken Dewar, Ph.D.
      Assistant Professor
      McGill University and Quebec Genome
      Steven Salzberg, Ph.D.
      Director, Center for Bioinformatics and Computational Biology
      University of Maryland
      Gabor Marth, Ph.D.
      Professor of Bioinformatics
      Boston College
      Elliott Margulies, Ph.D.
      Genome Informatics Section
      National Human Genome Research Institute
      National Institutes of Health
      Scientific Advisory Board
    • 21. EdgeBio
    • 22. Edge Bio
    • 23. Bioinformatics
      Cloud Computing (Iaas, PaaS)
      Amazon, Google, Others
      NGS Software and Algorithms
      Commercial (CLC) and Open Source
      (cloud)Biolinux, Hadoop and Chef
      Data Sharing and Standards (GSC/M5)
    • 24. Cloud
    • 25. Cloud
      Not a talk on cloud computing…
      Either you already know what it is
      – OR –
      Other can do it more justice with more time.
      The 4 dollar genome.
    • 26. An Academic Problem
      Have 100K+ free computes avail (Teragrid)
      Can’t get to them easily
      Have unlimited pool of computes (Amazon)
      Can’t figure out how to pay for them
      If you have figured those out…
      Traditional Issues
      Pipes too small
    • 27. Edge Science Gateway (ESG)
      Easily leverage any source at the back end
      Internal HPC Cluster
      Internal cloud (Eucalyptus)
      Commercial partners provide thin clients layer
      CLC Bio
    • 28. Edge Science Gateway (ESG)
      Plug and Play Tools
      Chef and (cloud)Bio-Linux
      Real people, not services underneath it all.
      IFX and IT consulting
    • 29. Edge Exome Analysis Pipeline
      Base Call, Quality Filter
      Exon junctions
      Variant Analysis
      Variant Annotation
      Refseq (etc)
      SIFT, PolyPhen
      Repeat Database
      Functional and Structural Analysis
    • 30. Sometimes money isn’t enough
      Traditional Infrastructure or New Era Clouds
      Still costs, whether up front or on back end
      Always want to minimize cost
      Frameworks and Algorithms R&D
      NGS Software and Algorithms
    • 31. NGS Software and Algorithms
      Best of Breed though pluggable architecture
      Make them faster…
      Map Reduce Blast & GPU Enable Blast
      SIMD Accelerated HMMR, ClustalW, SW (CLC Bio)
      …or run them less.
      Clustering algorithms
      Efficient data refreshes
      Sharing of results
    • 32. Frameworks
      Easily deploy others software though virtualization
      Chef (an Intro)
      Open Source configuration management for your entire infrastructure
      MPI and Hadoop
      Speed up and I/O issue resolution with MPI
      CloudBurst – mapReduce based NGS mapping
    • 33. Edge BioServ Services
      Project goals and timelines
      Number of samples
      Number of reads/tags per sample
      Experiment and Project Design
      Sample Preparation
      Library Preparation
      Sample Capture
      Library Construction
      Sample QC and Quantification
      Adaptor ligation
      Amplification & Sequence
      Fragment amplification
      Next Generation Sequencing run
      Align sequence to reference genome
      or RNA database
      Secondary and Tertiary Analysis
      Data Analysis
    • 34. Real World Examples
      1500+ Sample Epigenetic Study
      • Mix of Commercial and Open Tools
      • 37. Geospiza
      • 38. CLC Bio
      • 39. Customs Algorithms
      • 40. HPC and Storage
      • 41. Onsite 200 TB NAS
      • 42. S3 for Backup (Soon for Delivery)
    • Real World Examples
      Hundreds of exomes over the next 6 months.
      Pipeline for mapping and variant analysis
      Mix of commercial, in house, and open source tools.
    • 43. Edge Exome Analysis Pipeline
      Base Call, Quality Filter
      Exon junctions
      Variant Analysis
      Variant Annotation
      Refseq (etc)
      SIFT, PolyPhen
      Repeat Database
      Functional and Structural Analysis
    • 44. EdgeBioExon Coverage StatisticsHow well is the exome covered?
      ~3 Quads on SOLiD 3 Plus
      • <1% of exons have 0 coverage
      • 45. 3% of exons have 0-5x coverage
      • 46. 5% of exons have 0-10x coverage
      • 47. 95% of exons have >10x coverage
      ~1 Quad on SOLiD 3 Plus
      • <2% of exons have 0 coverage
      • 48. 10% of exons have 0-5x coverage
      • 49. 17% of exons have 0-10x coverage
      • 50. 83% of exons have >10x coverage
    • Real World Examples
      Transcriptomes from microbes to mice.
      Rapidly evolving field
      Again leveraging tools across the board via ESG
      Plug and Play Best of Breed.
    • 51. Visualization
    • 52. Re$ources
    • 53. Re$ources
    • 54. Re$ources
    • 55. Re$ources
    • 56. Re$ources
    • 57. Questions?
      Thank You
      Twitter: @BioInfo & @EdgeBio
    • 58.
    • 59. …Yet
      1000 Genomes+ 1500