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An Introduction to CAMERA and Underlying Technologies

An Introduction to CAMERA and Underlying Technologies. Philip Papadopoulos University of California, San Diego San Diego Supercomputer Center California Institute of Telecommunications and Information Technology (Calit2). PI Larry Smarr. Announced 17 Jan 2006. Public Release 13 March 2007

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An Introduction to CAMERA and Underlying Technologies

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  1. An Introduction to CAMERA and Underlying Technologies Philip Papadopoulos University of California, San Diego San Diego Supercomputer Center California Institute of Telecommunications and Information Technology (Calit2)

  2. PI Larry Smarr Announced 17 Jan 2006. Public Release 13 March 2007 $24.5M Over Seven Years

  3. DNA Basics for Non-Biologists • Nucleotide bases of DNA • ACTG (Adenine, Cytosine, Guanine, Thymine) • A Sequence of Bases Forms One Side of a DNA Strand • Complementary Bases form the other side of DNA • A matches T (pair) • C matches G (pair) • During cell replication, DNA is “unzipped” . The complementary side can then be replicated perfectly • Human DNA is about 3 billion base pairs on 26 Chromosomes

  4. Bases  Amino Acids • Triplets of nucleotide bases are called codons and define amino acids. • Amino acids are the basic building blocks of proteins • There are 20 amino acids, but 4^3 = 64 nucleotide combinations. • Many amino acids have multiple codons • Special codons (called start and stop codons) assist in DNA translation during cell replication. • Reading Frames of: GGGAAACCC • This raw sequence could be read as • GGGAAACCC (GGG AAA CCC) (Glycine, Lysine, Proline) • GGAAACCC (GGA AAC) (Glycine, Asparagine) • GAAACCC (GAA ACC) (Glutamic Acid, Threonine)

  5. Sequencing Tidbits • The Institute for Genomic Research (TIGR) sequenced the genome of the bacterium Haemophilus influenzae in 1995 using shotgun sequencing • 1.8 Million Base Pairs (Human: 3 Billion) • Sequencing does NOT tell you what function a particular gene plays • It is believed that only ~1.5% of human chromosome codes for expressed characteristics • The non-coding portions contain our genetic history • Unknown what function the rest our DNA plays

  6. Most of Evolutionary Time Was in the Microbial World You Are Here Tree of Life Derived from 16S rRNA Sequences Source: Carl Woese, et al

  7. Marine Genome Sequencing Project – Measuring the Genetic Diversity of Ocean Microbes Need Ocean Data Sorcerer II Data Will Double Number of Proteins in GenBank!

  8. Some CAMERA Goals • Provide an infrastructure where scientists from around the world can perform analysis on genetic communities • Global Ocean Sampling (GOS) is the initial large data set • ~ 8.5 Billion base pairs of raw Reads • Metadata is available for samples • Saline, Temperature, Geographic Location, Water Depth, Time of Day … • Other metadata will be correlated with samples (e.g. MODIS Satellite) • Allow others to search and compare input sequences against CAMERA data. • Overall provide a resource dedicated to metagenomics • Support new datasets • Support new analysis tools and web services

  9. Global Ocean Survey (GOS) Sequences are Largely Bacterial ~3 Million Previously Known Sequences ~5.6 Million GOS Sequences Source: Shibu Yooseph, et al. (PLOS Biology in press 2006)

  10. Reason for CAMERA • The Global Ocean Survey (GOS) is a huge influx of sequence data • Factors that interrelate microbes and microbial communities are not well known • Significant analysis requires large resources • All-to-all comparisons • Integration of other environmental (meta) data (weather, temperature, salinity,…) is essential • Raw Sequence Data sets are mid-sized • Current set of GOS Raw Reads is about 100GB (FASTA Files)

  11. Calit2 CAMERA ProductionCompute and Storage Complex is On-Line 512 Processors ~5 Teraflops ~ 200 Terabytes Storage

  12. User Map – 03 May 2007 • Site in production on 13 March 2007 • More than 500 Registered users from around the globe (~10 new users/day)

  13. Calit2’s Direct Access Core Architecture CAMERA’s Metagenomics Server Complex Dedicated Compute Farm (100s of CPUs) W E B PORTAL Data- Base Farm 10 GigE Fabric Local Environment Flat File Server Farm Direct Access Lambda Cnxns Web (other service) Local Cluster TeraGrid: Cyberinfrastructure Backplane (scheduled activities, e.g. all by all comparison) (10000s of CPUs) • Sargasso Sea Data • Sorcerer II Expedition (GOS) • JGI Community Sequencing Project • Moore Marine Microbial Project • NASA and NOAA Satellite Data • Community Microbial Metagenomics Data Traditional User Request Response + Web Services Source: Phil Papadopoulos, SDSC, Calit2

  14. Calit2 CAMERA ProductionCompute and Storage Complex is On-Line Compute Nodes 1 and 10 Gbit/s Switching 200 TB File Storage 10 Gbit/s Network Web, Application, DB Servers

  15. Global Elements • Data location – Storage Resource Broker Meta data catalog • Data-type aggregation, cross-correlation, integration – BIRN Data Mediator • Identity Management • Use Grid Security Infrastructure (GSI) Public Key System • Integrated Grid Accounts Management Architecture (GAMA) from SDSC for ease-of-use and Single Sign On • Portal Services • Based on GridSphere • Small Dedicated Compute Cluster (32 nodes)

  16. Logical Layout of Servers Single Sign On Layer Web Server Portal Server (Tomcat) Single Sign-on Server Public Net Private Net Cluster Frontend Blast Master (Jboss) Postgres Database GAMA Server Cluster Nodes and File Servers

  17. An Incomplete List of Software Components Postgres Database Apache Tomcat Jboss Servlet Container Google Web Toolkit Sun Grid Engine GAMA (Grid Accounting and Management Architecture)/GSI from Globus OPAL (Grid/Web Services Wrapper) GridSphere Portlet Container CAMERA Registration Portal Venter Application Portal NCBI Blast, MPIBlast, ClustalW, MrBayes, CDHit, and host of other Bio Software Ergatis Workflow Engine Jforums Drupl All Integrated with Rocks … Single Person Deployment

  18. OptIPortal– Another Rocks Cluster Termination Device for the OptIPuter Global Backplane • 20 Dual CPU Nodes, 20 24” Monitors, ~$50,000 • 1/4 Teraflop, 5 Terabyte Storage, 45 Mega Pixels--Nice PC! • Scalable Adaptive Graphics Environment ( SAGE) Jason Leigh, EVL-UIC Source: Phil Papadopoulos SDSC, Calit2

  19. Use of OptIPortal to Interactively View Microbial Genome 15,000 x 15,000 Pixels Acidobacteria bacterium Ellin345 (NCBI)Soil Bacterium 5.6 Mb Source: Raj Singh, UCSD

  20. Use of OptIPortal to Interactively View Microbial Genome 15,000 x 15,000 Pixels Acidobacteria bacterium Ellin345 (NCBI)Soil Bacterium 5.6 Mb Source: Raj Singh, UCSD

  21. A Look at Networking Introduction to Quartzite An Experimental Network

  22. Sunlight (10 Gigabit) Campus/WAN

  23. Using a Lambda Network for CAMERA • Many community databases • Protein Databank (PDB) • GenBank • SwissProt • Support only web or web services interfaces • New analysis/programs need access to raw databases/files • Usually, groups make a point-in-time copy of the database • We call this a data “fork” • Updates are not processed • Papers published with point-in-time data out of date by months or years • CAMERA “Direct Connect” will allow us to provide a high-speed connection to the backend servers • Try to eliminate data forking • Copies of CAMERA data is inevitable • Need mechanisms that allow others to keep their copies in synch with CAMERA

  24. UCSD Quartzite Core at Completion (Year 5 of OptIPuter) • Funded 15 Sep 2004 • Physical HW to Enable Optiputer and Other Campus Networking Research • Hybrid Network Instrument Reconfigurable Network and Enpoints

  25. 4x4 Wavelength Cross-Connect: 1x4 WSS 1x4 WSS 1x4 WSS 1x4 WSS combiners • All integrated optics (except optical amplifiers) • 4 1x4 WSS modules • 4 4x1 passive optical combiners • 4 x 40l x 40Gbps = 6.4Tbps switching capacity • currently using central 8l WSSs Optical Amps 4x4 WXC rack

  26. ASE source 4x1 switch 1x4 WSS OSA 1x4 WSS 1x4 WSS 1x4 WSS WXC performance demonstration: 8 lasers at centre of C-Band at 100GHz spacing use ASE source to illustrate wide bandwidth use external 4x1 switch to scan WXC ports alter switch states of WSS1 and WSS3 shown in movie on next page

  27. WXC performance demonstration:

  28. What Does it Cost to Drive the Network Dominant cost is DWDM optics Construction of Multiplexers is Simple, and not expensive ~ $250/Channel/End

  29. Layer 1 – Four Channel DWDM 10Gbps Switch X 4 Per Side (optional) DWDM Mux Transmit X 1 Per Side XFP Switch Module X 4 Per Side (optional) XFP DWDM Optics X 4 Per Side Used in Host or Switch DWDM DeMux Receive X 1 Per Side SC to LC Fiber 2M X 5 Per Side 1 Fiber Pair Channel 31 Channel 32 Channel 33 Channel 34 Corning 1U Rack Containing DWDM Mux / DeMux + SC to SC couplers, 1 Per side

  30. 1)Optics

  31. 2) Optional - Layer 2 Switch (10Gbps capable)

  32. 3) DWDM Mux DeMux

  33. 4) Corning Rack Mount, Couplers, Fiber

  34. Complete Solution

  35. 5) Optional- DWDM Media Converter

  36. Quartzite State Nov 2007 • Core Packet Switch with 68 10 GigE ports (More than ½ Terabit) • Approximately 30 Channels Lit • 64-port All-Optical Glimmerglass Switch - All Fiber into Quartzite is switchable • 4 port x 8 Lambda DWDM switch at Lucent (On site at Calit2 in Dec) • 4 Channel DWDM Between Calit2 and SDSC • One channel is used for 10Gigabit Production to BIRN Data Racks. • Ordered, but waiting for fulfillment • 20 Mux/Demux (8 C-band DWDM Channels + 1 1310 (LR) Passband) • 32 DWDM XFPS (Channel 40-43 – will fill out rest of channels in 2008)

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