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OGCE SC10 presentation as the IU booth

OGCE SC10 presentation as the IU booth

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  • Background on gateways, needs- Software environment major issueWhy GWT gadgets?Why PMRPC?
  • Springboard is HUBzero integrated with TeraGrid (and potentially its successor XD once the architecture is known). More Springboard is based on the HUBzero'sJoomula web platform, integrated with MyProxy authentication (so TG users can login with their TG crendentials), providing interactive communication between online TG users and support staff, providing collaboration space (application/tool publication and sharing, data sharing,  user created project group spaces, forums, documents/tutorials/course and other materials), etc.

OGCE SC10 OGCE SC10 Presentation Transcript

  • Open Gateway Computing Environments Marlon Pierce, Suresh Marru, Yan Liu, Carol Song, SudhakarPamidighantam, and Emre Brookes
  • Workshop AgendaAbout OGCEThe OGCE Gadget ContainerBuilding SimpleGridGadgetsGWT Gadgets and HUBZero PortabilityBioinformatics Workflows in the Cloud: BioVLABComputational Chemistry Workflows: GridChemManaging Biophysical Data Analysis: UltraScan
  • About OGCE http://www.collab-ogce.org http://collab-ogce.blogspot.comBack View slide
  • Open Gateway Computing Environments• The OGCE team develops software for building secure, Web-based Science Gateways – Chemistry, Bioinformatics, Biophysics, Environmental Sciences• OGCE is funded by the National Science Foundation’s Software Development for Cyberinfrastructure (SDCI) program.Back View slide
  • OGCE Funds Full Gateway Software LifecyleBack
  • OGCE SoftwareName DescriptionOGCE Gadget Container AnOpenSocial and Google gadget-compatible Web container for running Web gadgets.GFAC A Web service for generating, securely invoking, and managing the lifecycle of scientific applications on Grids and CloudsWorkflow Tools Composer (XBaya), enactment engines, event system, and service registry to support scientific workflows on Grids and Clouds.Gadgets and Gadget Tools for building secure Google-gadget based Science Gateways.Building Tools Back
  • OGCE Partners and PeopleInstitution PeopleIndiana University Marlon Pierce, Suresh Marru, Raminder Singh, ArchitKulshrestha, Gerald GuoNCSA/UIUC SudhakarPamidighantam, Shaowen Wang, Yan LiuPurdue University Carol Song, Lan Zhao, David Braun, Shawn WuUTHSCSA Emre Brookes, BorriesDemeler, Bruce Dubbs Back
  • OGCE Components in ActionFeaturedGateway OGCE Components UsedUltraScan GFAC scientific application management serviceGridChem,ParamChem XBaya workflow composer, OGCE Messenger Service, XRegistrySimpleGrid OGCE Gadget Container (in development)Purdue CCSM Portal Gadget Container and gadget building libraries (in development)BioVLAB GFAC, XBaya,XRegistry, Workflow Interpreter Service Back
  • OGCE Alumni• We also gratefully acknowledge the contributions of participants in previous incarnations of the OGCE: – TACC: MaytalDahan, Rion Dooley – SDSU: Mary Thomas – SDSC: Nancy Wilkins-Diehr, Jeff Sale – LSF: SrinathPerera, SanjivaWeeravarnaBack
  • More Information• OGCE Web Site: http://www.collab-ogce.org• News Feed/Blog: http://collab-ogce.blogspot.com• Contact us: – ogce-discuss@googlegroups.com – http://groups.google.com/group/ogce-discuss/• Software Downloads: Software is available as tagged SVN releases from our SourceForge project. – http://sourceforge.net/projects/ogce/ – See http://www.collab-ogce.org/ogce/index.php/Portal_download Back
  • The OGCE Gadget Container Managing layouts, look and feel, and behind-the-scenes services for aggregated Web gadgetsBack
  • The OGCE Gadget Container allows you to build portals out of public and private Google Open Social gadgets. Supports HTTPS. Downloadable, packaged software. Back
  • The OGCE Application Registry gadget allows users to interactively register hosts and applications that are dynamically wrapped as Web services.Back
  • The OGCE Experiment Builder gadget allows users to create projects and experiments out of previously composed workflows.Back
  • Google Gadget-Based Science Gateways PolarGridLEAD Back
  • Mobile Support Gadget Container is built with HTML, JavaScript and CSS. Works in both iPhone and Android native browsers with out modification. Developing layout managers better suited to limited screen real estate.
  • Feature Groups FeaturesLook and Feel Tabbed and Tree layout managers, 2 and 3 column layouts, default maximized views of gadgets, customizable color styling.Security Supports end-to-end SSL between browser, container, and gadgets; OpenIDauthentation; OAuth-secured gadgets; MyProxy logins; limited Grid credential sharing between gadgets; CILogon for InCommon loginInter-Gadget Supports OpenAjax publish-subscribe style messaging between gadgets. PMRPCCommunication JavaScript messaging support in developmentREST Service API Layouts, logins, sign-ups, user administration, user identification, and Grid credentials all accessible via REST service calls as well as the user interface.Open Source Social All code is open source and builds on Apache Shindig 2.0.NetworkingGadget Development Support for GWT-based gadgets and YUI JavaScript libraries in development. Back
  • Bioinformatics Workflows in the CloudBack
  • BioVLAB• BioVLAB- A Reconfigurable Cloud Computing Environment for Bioinformatics.• Collaboration between OGCE and Prof. Sun Kim’s group, School of Informatics and Computing, Indiana University.• Used for executing Bioinformatics applications in Cloud since late 2006.• BioVLAB-Proteins published in Nature News, 24 October 2007.• BioVLAB-Microarray published in eScience 2008• BioVLAB-MMIA, BioVLAB-mCpG – In Preparation Back
  • Architecture – Complete ViewBack
  • How to use BioVLAB1. Get an Amazon account2. Download workflow3. Run the workflowUsability!Back
  • BioVLAB Application Development ProcedureUser • Develop a command line app. Gfac Registration form • Install the app. in Amazon EC2 • Let the app. store any output to Amazon S3 /Admin Microsoft Application-Based Storage • Make a virtual machine image • Register the app. by using GfacUser • Instantiate EC2 and run the app. by using XBaya Back
  • BioVLAB-Microarray• Analysis of high throughputmicroarray experiment• Multiple tasks in a singlebatch• Output of a task can pluggedinto another task• Repeat the same set of taskswith small changes ofparameters Back
  • EXPERIMENTSBack
  • • MicroRNAs (miRNAs) • small (19-22 nucleotide) non-protein- coding RNA molecules • regulate the expression of specific gene products • effect translational blockade or message degradation• MMIA: microRNA and mRNA integratedanalysis BioVLAB-MMIA • Computation in the Cloud • MMIA expertise in workflow Back
  • Back
  • BioVLAB-mCpGBack
  • BioVLAB Summary• Usability (Reconfigurable environments) – As an adoption of the SaaS model of Cloud Computing for BioVLAB, end-users only need to launch the pre- composed BioVLAB workflows. With XBaya, users can easily customize it by modifying just a few components and input parameters.• Flexibility (Full privileges) – As a way of the IaaS model, BioVLAB workflow developers can have flexibility for handling computing resources and implementing applications with Amazon Cloud. They can choose specific systems resources to satisfy their needs with a fully controlled access power.• Reducing processing time & Cost effective – Users can have number of servers, and control their usage time as they want. That reduces researching cost and initial time to construct physical infrastructure for research. Back
  • Building SimpleGrid Gadgets Yan Liu, UIUCBack
  • SimpleGrid Toolkit• http://simplegrid.org• New TeraGrid science gateway development support• Hands-on tutorials at TeraGrid ‘07, ‘08, ‘09, ‘10, SciDAC’09, ’10, I- CHASS’08• Education program at SC’07 Back
  • SimpleGrid Science Gateway • Web 2.0 Rich Client • Web Server • Application Web Service • SimpleGrid API • TeraGrid Middleware • TeraGrid ResourcesBack
  • SimpleGrid User Environment• Usability-centric Web environment for user-friendly online analysis• Transparent access to TeraGrid• User interface – YUI2 and YUI3 – YUI components used • Menu, layout, overlay, dialog, data source, data table, event handling for user input (e.g., drag&drop), buttons• Logic control – Browser-centered logic control – Server is needed for data feeding, messaging, and user request handling• Browser-server communication – AJAX-based asynchronous communication • For data/parameter selection, job submission and monitoring, data uploading and transfer, and result visualization – Event programming• Online services – Twitter for job status notification and user collaboration Back
  • Application Example: TeraGrid-based Spatial InterpolationBack
  • SimpleGrid APIBack
  • Web Service Development • A Simple Tool for Automatic Web Service Package Generation • Axis2-basedBack
  • SimpleGrid Gadgets• Benefits of using gadget container – Loosely-coupled integration with gadgets • Web 2.0 features in gadgets do not interfere with container layout – Enhanced usability • Through easy integration with Open Social containers, e.g., OGCE, iGoogle – Enabling Web-based collaborative scientific computing activities • Domain-specific customization of community-contributed gadgets • Standard gadget-container and gadget-gadget communication for integrated use • Workflow support within gadget container – Inter-gadget communication and event-handling, e.g., drag & drop between two gadgets• SimpleGrid gadgets design – Standalone Gadgets and Services • Job management • Visualization • Job tracking through social networking – Reusable, composable, interoperable, customizableBack
  • SimpleGrid Gadgets Implementation• Integration with Gadget Container – Security Requirements • Single sign-on with gadget container for better usability – Gadget-gadget Communication • Messaging and Event-handling – Notification of job completion for visualization in the job gadget – Visualization request-handling in the visualization gadget • Implementation – OpenSocial RPC: gadgets.rpc – Follow AJAX sandbox security requirement by using container-forwarding and leveraging YUI’s flexible API for response handling• Ongoing work – Integrate single sign-on authentication and authorization – Seamless Grid credential management through single sign-on – OpenAjax-based gadget-gadget communication – Drag & drop feature between two gadgets Back
  • Building GWT Gadgets and Gadget Integration Across OGCE and HUBZero Carol Song, PurdueBack
  • Purdue Participation in OGCE• Gadget portability between iGoogle, OGCE gadget container and the HUBzero framework• Google Web Toolkit (GWT) gadget development• PMRPC for inter-gadget communication• Application gateways (climate modeling, scientific data gateways)
  • The TeamInstitution PeopleLead and coordinator for Carol SongPurdueArchitecture, web David Braun, Shawn Wutechnology, commoncomponentsScience gateway gadget Lan Zhao, Shawn Wu, Carol Songdevelopment
  • GWT gadget development• Developing GWT gadgets for data management• Why GWT? – Write in Java (thus the availability of rich application dev and debugging tools, etc) – Code translated into cross-browser JavaScript at deployment – GWT gadgets library simplifies gadget development ☼GWT gadgets can be hosted in iGoogle and OGCE gadget containers, and in HUBzero based gateways.
  • Inter-gadget communication• Using PMRPC – HTML5 JavaScript library for – Message passing – Remote procedure call – Publish-subscribe cross-context communication in browser• Using PMRPC to facilitate communication between two gadgets• How does it work – A simple API for exposing and calling procedures between browser windows, iFrames and web workers, even between different origins.
  • PMRPC Example BrowserData Browser Image ViewerGadget (client) Gadget (server) Register view function view call view pmrpc pmrpc
  • Gadget Portability• Write once, host it in different gateway platforms• OGCE, HUBzero, iGoogle• HUBzero – Web platform based on Joomla , developed by Purdue to support online simulations and scientific collaboration – A different model from OGCE: turnkey, end to end solution for building gateways – 25+ hubs are in production or being actively developed, with nanohub.org being the grandfather of all.• Add gadget support in HUBzero – Integrate Apache Shindig -- an OpenSocial container – OGCE gadgets work as-is in a hub
  • Same gadget in three environments
  • Domain science gateways• Climate Model (CCSM) science gateway – In production – GridSphere based – Uses TeraGrid resources• Scientific data gateway – Heterogeneous data (radar, model output, remote sensing, hydrology, … social science data in the future)
  • Computational Chemistry Workflows: GridChem SudhakarPamidighantamBack
  • GridChem Workflow Demo
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  • Managing Biophysical Data Analysis: UltraScan Emre Brookes, UTHSCSABack
  • OGCE: UltraScan: High-resolution Modeling of Analytical Ultracentrifugation Experiments on TeraGrid Emre Brookes BorriesDemeler Department of Biochemistry 16 November 2010Back
  • Overview Background What is Analytical Ultracentrifugation (AUC)? What does an AUC experiment provide? How do we obtain results? Example results TG Science Gateway GFAC Integration User community Publications FutureBack
  • Background: What is AUC ? AUC is an important technique for the solution study ofmacromolecules Molecules are not fixed to a microscope grid Molecules are not distorted by crystal packing forces (vs X-Raycrystallography) Very large size range (complements cryo-EM and NMR) Dynamic processes can be studied Conformational changes Back
  • Background: What is AUC ? Sample placed in cell Run Ultracentrifuge Usually 20-60k RPM Collect data 4 to 24 hours or more Analyze the dataBack
  • Background: What does it provide?  Time series of radial concentration profiles  From this, we can determine: How many different types of molecules are present in the solution What are there molecular weights and shapes (one dimension of shape – spherical to ellipsoidal) Are interactions present Concentration RadiusBack
  • Background: How do we obtain results? The Lamm equation is a PDE which describes an ideal solute (a molecule insolution). ∂C ∂t r = − 1 ∂ r ∂r [s  r2 C − D r 2 ∂C ∂r ] t Two solute-specific parameters (s, D) Other parameters are global to the experimentBuild finite element models (FEM) for each (s,D) in rangeFit collections of (s,D) FEMs to experimental data. Multistep procedure Back
  • Background: How do we obtain results? Key breakthrough algorithms: 2DSA Solves arbitrarily large non-negative least squares problems Breakthrough algorithm which allowed our advanced analysis techniques Brookes, Boppana, Demeler, Computing Large Spare Multivariate Optimization Problems with an Application in Biophysics. SC06 ACM 0-7695-2700-0/06 GA Parsimonious regularization “sharpens” for sparse solution space (vs. “smoothing” of max-entropy or Tikhonov) Brookes, Demeler, Parsimonious Regularization using Genetic Algorithms Applied to the Analysis of Analytical Ultracentrifugation Experiments. GECCO07 ACM 978-1-59593-697-4/07/0007 Back
  • Example Results: Fit of DNA digestDigest of pPOL-1 208-12. Individual fragments can be distinguished. Back
  • Example Results: Protein – 1 day old CuZn Superoxide Dismutase Mutant - Metalated form, freshlyBack purified (Data provided by P.J. Hart &SaiVenkateshSeetharaman)
  • Example Results: Protein – 7 days oldBack Apo-form showing clear signs of degradation
  • A B BC D Example: Clathrin baskets assembling from clathrintriskelia (A). The sample also displays several nonglobular species which represent the building block subunits required for assembly of intact baskets (B, D). Sample shows a large heterogeneity of different sized baskets that assume a mostly globular form with Back a unity frictional ratio (B,C). (Data kindly provided by E. Lafer, UTHSCSA, Dept. of Biochemistry)
  • TeraGrid Science Gateway •Center for Analytic Ultracentrifugation of Macromolecular Assemblies •http://cauma.uthscsa.eduBack
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  • TG SG Usage 2007-10• Job statistics for UltraScan project forapproximately the last 4 years.• Only partial data is available for 2007(2nd half) and 2010 (thru June), and onlysuccessful runs are included. •Totals of CPU hours consumed from TeraGrid, UTHSCSA and international resources •Number of investigators whose data were analyzed (left Y-axis), and number of submitted jobs (right Y-axis).• Both panels indicate increasing usageand need for TeraGrid resources and anincreasing number of investigatorsrequiring access to these resources. Back
  • GFAC Integration UltraScan job submission previously relied on GRAM4 GFAC integrated as middleware to abstract submission process  GRAM5, UNICORE and any future mechanism Science Gateway is in active use Initial testing done on IU quarry node Extensively tested job submission process using GFAC to LONIsQueenBee and TACCs Ranger Deployed 26 October 2010 Implementation details available http://wiki.bcf.uthscsa.edu/cauma/wiki/US2GFACTesting Back
  • User Community: Publications Since the development of our advanced methods, virtually every publication from our lab has used these methods We currently count 35 peer reviewed journal publications and poster abstracts Many additional presented talks where these methods have provided important new detail to the investigations of biological as well as synthetic polymer systems We are aware of at least another 25 publications that were facilitated by our methods from other laboratories using our TeraGrid applications Back
  • User Community: Publications Major problems successfully addressed with our methods include: Studies of aggregation inhibition of amyloid beta peptide by designed beta- sheet breaker peptides, the structure of the Hsp110:Hsc70 nucleotide exchange machineSchuermann JP, Jiang J, Cuellar J, Llorca O, Wang L, Gimenez LE, Jin S, Taylor AB, Demeler B, Morano KA, Hart PJ, Valpuesta JM, Lafer EM, Sousa R. Structure of the Hsp110:Hsc70 nucleotide exchange machine. Mol Cell. 2008 Jul 25;31(2):232-43. Epub 2008 Jun 12.PMID: 18550409 De-amidation effects on aggregation of eye lens protein betaA3-crystallin Takata T, Oxford JT, Demeler B, Lampi KJ. Deamidation destabilizes and triggers aggregation of a lens protein, betaA3-crystallin. Protein Sci. 2008 Sep;17(9):1565-75. Epub 2008 Jun 20.PMID: 18567786 Studies of band-gaps of CdTenanoparticles using the innovative multi- wavelength analysis Back
  • User Community: Publications• A few additional publications: Lee YS, Lee S, Demeler B, Molineux IJ, Johnson KA, Yin YW. Each monomer of the dimeric accessory protein for human mitochondrial DNA polymerase has a distinct role in conferring processivity. J Biol Chem. 2009 Oct 28. [Epub ahead of print] PMID: 19858216 Whidby J, Mateu G, Scarborough H, Demeler B, Grakoui A, Marcotrigiano J. Blocking hepatitis C virus infection with recombinant form of envelope protein 2 ectodomain. J Virol. 2009 Nov;83(21):11078-89. Epub 2009 Aug 26.PMID: 19710151 Xiao F, Cai Y, Wang JC, Green D, Cheng RH, Demeler B, Guo P. Adjustable ellipsoid nanoparticles assembled from re-engineered connectors of the bacteriophage phi29 DNA packaging motor. ACS Nano. 2009 Aug 25;3(8):2163-70.PMID: 19634910 Nagel-Steger L, Demeler B, Meyer-Zaika W, Hochdörffer K, Schrader T, Willbold D. Modulation of aggregate size- and shape-distributions of the amyloid-beta peptide by a designed beta-sheet breaker. EurBiophys J. 2009 Feb 24. [Epub ahead of print]PMID: 19238376 Demeler B, Brookes E, Nagel-Steger L. Analysis of heterogeneity in molecular weight and shape by analytical ultracentrifugation using parallel distributed computing. Methods Enzymol. 2009;454:87-113.PMID: 19216924 Chinnaswamy S, Yarbrough I, Palaninathan S, Kumar CT, Vijayaraghavan V, Demeler B, Lemon SM, Sacchettini JC, Kao CC.A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase. J Biol Chem. 2008 Jul 18;283(29):20535-46. Epub 2008 Apr 28.PMID: 18442978 Yuan P, Leser GP, Demeler B, Lamb RA, Jardetzky TS. Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein. Virology. 2008 Sep 1;378(2):282-91. Epub 2008 Jul 2.PMID: 18597807 Back
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  • User Community: Laboratories• 1. Academia Sinica, Institute of Biological Chemistry - Taiwan• 2. Amylin Pharmaceuticals, Inc. - San Diego, California• 3. A. H. Bakh Institute of Biochemistry - Russian Academy of Sciences, Moscow, Russia• 4. Burnet Institute - Melbourne, Australia• 5. Charles University - Prague, Czech Republic• 6. Center for Analytical Ultracentrifugation, EMBL - Heidelberg, Germany• 7. Colorado State University - Fort Collins, Colorado• 8. EcolePolytechniqueFédérale de Lausanne - Lausanne, Switzerland• 9. Florida State University - Tallahassee, Florida• 10. ForschungsinstitutfürMolekularePharmakologie - Berlin, Germany• 11. Heinrich Heine University - Düsseldorf, Germany• 12. IGBMC - Strassbourg, France• 13. Indiana University - Bloomington, Indiana• 14. Keck Biophysics Facility, Northwestern University - Evanston, Illinois• 15. Marshall University - Huntington, West Virginia• 16. Max Planck Institute for Colloids and Interfaces - Golm, Germany• 17. McGill University - Montreal, Canada• 18. MD Anderson Cancer Center - Houston, Texas• 19. NIH - NHLBI - Bethesda, Maryland• 20. Oregon State University - Oregon State University, Corvallis, Oregon• 21. Osaka University - Osaka Japan• 22. Pasteur Institute - Paris, France• 23. Public LIMS Portal - Open Access Back
  • User Community: Laboratories• 24. Rice University - Houston, Texas• 25. Shriners Hospital for Crippled Children - Portland, Oregon• 26. Southern Illinois University Carbondale - Carbondale, Illinois• 27. State University New York (SUNY) - Albany, New York• 28. Stony Brook University - Stony Brook, New York• 29. TechnischeUniversitätMünchen - Garching, Germany• 30. Texas A&M University - College Station, Texas• 31. University of Bristol - Bristol, UK• 32. University of Illinois, Chicago - Chicago, Illinois• 33. University of Mainz, Molecular Biophysics - Mainz, Germany• 34. University of Massachusetts, Medical School - Worcester, Massachusetts• 35. University of Melbourne, Australia - Melbourne, Victoria• 36. University of Michigan - Ann Arbor, Michigan• 37. University of Missouri, Columbia - Columbia, Missouri• 38. University of Montana - Missoula, Montana• 39. National Center for Macromolecular Hydrodynamics, University of Nottingham - Nottingham, UK• 40. University of Texas at Austin - Austin, Texas• 41. University of Texas Health Science Center - San Antonio, Texas• 42. University of Toronto - Toronto, Canada• 43. University of Utrecht - Utrecht, Netherlands• 44. University of Victoria - British Columbia, Canada• 45. University of Washington - Seattle, Washington• 46. University of Washington, Klevit Lab - Seattle, Washington Back
  • Future Improved gateway ASTA, GFAC Multiwavelength data Datasets 3 orders of magnitude larger MD simulation DMD BD Global solution studies Multiple AUC experiments DLS SAXS/SANS Back
  • AcknowledgmentsThanks to: IU Raminder Singh, Suresh Marru, Marlon Pierce TACC: Chris Hempel, Margaret Murray, Jay Boisseau SDSC Nancy Wilkins-Diehr LONI Our team at UTHSCSA: Jeremy Mann, Bruce Dubbs, Dan Zollars, Gary Corbet, Virgil Schiff.Support  To Demeler: NIH/NCRR 1R01 RR022200 NIH/NCRR 3R01RR022200-03S1 NSF TG-MCB070039,40 NSF/ASTA TG-MCB07038  To Brookes NIH/NIGMS 1K25GM090154-01A1Back NSF OCI-1032742
  • Thank YouThe OGCE Project is funded by the NSF Office of Cyberinfrastructure SDCI Program