The document discusses Open Gateway Computing Environments (OGCE) and its software components. OGCE develops secure web-based science gateways for fields like chemistry, bioinformatics, biophysics, and environmental sciences. It is funded by the NSF. Key OGCE software includes the Gadget Container, GFAC for invoking scientific applications on grids and clouds, and workflow tools. Partners include Indiana University, NCSA, Purdue University, and UTHSCSA. The document provides examples of OGCE components in action, like UltraScan, GridChem, and BioVLAB. It also discusses building simple grid gadgets and computational chemistry workflows with GridChem.

1. Open Gateway Computing Environments
Marlon Pierce, Suresh Marru, Yan Liu,
Carol Song, SudhakarPamidighantam, and
Emre Brookes

2. Workshop Agenda
About OGCE
The OGCE Gadget Container
Building SimpleGridGadgets
GWT Gadgets and HUBZero Portability
Bioinformatics Workflows in the Cloud: BioVLAB
Computational Chemistry Workflows: GridChem
Managing Biophysical Data Analysis: UltraScan

3. About OGCE
http://www.collab-ogce.org
http://collab-ogce.blogspot.com
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4. 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.
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5. OGCE Funds Full Gateway Software Lifecyle
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6. OGCE Software
Name Description
OGCE 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 Clouds
Workflow 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
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7. OGCE Partners and People
Institution People
Indiana University Marlon Pierce, Suresh Marru, Raminder Singh,
ArchitKulshrestha, Gerald Guo
NCSA/UIUC SudhakarPamidighantam, Shaowen Wang, Yan Liu
Purdue University Carol Song, Lan Zhao, David Braun, Shawn Wu
UTHSCSA Emre Brookes, BorriesDemeler, Bruce Dubbs
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8. OGCE Components in Action
FeaturedGateway OGCE Components Used
UltraScan GFAC scientific application management service
GridChem,ParamChem XBaya workflow composer, OGCE Messenger Service, XRegistry
SimpleGrid OGCE Gadget Container (in development)
Purdue CCSM Portal Gadget Container and gadget building libraries (in development)
BioVLAB GFAC, XBaya,XRegistry, Workflow Interpreter Service
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9. 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, SanjivaWeeravarna
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10. 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
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11. The OGCE Gadget Container
Managing layouts, look and feel, and
behind-the-scenes services for
aggregated Web gadgets
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12. The OGCE Gadget Container allows you to build portals out of public and private Google
Open Social gadgets. Supports HTTPS. Downloadable, packaged software.
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13. The OGCE Application Registry gadget allows users to interactively register hosts and
applications that are dynamically wrapped as Web services.
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14. The OGCE Experiment Builder gadget allows users to create projects and
experiments out of previously composed workflows.
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15. Google Gadget-Based Science Gateways
PolarGrid
LEAD
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16. 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.

17. Feature Groups Features
Look 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 login
Inter-Gadget Supports OpenAjax publish-subscribe style messaging between gadgets. PMRPC
Communication JavaScript messaging support in development
REST 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.
Networking
Gadget Development Support for GWT-based gadgets and YUI JavaScript libraries in development.
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18. Bioinformatics Workflows in the Cloud
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19. 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
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20. Architecture – Complete View
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21. How to use BioVLAB
1. Get an Amazon account
2. Download workflow
3. Run the workflow
Usability!
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22. BioVLAB Application
Development Procedure
User
• 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 Gfac
User
• Instantiate EC2 and run the app. by using XBaya
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23. BioVLAB-Microarray
• Analysis of high throughput
microarray experiment
• Multiple tasks in a single
batch
• Output of a task can plugged
into another task
• Repeat the same set of tasks
with small changes of
parameters
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24. EXPERIMENTS
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25. • 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 integrated
analysis
BioVLAB-MMIA
• Computation in the Cloud
• MMIA expertise in workflow
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26. Back

27. BioVLAB-mCpG
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28. 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.
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29. Building SimpleGrid Gadgets
Yan Liu, UIUC
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30. 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
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31. SimpleGrid Science Gateway
• Web 2.0 Rich Client
• Web Server
• Application Web Service
• SimpleGrid API
• TeraGrid Middleware
• TeraGrid Resources
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32. 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
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33. Application Example: TeraGrid-based
Spatial Interpolation
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34. SimpleGrid API
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35. Web Service Development
• A Simple Tool for
Automatic Web
Service Package
Generation
• Axis2-based
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36. 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, customizable
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37. 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
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38. Building GWT Gadgets and Gadget
Integration Across OGCE and HUBZero
Carol Song, Purdue
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39. 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)

40. The Team
Institution People
Lead and coordinator for Carol Song
Purdue
Architecture, web David Braun, Shawn Wu
technology, common
components
Science gateway gadget Lan Zhao, Shawn Wu, Carol Song
development

41. 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.

42. 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.

43. PMRPC Example
Browser
Data Browser Image Viewer
Gadget (client) Gadget (server)
Register view
function view
call view
pmrpc pmrpc

44. 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

45. Same gadget in three environments

47. 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)

48. Computational Chemistry Workflows:
GridChem
SudhakarPamidighantam
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49. GridChem Workflow Demo

50. Back

51. Managing Biophysical Data Analysis:
UltraScan
Emre Brookes, UTHSCSA
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52. OGCE: UltraScan: High-resolution Modeling of Analytical
Ultracentrifugation Experiments on TeraGrid
Emre Brookes
BorriesDemeler
Department of Biochemistry
16 November 2010
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53. 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
 Future
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54. Background: What is AUC ?
 AUC is an important technique for the solution study of
macromolecules
 Molecules are not fixed to a microscope grid
 Molecules are not distorted by crystal packing forces (vs X-Ray
crystallography)
 Very large size range (complements cryo-EM and NMR)
 Dynamic processes can be studied
 Conformational changes
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55. Background: What is AUC ?
 Sample placed in cell
 Run Ultracentrifuge
Usually 20-60k RPM
 Collect data
4 to 24 hours or more
 Analyze the data
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56. 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
Radius
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57. Background: How do we obtain results?
 The Lamm equation is a PDE which describes an ideal solute (a molecule in
solution).
∂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
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58. 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
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59. Example Results: Fit of DNA digest
Digest of pPOL-1 208-12. Individual fragments can be distinguished.
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60. Example Results: Protein – 1 day old
CuZn Superoxide Dismutase Mutant - Metalated form, freshly
Back purified
(Data provided by P.J. Hart &SaiVenkateshSeetharaman)

61. Example Results: Protein – 7 days old
Back Apo-form showing clear signs of degradation

62. A
B
B
C 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)

63. TeraGrid Science Gateway
•Center for Analytic Ultracentrifugation of Macromolecular Assemblies
•http://cauma.uthscsa.edu
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66. Back

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68. Back

69. Back

70. TG SG
Usage 2007-10
• Job statistics for UltraScan project for
approximately the last 4 years.
• Only partial data is available for 2007
(2nd half) and 2010 (thru June), and only
successful 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 usage
and need for TeraGrid resources and an
increasing number of investigators
requiring access to these resources.
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71. 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 LONI'sQueenBee and
TACC's Ranger
Deployed 26 October 2010
Implementation details available
http://wiki.bcf.uthscsa.edu/cauma/wiki/US2GFACTesting
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72. 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
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73. 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
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74. 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
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75. Back

76. 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
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77. 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
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78. 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
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79. Acknowledgments
Thanks 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 1K25GM090154-01A1
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80. Thank You
The OGCE Project is funded by the NSF
Office of Cyberinfrastructure SDCI
Program