Overview ofAnalysis Result Manager         (ARM)      Jeremy Magland       27 October, 2011  brainomics group @ Penn
Motivations for ARMO Motivation #1:VisualizationI wanted to be able toSEE my fMRI data,intermediate files, andprocessing r...
Motivations for ARMO Motivation #2:                            Bone-Water Study                            Real-time Study...
Motivations for ARMO Motivation #3:Computing PowerUtilize the processingpower of servercomputers (CPUpower, RAM,automatic ...
Motivations for ARMO Motivation #4:Provenance TrackingTrack the processingsteps required toreproduce eachintermediate obje...
Challenge: Richly Interactive,Web-based Data VisualizationO Browser-based                           O RemoteWidgets:  appl...
RemoteWidgets: Overview                           SeegullO Write a GUI for the  web using only one                 ARM  pr...
RemoteWidgets:     One App, Two Access Options                       Seegull in Web BrowserO Web Browser  Interface (jQuer...
RemoteWidgets: Hello, World!
RemoteWidgets:      Server-Side Event HandlingO Handling GUI events is as easy as connecting Qt signals and slots on the s...
RemoteWidgets: IdeaO Interactive, desktop-style visualization tools  available from the convenience of a web  browser.
Analysis Result Manager             (ARM)O Cloud-based  approach to fMRI  data management,  visualization, and  analysis.O...
Tradeoff Between    Scripting and GUI for fMRI ProcessingO Scripting is way more powerful for research purposes.  And, if ...
ARM: Script-Generated WorkflowsWith Robust Tracking of Provenance Data   The multi-threaded processing     The script imme...
Processors are Generic PluginsC++ Wrappers (for FSL, SPM, etc) Views are also plugins… (custom views of custom datatypes)
Live ARM DemonstrationO   Upload Scan Data                   O   View processing results andO   Online view, change view  ...
Live Seegull DemonstrationO It is often desirable to SHARE results with others.  But you don’t always want to give them ac...
Summary and FutureO Share interactive views of dataO Taking full advantage of cloud technology    to manage, process, visu...
Especially Thank You to…O Anna Rose ChildressO Felix WehrliO Charlie EpsteinAnd…O   Benny Lam        O   John Detre     O ...
Analysis Result Manager (ARM)
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Analysis Result Manager (ARM)

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Introduction to a new web-based functional MRI study management system.

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Analysis Result Manager (ARM)

  1. 1. Overview ofAnalysis Result Manager (ARM) Jeremy Magland 27 October, 2011 brainomics group @ Penn
  2. 2. Motivations for ARMO Motivation #1:VisualizationI wanted to be able toSEE my fMRI data,intermediate files, andprocessing results,and to share thesewith my collaborators.
  3. 3. Motivations for ARMO Motivation #2: Bone-Water Study Real-time Study Subject AP-1Data Management REAL_23 Localizer Sample Session 1 Baseline, TR=300Organize fMRI data text Raw fMRI series Follow-up 1, TR=300 About Anatomic localizeron a central server, study Session 2 Bone-Water Study Stuff REAL_36 Subject AP-1and access it from To fill Session 1 Localizer sapace Session 2 Baseline, TR=300anywhere (cloud Follow-up 1, TR=300style)
  4. 4. Motivations for ARMO Motivation #3:Computing PowerUtilize the processingpower of servercomputers (CPUpower, RAM,automatic parallelprocessing)
  5. 5. Motivations for ARMO Motivation #4:Provenance TrackingTrack the processingsteps required toreproduce eachintermediate object andprocessing result.Advantages:* reproducibility* auto-non-redundantprocessing
  6. 6. Challenge: Richly Interactive,Web-based Data VisualizationO Browser-based O RemoteWidgets: applications are very convenient but often O Framework for have limited developing functionality.O Desktop applications desktop can have rich applications in Qt4 functionality. However with option to there are some cons: O software deploy on browser. downloads/updates O OS incompatibility O Security risks O Etc.
  7. 7. RemoteWidgets: Overview SeegullO Write a GUI for the web using only one ARM programming language: Qt4/C++O Rapid development Pickles of highly interactive web applications.O Direct access to Math Puppy server-side processes.
  8. 8. RemoteWidgets: One App, Two Access Options Seegull in Web BrowserO Web Browser Interface (jQuery)O Desktop Interface (thin client download) Seegull on Desktop
  9. 9. RemoteWidgets: Hello, World!
  10. 10. RemoteWidgets: Server-Side Event HandlingO Handling GUI events is as easy as connecting Qt signals and slots on the server… no javascript coding needed.
  11. 11. RemoteWidgets: IdeaO Interactive, desktop-style visualization tools available from the convenience of a web browser.
  12. 12. Analysis Result Manager (ARM)O Cloud-based approach to fMRI data management, visualization, and analysis.O ARM is a RemoteWidgets application, and can therefore be accessed remotely via a web browser.
  13. 13. Tradeoff Between Scripting and GUI for fMRI ProcessingO Scripting is way more powerful for research purposes. And, if you have a good script interface, you could always throw a GUI on top of it.O But… some problems with Matlab-style scripting: O Need to manually shuffle data around in files/folders O Not easy to remember exactly which parameters were used >2 days ago O Run a 10-hour script, and discover the last line had a bug.
  14. 14. ARM: Script-Generated WorkflowsWith Robust Tracking of Provenance Data The multi-threaded processing The script immediately sets up module then executes each a workflow, creating all processors as soon as all input intermediate and result objects objects have been defined. ahead of the processing, storing detailed information about how objects are related via processes.
  15. 15. Processors are Generic PluginsC++ Wrappers (for FSL, SPM, etc) Views are also plugins… (custom views of custom datatypes)
  16. 16. Live ARM DemonstrationO Upload Scan Data O View processing results andO Online view, change view intermediate files. settings O Show provenance (processO Super-efficient browsing of huge history) of the output objects. data files. O Explain that changing scan id’sO Browser access to same app and even names of theO View example script processors causes no problems. Key assumption:O Running script does nothing objects, once created, never because processing has already change. completed O Clean up by deleting results. (InO Change design function and re- future, intermediate files will be run script – show how auto-removed after a period if processes are queued and they are no longer linked to executed in proper order (No results) redundant processing). O In development – share a processing result by a button click.
  17. 17. Live Seegull DemonstrationO It is often desirable to SHARE results with others. But you don’t always want to give them access to a huge system. Furthermore, since ARM is highly dynamic, you want to be sure that a result, once shared, is available for ever after (snapshot of a result)O Hence, Seegull
  18. 18. Summary and FutureO Share interactive views of dataO Taking full advantage of cloud technology to manage, process, visualize, compare fMRI data analysesO Script-generated workflowsO Automatic provenance trackingO Convenient access via web browserO Import publicly available fMRI studies into system (powerful meta-analyses)
  19. 19. Especially Thank You to…O Anna Rose ChildressO Felix WehrliO Charlie EpsteinAnd…O Benny Lam O John Detre O Chris TjoaO Oscar Bartra O Jesse Lupardus O Brian AvantsO Kimberly Young O Ning ZhangO Dan Willard O Cheng LiO Rob Fabianski O Ze Wang

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