IPlant Collaborative Hands-on Cyberinfrastructure Workshop – Part 2 R. Walls University of Arizona...
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Transcript of IPlant Collaborative Hands-on Cyberinfrastructure Workshop – Part 2 R. Walls University of Arizona...
![Page 1: IPlant Collaborative Hands-on Cyberinfrastructure Workshop – Part 2 R. Walls University of Arizona Biodiversity Information Standards (TDWG) Sep. 29, 2015,](https://reader035.fdocuments.us/reader035/viewer/2022062315/56649f065503460f94c1b595/html5/thumbnails/1.jpg)
iPlant CollaborativeHands-on Cyberinfrastructure
Workshop – Part 2R. Walls
University of ArizonaBiodiversity Information Standards (TDWG)
Sep. 29, 2015, Nairobi, Kenya
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iPlant data analysis platformsDiscovery Environment (DE): web based graphical user
interface
Atmosphere: Cloud computing
Bisque: Image management and analysis
Agave: “Science as a service” API
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Discovery Environment (DE): Web-based graphical interface for
high-performance computing
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Manage data using metadata
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Atmosphere: Free cloud computing
https://atmo.iplantcollaborative.org/
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Bisque: Image management
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Bulk image analysis
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Agave API: Science as a Service platform
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http://agaveapi.co/tools/command-line-interface/
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http://preview.agaveapi.co/tools/client-sdk/
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Hands-on activity1. Using the DE for analyzing data
2. Introduction to Bisque
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1. Data analysis using the Discovery Environment
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Setting DE preferences
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Analysis window in DE
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2. Bisque: Enabling Cloud and Grid PoweredImage Analysis
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Bisque-iPlant TeamBisque (U. California, Santa Barbara)
B. S. ManjunathKris KvelikvalDmitry Fedorov
iPlant (U. Arizona, Tucson)Nirav MerchantMartha NarroRamona Walls
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BisqueImage Management, Analysis, Sharing System
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Why Bisque?Biologists can
Manage images using metadataChoose from multiple analysis options Overlay results to validate findingsAnnotate imagesShare images, results, annotations via secure links
Algorithm developers can Publish new analysis methods, easily make them web
accessibleProduce interactive plots, visualizations using built-in API
Integrated with iPlant storage and computation infrastructure for scalability
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Bisque Features
Web application
Tiling, zooming, step through image stacks, play as movie
Display 20K x 20K pixel images in web browser
Handles 100+ image, video formats
Import large image sets (≤ 40 GB via Bisque), extremely large ones (> 40 GB via iPlant Data Store)
Scale analyses using distributed computing (connected to XSEDE) and workflow engines (Pegasus, Condor)
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Cleared Leaf Image Database: http://charlus.iplantcollaborative.org/
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Main application:http://bisque.iplantcollaborative.org/
Bisque user manual on iPlant: https
://pods.iplantcollaborative.org/wiki/display/BIS/Using+the+Bisque+Image+Analysis+System
Bisque video tutorials:http://bovary.iplantcollaborative.org/client_service/help
Supporthttp://ask.iplantcollaborative.org
Bisque wiki:http://biodev.ece.ucsb.edu/projects/bisquik/wiki
Useful Links
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Import and Export
•support for multiple files•plugin free HTML5 uploads•drag/drop• import annotations•processing compressed files•compose 5D from multiple files
•on the file streaming export•dataset export•export annotations•compressed files: Tar, GZip, Zip, BZip
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Sharing
Easy modes: “Private” and “Published”
Flexible sharing for resourcesUsing E-mails of
collaborators Read-only or Full
access
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Example Analysis: Seed SizeHigh resolution flat bed scanner image of seeds
Edge detection and analysis by Bisque
Source: Edgar Spalding