iplant collaborative hands-on cyberinfrastructure workshop – part 2 r. walls university of arizona...
TRANSCRIPT
iPlant CollaborativeHands-on Cyberinfrastructure
Workshop – Part 2R. Walls
University of ArizonaBiodiversity Information Standards (TDWG)
Sep. 29, 2015, Nairobi, Kenya
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
Discovery Environment (DE): Web-based graphical interface for
high-performance computing
Manage data using metadata
Atmosphere: Free cloud computing
https://atmo.iplantcollaborative.org/
Bisque: Image management
Bulk image analysis
Agave API: Science as a Service platform
http://agaveapi.co/tools/command-line-interface/
http://preview.agaveapi.co/tools/client-sdk/
Hands-on activity1. Using the DE for analyzing data
2. Introduction to Bisque
1. Data analysis using the Discovery Environment
Setting DE preferences
Analysis window in DE
2. Bisque: Enabling Cloud and Grid PoweredImage Analysis
Bisque-iPlant TeamBisque (U. California, Santa Barbara)
B. S. ManjunathKris KvelikvalDmitry Fedorov
iPlant (U. Arizona, Tucson)Nirav MerchantMartha NarroRamona Walls
BisqueImage Management, Analysis, Sharing System
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
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)
Cleared Leaf Image Database: http://charlus.iplantcollaborative.org/
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
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
Sharing
Easy modes: “Private” and “Published”
Flexible sharing for resourcesUsing E-mails of
collaborators Read-only or Full
access
Example Analysis: Seed SizeHigh resolution flat bed scanner image of seeds
Edge detection and analysis by Bisque
Source: Edgar Spalding