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

Upload and download

Upload the file ex.pl.fasta from http://bit.ly/1euy02s

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