iPlant Collaborative Hands-on Cyberinfrastructure Workshop – Part 2 R. Walls University of Arizona Biodiversity Information Standards (TDWG) Sep. 29, 2015, Nairobi, Kenya

iPlant data analysis platforms Discovery Environment (DE): web based graphical user interface Discovery Environment Atmosphere: Cloud computing Atmosphere Bisque: Image management and analysis Bisque Agave: “Science as a service” API Agave

Discovery Environment (DE): Web-based graphical interface for high-performance computing

Manage data using metadata

Atmosphere: Free cloud computing

Bisque: Image management

Bulk image analysis

Agave API: Science as a Service platform

Hands-on activity 1. 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

Setting DE preferences

Analysis window in DE

2. Bisque: Enabling Cloud and Grid PoweredImage Analysis

Bisque-iPlant Team Bisque (U. California, Santa Barbara) B. S. Manjunath Kris Kvelikval Dmitry Fedorov iPlant (U. Arizona, Tucson) Nirav Merchant Martha Narro Ramona Walls

Bisque Image Management, Analysis, Sharing System

Why Bisque? Biologists can Manage images using metadata Choose from multiple analysis options Overlay results to validate findings Annotate images Share images, results, annotations via secure links Algorithm developers can Publish new analysis methods, easily make them web accessible Produce 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:

Main application: Bisque user manual on iPlant: Bisque+Image+Analysis+System Bisque+Image+Analysis+System Bisque video tutorials: Support Bisque 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 resources Using s of collaborators Read-only or Full access Easy modes: “Private” and “Published” Flexible sharing for resources Using s of collaborators Read-only or Full access

Example Analysis: Seed Size High resolution flat bed scanner image of seeds Edge detection and analysis by Bisque Source: Edgar Spalding