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

2. 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

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

4. Manage data using metadata

5. Atmosphere: Free cloud computing https://atmo.iplantcollaborative.org/

6. Bisque: Image management

7. Bulk image analysis

8. Agave API: Science as a Service platform

9. http://agaveapi.co/tools/command-line-interface/

10. http://preview.agaveapi.co/tools/client-sdk/

11. Hands-on activity 1. Using the DE for analyzing data 2. Introduction to Bisque

12. 1. Data analysis using the Discovery Environment

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

14. Setting DE preferences

15. Analysis window in DE

16. 2. Bisque: Enabling Cloud and Grid PoweredImage Analysis

17. 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

18. Bisque Image Management, Analysis, Sharing System

19. 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

20. 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)

21. Cleared Leaf Image Database: http://charlus.iplantcollaborative.org/ http://charlus.iplantcollaborative.org/

22. Main application: http://bisque.iplantcollaborative.org/ Bisque user manual on iPlant: https://pods.iplantcollaborative.org/wiki/display/BIS/Using+the+ Bisque+Image+Analysis+System https://pods.iplantcollaborative.org/wiki/display/BIS/Using+the+ Bisque+Image+Analysis+System Bisque video tutorials: http://bovary.iplantcollaborative.org/client_service/help Support http://ask.iplantcollaborative.org Bisque wiki: http://biodev.ece.ucsb.edu/projects/bisquik/wiki Useful Links

23. 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

24. Sharing Easy modes: “Private” and “Published” Flexible sharing for resources Using E-mails of collaborators Read-only or Full access Easy modes: “Private” and “Published” Flexible sharing for resources Using E-mails of collaborators Read-only or Full access

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