1. iPlant Collaborative Hands-on Cyberinfrastructure Workshop - Part 1 R. Walls University of Arizona Biodiversity Information Standards (TDWG) Sep. 28, 2015, Nairobi, Kenya

2. iPlant Cyberinfastructure It’s not just for plants! http://www.ssec.si.edu/blog/phylogenetic_trees#.VciwmUU7Rek

3. Cyberinfrastructure (CI) is: data storage software hardware high-performance computing people …used to solve problems of size and scope that would not otherwise be solvable.

4. iPlant Campus Champions

5. iPlant: Layer Cake

6. iPlant Data Store is the heart of our CI All registered users have 100 GB free allocation, can easily request 1TB or more for shared projects Cyberduck

7. Fast Parallel Data Transfers SourceTime (sec) CD320 Berkeley Server150 External Drive36* USB2.0 Flash30 iPlant Data Store 18* My Computer15 Time to move 1GB of data from UC Berkeley to iPlant Data Store and other locations. Based on 100 GB transfer. Will be limited by local network speed.

8. Multiple Access Modes https://pods.iplantcollaborative.org/wiki/display/DS/Accessing+Data+in+t he+iPlant+Data+Store

9. iPlant Tools and Services https://community.lego.com/t5/LEGO-General/What- does-LEGO-mean/td-p/4318550

10. tnrs.iplantcollaborative.org

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

12. Tutorial: https://pods.iplantcollaborative.org/wiki/display/sciplant/NCBI+Sequence+Read+Archiv e+%28SRA%29+Submission+-+Workflow+and+Tutorial SRA sequence submission pipeline through the DE Apps for submitting via an existing or new BioProject Biosamples created as part of the pipeline Metadata templates for all SRA sample types Handles generation of XML file, data transfer, validation

13. Manage data with metadata

14. Atmosphere: Free and easy cloud computing https://atmo.iplantcollaborative.org/

15. Bisque: Image management

16. Graphical and text annotations total_length scale Custom graphical annotation types 140,319,0,0,0; 467,317,0,0,0;

17. Bulk image analysis

18. Agave API: Science as a Service platform

19. Interacting with iPlant Extended Collaborative Support (ECS) – Take advantage of iPlant’s existing components to build and share a new workflow. Powered by iPlant – develop your own front end, use our authentication, storage, and permission services and APIs iPlant Community Collaborations – use iPlant to host data and analyses for your research community

20. http://www.iplantcollaborative.org/ https://pods.iplantcollaborative.org/wiki/display/start/Getting+ Started+with+iPlant

21. http://www.iplantcollaborative.org/learning-center/get-started

22. Hands-on activity Accessing the iPlant Data Store http://bit.ly/1euy02s

23. Public access without login http://mirrors.iplantcollaborative.org/

24. Accessing data via the DE

25. Upload and download

26. Sharing permissions

27. Sharing a file with a public link

28. Cyberduck To install Cyberduck for your operating system for the first time: https://cyberduck.io/.https://cyberduck.io/ Configure Cyberduck for use with the Data Store (one-time only) Browse your folders in the data store upload and download a file Browse anonymous data Transfer file from ftp site https://pods.iplantcollaborative.org/wiki/display/DS/Using+Cyberduck+for+U ploading+and+Downloading+to+the+Data+Store

29. iCommands https://pods.iplantcollaborative.org/wiki/display/DS/Using+ iCommands iinit – authentication ils – list constents of a directory icd – change directories iget – download a file iput – upload a file