1. The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop iCommands and Other Data Store Resources

2. Access the Data Store with iCommands Advantage + Disadvantage - Customizability Requires some expertise  Ability to script and automate  Access from terminal/server  Can resume transfers

3. Access the Data Store with iCommands From DE: /iplant/home/jdebarry/UGA_DEMO  iget./HAL-AnnotatedProteins.fasta. From Local Folder: /Users/jdebarry/Dropbox/UGA_Workshop/0_To_Data_Store  iput HAL-AnnotatedProteins.fasta. https://pods.iplantcollaborative.org/wiki/display/DS/Using+iCom mandshttps://pods.iplantcollaborative.org/wiki/display/DS/Using+iCom mands

4. Tips -f force - overwrite local files -P output the progress of the download. -r recursive - retrieve subcollections (directories) -T renew socket after 10 min.(use with large files) -V Very verbose Useful iget / iput options:

5. iCommands to view and edit metadata Ability to interact with metadata at the command line Already installed as part of iCommands Documentation is a little wimpy Try Here and HereHere

6. Associate Metadata with iCommands From DE/iplant/home/jdebarry/HT_TEST_Data  imeta ls –D PiroplasmaDB- 3.0_BmicrotiRI_AnnotatedProteins.fasta  imeta add -D PiroplasmaDB- 3.0_BmicrotiRI_AnnotatedProteins.fasta test_attribute test_value  imeta rm -D PiroplasmaDB- 3.0_BmicrotiRI_AnnotatedProteins.fasta test_attribute test_value

7. Tips At the moment, metadata added via template is not available from the command line

8. iDrop Desktop Synchronization 1.Click on Settings 2.Click on the Synchronization tab 3.Click New to start a new synchronization 4.Enter a name (e.g. Project 1 sequence data) 5.Click Choose Local Folder to select a folder 6.Select a synchronization mode 7.Select a frequency for synchronization 8.Click Choose iRODS Folder to select the location to synch to 9.Click Update to save your synchronization

9. Tips  Choose one of three methods to synchronize files: Local > iRODS – files will copied at synch to Data Store Local < iRODS – Data Store files copied to local computer at sync Local <> iRODS –Data Store files and local computer both synced If syncing to a DropBox folder, Dropbox must be paused during set up

10. From Data to Project Management The iPlant Data Commons (coming soon)

11. Data, Project, Research Management In the iPlant Data Commons Manage projects and track analyses over the data lifecycle Metadata templates and workflows for common analysis types Automated gap analyses for metadata standards Publish data/metadata to the Data Commons and supported external repositories with appropriate long-term identifiers and licenses (e.g., DOIs) Home for high-value public dataset to be used with iPlant analysis tools Data will be static, discoverable, reusable, and linked to external repositories Development underway…

12. Data Commons Development Plans

13. Goal: Data models and workflows for the entire data lifecycle specimen collection analysis project creation publication

14. NCBI Sequence Read Archive Tease… Simplify as part of Data Commons ‘Push Button’ Gap analysis to collect missing metadata Generate submission package Testing, in progress for other repositories

15. We Look Forward to Working With You! Get your account at www.iplantcollaborative.org/www.iplantcollaborative.org/ iPlant Learning Center for tutorials and documentationiPlant Learning Center ask.iplantcollaborative.org/questions/ jdebarry@iplantcollaborative.org

16. Detailed instructions with videos, manuals, documentation in Learning Center Keep asking: ask.iplantcollabortive.org

17. The iPlant Collaborative is funded by a grant from the National Science Foundation Plant Cyberinfrastructure Program (#DBI-0735191).