iplant collaborative hands-on cyberinfrastructure workshop - part 1 r. walls university of arizona...
TRANSCRIPT
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iPlant CollaborativeHands-on Cyberinfrastructure
Workshop - Part 1R. Walls
University of ArizonaBiodiversity Information Standards (TDWG)
Sep. 28, 2015, Nairobi, Kenya
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iPlant CyberinfastructureIt’s not just for plants!
http://www.ssec.si.edu/blog/phylogenetic_trees#.VciwmUU7Rek
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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.
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iPlant Campus Champions
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iPlant: Layer Cake
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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
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Fast Parallel Data Transfers
Source Time (sec)
CD 320
Berkeley Server 150
External Drive 36*
USB2.0 Flash 30
iPlant Data Store 18*
My Computer 15
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.
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Multiple Access Modes
https://pods.iplantcollaborative.org/wiki/display/DS/Accessing+Data+in+the+iPlant+Data+Store
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iPlant Tools and Services
https://community.lego.com/t5/LEGO-General/What-does-LEGO-mean/td-p/4318550
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tnrs.iplantcollaborative.org
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Discovery Environment (DE): Web-based graphical interface for
high-performance computing
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Tutorial: https://pods.iplantcollaborative.org/wiki/display/sciplant/NCBI+Sequence+Read+Archive+%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
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Manage data with metadata
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Atmosphere: Free and easy cloud computing
https://atmo.iplantcollaborative.org/
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Bisque: Image management
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Graphical and text annotations
total_lengthscale
Custom graphical annotation types
140,319,0,0,0; 467,317,0,0,0;
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Bulk image analysis
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Agave API: Science as a Service platform
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Interacting with iPlantExtended 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
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http://w
ww.iplantcolla
borative.org
/
https://pods.iplantcollaborative.org/wiki/display/start/Getting+Started+with+iPlant
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http://www.iplantcollaborative.org/learning-center/get-started
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Hands-on activityAccessing the iPlant Data Store
http://bit.ly/1euy02s
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Public access without login
http://mirrors.iplantcollaborative.org/
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Accessing data via the DE
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Upload and download
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Sharing permissions
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Sharing a file with a public link
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Cyberduck
To install Cyberduck for your operating system for the first time: https://cyberduck.io/.
Configure Cyberduck for use with the Data Store (one-time only)
Browse your folders in the data storeupload and download a file
Browse anonymous data
Transfer file from ftp site
https://pods.iplantcollaborative.org/wiki/display/DS/Using+Cyberduck+for+Uploading+and+Downloading+to+the+Data+Store
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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