iPlant CollaborativeHands-on Cyberinfrastructure

Workshop - Part 1R. Walls

University of ArizonaBiodiversity Information Standards (TDWG)

Sep. 28, 2015, Nairobi, Kenya

iPlant CyberinfastructureIt’s not just for plants!

http://www.ssec.si.edu/blog/phylogenetic_trees#.VciwmUU7Rek

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.

iPlant Campus Champions

iPlant: Layer Cake

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

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.

Multiple Access Modes

https://pods.iplantcollaborative.org/wiki/display/DS/Accessing+Data+in+the+iPlant+Data+Store

iPlant Tools and Services

https://community.lego.com/t5/LEGO-General/What-does-LEGO-mean/td-p/4318550

tnrs.iplantcollaborative.org

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

high-performance computing

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

Manage data with metadata

Atmosphere: Free and easy cloud computing

https://atmo.iplantcollaborative.org/

Bisque: Image management

Graphical and text annotations

total_lengthscale

Custom graphical annotation types

140,319,0,0,0; 467,317,0,0,0;

Bulk image analysis

Agave API: Science as a Service platform

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

http://w

ww.iplantcolla

borative.org

/

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

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

Hands-on activityAccessing the iPlant Data Store

http://bit.ly/1euy02s

Public access without login

http://mirrors.iplantcollaborative.org/

Accessing data via the DE

Upload and download

Sharing permissions

Sharing a file with a public link

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

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