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Introduction to CyVerse

Goals

  • Introduce NEON scientists and staff to CyVerse and its resources.

  • Demonstrate via hands-on exercises the CyVerse Data Store, Data Science Workbench (Discovery Environment), Cloud (Atmosphere), BisQue image analysis, Data Commons, and Powered By features.

  • Open discussion about how NEON staff or academic scientists working with NEON data could begin to utilize CyVerse at scale.

    Suggested topics:

    • Identify NEON’s computational and data storage|sharing bottlenecks that CyVerse can ameliorate.
    • Identify missing components from the current CyVerse infrastructure that NEON requires.

Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise Register
Atmosphere access You must have access to Atmosphere Request Access
CyVerse Data Store allocation increase (Optional) You must be registered for CyVerse Request Increase (form #2)
Jetstream access (Optional) You must have registered with XSEDE Request Access
Cyberduck (Optional) Standalone program for uploading/downloading data to Data Store Download
Windows 10 Linux Subsystem (Optional) Install Ubuntu Bash on a Windows OS Installation Instructions
iCommands Installation (Optional) Install iCommands for Linux, Windows, or Mac OSX Installation Instructions

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Quick Start
Data Store GUI/Command line Data Store Data Store Manual Data Store Guide
Discovery Environment Web/Point-and-click Discovery Environment DE Manual Discovery Environment Guide
Atmosphere Command line (ssh) and/or Desktop (VNC) Atmosphere Atmosphere Manual Atmosphere Guide
BisQue Web/Point-and-click and/or Command-line (API) BisQue BisQue Manual (See Manual)
DNA Subway Web/Point-and-click DNA Subway (See Guide) DNA Subway Guide
SciApps Command-line (API) SciApps (See Guide) SciApps Guide
Agave API Command-line (API) Agave API Agave Live Docs Agave Guide

Application(s) used

Discovery Environment App(s):

App name Version Description App link Notes/other links
Muscle 3.8.31 Multiple sequence aligner DE Application URL Original App Documentation
Jupyter-Lab 0.0.3 Base Jupyter Lab Image VICE Application URL VICE Manual
RStudio Geospatial 3.5.0 Based on Rocker Geospatial RStudio Image VICE RStudio URL Rocker Docker
Shiny Apps 1.5.9 R Shiny with Geospatial dependencies (GDAL, GEOS, etc) Geospatial Shiny App Rocker Shiny

Atmosphere Image(s):

Image name Version Description Link Notes/other links
CyVerse CentOS 6.8 GUI Base 1.0 base image CentOS 6.8 with GNOME GUI Atmosphere Image 1  
Ubuntu 18.04 GUI XFCE Base 1.0 base Ubuntu 18.04 with GNOME GUI Atmosphere Image 2  

Input and example data

In order to complete this tutorial you will need to have the following inputs prepared

Input File(s) Format Preparation/Notes Example Data
       

Fix or improve this documentation

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