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AG2PI Foundations of Computation: An Introduction for Biologists Workshop

Times: 11:00 - 16:00 EST/08:00-13:00 PST

Dates: Tuesday 19th, Thursday 21st, and Friday 22nd January 2021

Ready to join the workshop? Follow these steps:

Step 1: Create CyVerse Account (free) CyVerse User Portal

Please use your institutional email address, and if you don’t have an ORCID ID - sign up for one of those too, they’re super important and valuable!

Step 2: Sign up for Workshop Workshop Enrollment

Step 3: Review this website – all of our training materials will be posted or linked from here

Goal

The goals of the workshop are to allow you as new data scientists to leave with an understanding of using CyVerse resources, the command line, and the basics of R and Rstudio programming.

You will have opportunities to work in your preferred Integrated Development Environment (IDE) in the public research cyberinfrastructure. CyVerse enables us to work with large and very large analyses.

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Tutorial Maintainer(s)

Who to contact if this guide needs fixing.

Maintainer	Institution	GitHub Username
Ryan Bartelme	CyVerse / University of Arizona	rbartelme
Tyson Swetnam	CyVerse / University of Arizona	tyson-swetnam

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Content Links

Use the table of contents on the left side of the page to navigate

• Home
• Code of Conduct
• Agenda
  • Day 1 2021-01-19
  • Day 2 2021-01-21
  • Day 3 2021-01-22
• Discovery Environment Overview
  • The Data Store
    • Walkthrough
  • The App Catalog
    • Walkthrough
  • Analyses
    • Walkthrough
• Visual Interactive Computing
  • Starting a VICE app
  • Stopping a VICE app
• Managing data in the cloud
  • Setting up iCommands
  • Uploading with iCommands
  • Downloading with iCommands
  • Downloading with WebDav
• Data Science Workspaces
  • Starting the VICE app
• Introducing the Shell
  • Background
  • Getting Started
    • Opening The Shell Via CyVerse
    • Command not found
• Navigating Files and Directories
  • The File System
    • Home Directory Variation
    • Slashes
    • Clearing your terminal
  • General syntax of a shell command
  • Getting help
    • The --help option
    • Unsupported command-line options
    • The man command
    • Manual pages on the web
  • Exploring More ls Flags
    • Listing in Reverse Chronological Order
  • Exploring Other Directories
    • Other Hidden Files
    • Orthogonality
    • Two More Shortcuts
    • Absolute vs Relative Paths
    • Relative Path Resolution
    • ls Reading Comprehension
  • Challenge - Nelle’s Pipeline: Organizing Files
    • Sorting Output
• Working With Files and Directories
  • Creating Directories
    • Step one: see where we are and what we already have
    • Step two: Create a directory
      • Two ways of doing the same thing
      • Good names for files and directories
  • Create a text file
    • Which Editor?
      • Control, Ctrl, or ^ Key
    • Creating Files a Different Way
      • What’s In A Name?
      • Moving files and directories
    • Moving Files to a new folder
    • Copying files and directories
    • Renaming Files
    • Moving and Copying
    • Removing files and directories
      • Deleting Is Forever
    • Using rm Safely
  • Operations with multiple files and directories
    • Copy with Multiple Filenames
    • Using wildcards for accessing multiple files at once
      • Wildcards
    • List filenames matching a pattern
      • More on Wildcards
  • Organizing Directories and Files
    • Reproduce a folder structure
• Pipes and Filters
• Finding Things
• Introducing R and Rstudio
  • Why Learn R? What is RStudio?
  • Optional Local Setup
  • Introduction
  • Navigating & Interacting with R Studio
    • Basic Layout
    • Calculating with R
    • HELP!
    • Installing packages
  • Data Structures
    • Types of Variables
    • Storing Variables
    • Vectors
    • Matrices & Dataframes
    • The R Environment
  • Exploring Data
    • Data Manipulation
    • Subsetting Data
  • Making Figures
    • Loading Data
    • Publication Quality Figures with ggplot2
    • Revisiting iRODS
    • Where to from here?

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
	You will need a CyVerse account to use our tools	CyVerse User Portal
	CyberDuck File manager (Windows and Mac OS X only)	Download Cyberduck

Platform(s)

We provide ready-to-use examples of (1) Docker containers with pre-configured software development environments, (2) Example datasets, & (3) ReadTheDocs style documentation that will allow for self-paced asynchonous learning as well as opportunities for in-person live coding.

We will use the following CyVerse platform(s):

Platform	Interface	Link	Platform Tour
Data Store	GUI/Command line	Data Store	Data Store Guide
Discovery Environment	Web/Point-and-click	Discovery Environment	Discovery Environment Guide
Learning Center	ReadTheDocs	This website	CyVerse Learning Center

Application(s) used

Discovery Environment App(s):

App name	Version	Description	Quick Launch	GitHub repositories
RStudio	3.6.3	RStudio Tidyverse		CyVerse RStudio GitHub
Jupyter Lab SciPy	2.2.5	Jupyter Lab SciPy Official		CyVerse JupyterLab GitHub

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
Sample Datasets	various	Example datasets cached on the CyVerse Data Store	WebDav

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Fix or improve this documentation

• Search for an answer: CyVerse Learning Center

• Ask us for help: click on the lower right-hand side of the page

• Report an issue or submit a change: Github Repo Link

• Send feedback: learning@CyVerse.org

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