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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.


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


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_globe

You will need a CyVerse account to use our tools

CyVerse User Portal

cyberduck

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

rstudio-verse

CyVerse RStudio GitHub

Jupyter Lab SciPy

2.2.5

Jupyter Lab SciPy Official

jupyterlab-scipy-2.2.5

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


Fix or improve this documentation


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