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CyVerse Tools, Services, and Reproducibility, Workshop

Tools and services workshops cover the major platforms of the CyVerse cyberinfrastructure ( including:

Day One

Introduction to CyVerse

This workshop covers CyVerse basics from data upload through to analysis and publication. Ultimately, we will use RNA-Seq as an example analysis. Topics include:

  • Data Store: Data storage, sharing, metadata management, and the Data Commons
  • Discovery Environment: A web-based, graphical interface to hundreds of bioinformatics tools
  • Atmosphere: Custom cloud computing for life science
  • RNA-Seq: A demonstration of data analysis, we will use the Kallisto/Sleuth workflow to analyze RNA-Seq data

Workshop Level

This workshop focuses on beginning users with little to no previous bioinformatics experience. For the RNA-Seq analysis, some familiarity with R will be helpful.

Day Two

Reproducible Science with CyVerse

This workshop focuses on essentials for reproducible science. The emphasis is on how to manage software and code to generate research that can be more easily replicated and that complies with modern publication and funding agency standards. Topics include:

  • Implementing FAIR: Understanding and implementing the FAIR principles and 4OSS recommendations
  • Jupyter Notebooks: Using notebooks for reproducible analysis
  • Docker: Using, managing, and creating containers for software reproducibility
  • Tool Installation on CyVerse: Deploying applications on CyVerse

Workshop Level

This workshop is more suited for intermediate and advanced users interested in extending and customizing CyVerse capabilities, including installing their own tools. Familiarity of Linux/command line is highly recommended.

Pre-Workshop Setup

Minimum Setup Instructions Day One

Prerequisite Notes Links
Wi-Fi-enabled laptop (Mac or Linux recommended) You should be able to use CyVerse from any laptop using Windows/MacOS/Linux. We Strongly recommend having access to a laptop running Windows/MacOS. While you will be able to use CyVerse components from any laptop, some of the tool installations may work better with those operating systems. For the day two workshop If you are using Windows, you may wish to install Linux Bash for Windows. We also strongly recommend Firefox or Chrome browser; We do not recommend Microsoft Edge Browser. It is helpful if you have administrative/install permissions on your laptop. Note: If specified, some workshops will be held in computer labs in which case a laptop is optional.
CyVerse Account Please ensure you have a CyVerse account and have verified your account by completing the verification steps in the email you got when you registered. You can test your account by logging into CyVerse User Portal Register for your CyVerse account at CyVerse User Portal Please register using an institutional email address (e.g. .edu/.gov/.org etc.)
Atmosphere Access After registering for a CyVerse account, you will need to request access to Atmosphere. Instructions for registering for access are here (See note marked Important). Atmosphere Access may take 24 hours so please do this in advance. Verify your Atmosphere Access by logging in: Atmosphere For justification, you can indicate you are requesting access for a workshop. Request Atmosphere access at the CyVerse user portal CyVerse User Portal.
Cyberduck Cyberduck is a third-party tool for uploading/downloading data to CyVerse. Currently, this tool is available for Windows/MacOS only. You will need to download Cyberduck and the connection profile. We will go through configuration and installation at the workshop. Download Cyberduck

Minimum Setup Instructions Day Two

Prerequisite Notes Links
Docker Docker is a technology for running individual software tools in a reproducible environment, and on any machine. We request you install The Desktop, Community Edition of Docker if you are using Windows or MacOS. The Docker CE x86_64 instructions are also available for Linux users. If you have installation problems, we will also have backup cloud instances available. Download Docker
Git Git is a version control software. If you are using Linux or MacOS, you most likely already have Git. Windows users may need to install Git. You can find instructions for Git installation at the link. Install Git
Text editor You will need to have a text editor suitable for working with code (Not Microsoft word, or other word processing software). We recommend Atom
Jupyter lab Jupyter is a popular data science workbench for reproducible analysis Install Juypyter lab
Windows Linux Subsystem (Windows PC only) This enables using Linux on Windows 10 PCs We suggested installing the Windows Linux Subsystem if you have a Windows 10 PC. Following the directions we also suggest installing an Ubuntu 18.04 LTS distribution.


Prerequisite Notes Links
Github We will make use of Github for managing documentation, and also any software/scripts developed (E.g. Docker files). Register for a GitHub account
Dockerhub Dockerhub is an online repository for the sharing and management of Docker images. Register for a Dockerhub account

Optional Download Extras

These are some extra downloads that aren’t required for the workshop, but which provide some options for functionalities we will cover.

Tool Notes Link
PuTTY (windows only) PuTTY allows SSH connection to a remote machine, and is designed for Windows users who do not have a Mac/Linux terminal. Download PuTTY
iCommands iCommands are third-party software for command-line connection to the CyVerse Data Store. Download and installation instructions available at CyVerse Learning Center


We will use the Etherpad at this link to share at the workshop: Etherpad

Let’s try this Google Doc

Agenda: Day One - CyVerse Tools and Services

Time Topic/Activity Slides Guides Notes/Links
9:30-10:00 Introduction to CyVerse slides    
10:00-10:30 Data Management Basics and Data upload with Cyberduck slides guide Download Cyberduck
10:30-10:45 Break      
10:45-11:00 Data Sharing within CyVerse   guide  
11:00-12:00 CyVerse Discovery Environment walkthrough and exercises slides guide
12:00-01:00 Lunch      
01:00-01:45 Cloud Computing with CyVerse Atmosphere slides guide  
01:45-02:15 Introduction to New RNA-Seq Methods Kallisto Tutorial  
02:15-02:30 Break      
03:00-04:30 Guided Sleuth Tutorial / Guided Tuxedo 2.0 Tutorial    
04:30 Wrap up/conclusion     Post Survey

Agenda: Day Two - Reproducible research with CyVerse

Time Topic/Activity Slides Guides Notes/Links
9:30-10:00 Introduction to Open Science principles    
10:00-10:30 Metadata Management with CyVerse     We will follow the Associating Metadata guide
10:30-10:45 Break      
10:45-11:30 Reproducibility Tutorial    
11:30-12:00 Starting a project with Docker    
12:00-01:00 Lunch      
01:00-02:00 Introduction to Docker      
02:00-03:00 Building with Snakemake      
02:15-02:30 Break      
03:00-04:30 Deploying tools on CyVerse      
04:30 Wrap up/conclusion      

Host Prep Instructions

These instructions are reminders for those hosting a CyVerse Workshop with us or on their own.

Internet and Wi-Fi

Good Wi-Fi is essential to this internet-based workshop. We would advise checking with your local IT on the ability to connect 20-40 laptops in the room you are using. Hopefully, you or others have experience on using the space you have reserved. In addition, please consider that not every attendee may be local (including your CyVerse trainer) and so restriction-free/guest public Wi-Fi access should be available.


On Guest/public Wi-Fi it is not uncommon for certain ports needed to communicate with CyVerse services may be blocked. In our experience, IT is usually willing to open these ports (or provide temporary guest login) for the duration of the workshop. The following ports are needed for the workshop:

  • iRODS/Data Store: 1247 and 20000-20399
  • SSH: 22
  • VNC: 5900-5910
  • RStudio: 8787
  • Jupyter: 8000

Your CyVerse instructor will test connection prior to the workshop, or work with you to test connection to services.

Room Spaces/Computer labs

Our workshops are one to several days in length. A good space will have:

  • Windows (with shades), ventilation and reasonably comfortable chairs
  • Sufficient power strips or power access for laptop users.
  • One or more large projection screens with bright projectors
  • Accommodation for attendees with mobility/hearing/vision difficulties

If using a Computer Lab, we recommend having the Prerequisite and Download Extras installed if possible.

About CyVerse

CyVerse Vision: Transforming science through data-driven discovery.

CyVerse Mission: Design, deploy, and expand a national cyberinfrastructure for life sciences research and train scientists in its use. CyVerse provides life scientists with powerful computational infrastructure to handle huge datasets and complex analyses, thus enabling data-driven discovery. Our powerful extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, APIs, and more.

While originally created with the name iPlant Collaborative to serve U.S. plant science communities, CyVerse cyberinfrastructure is germane to all life sciences disciplines and works equally well on data from plants, animals, or microbes. By democratizing access to supercomputing capabilities, we provide a crucial resource to enable scientists to find solutions for the future. CyVerse is of, by, and for the community, and community-driven needs shape our mission. We rely on your feedback to provide the infrastructure you need most to advance your science, development, and educational agenda.

CyVerse Homepage:

Funding and Citations

CyVerse is funded entirely by the National Science Foundation under Award Numbers DBI-0735191, DBI-1265383, and DBI-1743442.

Please cite CyVerse appropriately when you make use of our resources, CyVerse citation policy