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CyVerse Austria Workshop

Location: Technical University of Graz Lehrsaal VI (FS EG 076) Inffeldgasse 11 (with TUG Wifi)

This “Train-the-trainer” style workshop will be a week-long collaboration between CyVerse trainers and staff from CyVerse US as well as trainers and staff from CyVerse Austria. Over the week, the goal will be to help each CyVerse Austria trainer:

  1. Know the basic capabilities of CyVerse Austria infrastructure
  2. Give feedback to shape the development of CyVerse Austria infrastructure
  3. Be able to customize and install tools required by CyVerse Austria users
  4. Develop effective training and documentation skills to make CyVerse Austria a success for its users.

Currently, the CyVerse Austria cyberinfrastructure implements key capabilities of CyVerse infrastructure:

  • Data Store: Data storage, sharing, metadata management,
  • Discovery Environment: A web-based, graphical interface to hundreds of bioinformatics tools
  • Visual and Interactive Computing Environment: Jupyter labs, RStudio, and RShiny applications easily launched and managed in the Discovery Environment

Pre-Workshop Setup

Minimum Setup Instructions

We ask that all attendees download/install the following software tools prior to the workshop. If you have any difficulty, we will have time to help you with installation problems during the workshop.


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. 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.
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
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 installing Atom
Python (optional) For our documentation you will need Python 3 (3.8.0 or later) installed. this is likely already installed on Linux/MacOS systems Install Python
Python package manager PIP (optional) For our documentation you will need Python 3 (3.8.0 or later) installed Install Python PIP
Python sphinx (optional) For our documentation you will need sphinx and themes
# run this command at the terminal

$ pip install sphinx
$ pip install sphinx-autobuild
$ pip install sphinx_rtd_theme
Python RestView (optional) For our documentation RestView documentation.
# run this command at the terminal

$ pip install restview


Prerequisite Notes Links
CyVerse Austria 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 Austria User Portal. Register for your CyVerse account at CyVerse Austria User Portal. Please register using an institutional email address (e.g. .edu/.gov/.org etc.).
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
University VPN If you want to access data located at your home institution, you may want to have VPN (virtual private network) software installed. Contact your university IT department if you need assistance.

Optional and Extras

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

Tool Notes Link
VNC Viewer This tool enables connection to a remote Atmosphere Desktop. No installation or configuration is needed. Download VNC Viewer
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 - iCommands


We will Slack for shared notes and easy exchange of code, feedback, links, etc.: TBA


This workshop is will be interactive and collaborative (part training workshop, part coda-a-thon/hack-a-thon). For the most part, mornings will start with some lectures, discussion, and hands-on exercises. We will then decide as a group what the afternoon agenda should focus on. We also anticipate that attendees may want to different things and we will have some capacity to divide into smaller groups. Everything on the agenda is up for discussion, if something you would like to see is missing we can add it!

Monday 2019-11-18

Learning activities and goals

  • Answer questions about how CyVerse can be used
  • Explore what is possible now, possible soon, and what needs to be made possible
  • Get a basic understanding of how to use CyVerse to handle common data management tasks (Data import, sharing, and publication)
Time Topic/Activity Slides Guides Notes/Links
09:00-09:30 Computational Thinking with CyVerse      
09:30-10:00 Introductions and user needs discussions      
10:00-10:30 Cyberinfrastructure platform overview DE Slides   Introduction to CyVerse
10:30-11:00 Break      
11:00-11:30 Data Store Basics - Upload/Import DS Slides Data Store Guide
11:30-12:00 Data Store Basics - Metadata templates     Associating Metadata
12:30-01:30 Lunch      
  • Flexible PM Session (Break included)
  • Data Store Basics - Data Sharing
  • Data Store Basics - Data Commons
  • Data Store Basics - Data Management Planning
  • Data Store Additional topics - iCommands

Tuesday 2019-11-19

Learning activities and goals

  • Get more details on how scientific tools can be deployed on CyVerse
  • Learn the value of using Docker containers to manage tool
  • Understand how to obtain, deploy, and customize containers
  • Make science reproducible with documentation and notebooks
Time Topic/Activity Slides Guides Notes/Links
09:00-09:30 Data analysis with the Discovery Environment     Discovery Environment Guide
09:30-10:00 Docker Basics     Introduction to Docker
10:00-10:30 Docker basics (cont’d)      
10:30-11:00 Break      
11:00-11:30 Docker basics (cont’d)      
11:30-12:00 Introduction to VICE    
12:30-01:30 Lunch      
  • PM Session planning (Break included)
  • Creating open documentation with ReadTheDocs
  • More on Docker
  • Identifying tools with Bioconda, Biocontainers, Dockerhub
  • More on building Juypyter Notebooks

Wednesday 2019-11-20

Learning activities and goals

  • Work collaboratively on installing tools on CyVerse (DE/VICE)
  • Go through the major steps of tool deployment from importing, deployment, testing, and documenting.
  • Work on and reinforce topics from day I and II
Time Topic/Activity Slides Guides Notes/Links
09:00-09:30 Tool installation in the Discovery Environment     DE Tool Integration
09:30-10:00 Tool installation in the Discovery Environment      
10:00-10:30 Tool installation in the Discovery Environment      
10:30-11:00 Break      
11:00-11:30 Tool installation in the Discovery Environment      
11:30-12:00 Tool installation in the Discovery Environment      
12:30-01:30 Lunch      
  • PM Session planning (Break included)
  • Building scientific workflows
  • Introduction to Git and Github
  • Planning for day IV, V projects

Thursday 2019-11-21

Learning activities and goals

  • Working on complex scientific software (exploring the QIIME use case)
  • Individual project development and work
Time Topic/Activity Slides Guides Notes/Links
09:00-09:30 Introduction to QIIME    
09:30-12:30 Individual project work    
12:30-01:30 Lunch      
01:30-05:00 Report out and PM project work (Break included)      

Friday 2019-11-22

Learning activities and goals

  • Working on complex scientific software (exploring the QIIME use case)
  • Building teaching/training skills
  • Review of tools for collaboration
  • Group presentations and plans for the future
Time Topic/Activity Slides Guides Notes/Links
09:00-09:30 Improving your teaching/training skills with Carpentries    
09:30-10:00 Building a local community of practice     LifeSciTrainers Homepage
10:00-12:30 Individual Project Work (Break included)      
12:30-01:30 Lunch      
  • Group presentations
  • Wrap up discussion
  • Individual meetings
    Workshop Survey

Resources Bin

These are links to exercises, tutorials, and other learning materials. We may or may not cover all of these items in the workshop.

Resource Description Link
Kallisto RNA-Seq Tutorial RNA-Seq analysis using Kallisto and Sleuth. (Uses DE and RStudio)
QIIME2 v2019.10 Jupyter Lab QIIME2 Jupyter Lab tutorial QIIME2
CyVerse FAQ General CyVerse FAQs CyVerse FAQ

Code of Conduct

This workshop is run under a Code of Conduct - please respect it and your fellow attendees!

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