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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:
- Know the basic capabilities of CyVerse Austria infrastructure
- Give feedback to shape the development of CyVerse Austria infrastructure
- Be able to customize and install tools required by CyVerse Austria users
- 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
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.
Hardware/Software
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 |
Accounts
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
- CyVerse Austria User Portal: https://user.cyverse.tugraz.at/
- CyVerse Austria Discovery Environment: https://de.cyverse.tugraz.at/
- CyVerse Austria Data Store configuration:
- irods host: data.cyverse.tugraz.at
- irods zone: TUG
- irods port: 1247
- Instant Session Feedback: Feedback form
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!
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 | |||
01:30-05:00 |
|
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 | |||
01:30-05:00 |
|
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 | |||
01:30-05:00 |
|
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) |
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 | |||
01:30-03:00 |
|
|Workshop Survey| |
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| | |
CyVerse FAQ | General CyVerse FAQs | |CyVerse FAQ| |
This workshop is run under a Code of Conduct - please respect it and your fellow attendees!
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: http://www.cyverse.org
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