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CyVerse logo

CyVerse Tools and Services Workshop

Tools and services workshops cover the major platforms of the CyVerse cyberinfrastructure (http://www.cyverse.org/) including:

  • 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

Workshop topics build progressively along a ‘path’ most researchers will need to take from data upload through to analysis and publication, cluminating in an illustrative science use case (commonly RNA-Seq).

Who Should Attend

Faculty, Postdocs, graduate students who use and analyze biological data of all types (genomics, image data, from animals, plants, etc.).

Workshop Level

This workshop focused on beginning users with little to no previous bioinformatics experience.

Intermeidate and advanced users attend to better understand CyVerse capabilities and resources, including installing their own tools and extending these analyses into Cloud and HPC.


Pre-Workshop Setup

Minimum Setup Instructions

Prerequisite Notes Links
Wi-Fi-enabled laptop You should be able to use CyVerse from any laptop using Windows/MacOS/Linux. We 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 verfied your account by completing the verification steps in the email you got when you registered. You can test your account by logging into http://user.cyverse.org/. Register for your cyverse account at http://user.cyverse.org/. 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 here. For justification, you can indicate you are requesting access for a workshop. Request Atmosphere access at the CyVerse user portal http://user.cyverse.org/
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.

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
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

Agenda

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
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      
03:00-04:45 Guided Sleuth Tutorial / Guided Tuxedo 2.0 Tutorial    
04:45-05:00 Wrap up/conclusion     Post Survey

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 traininer) and so restruction-free/guest public Wi-Fi access should be available.

Important

On Guest/public Wi-Fi it is not uncommon for certian ports needed to communicate with CyVerse services may be blocked. In our experience, IT is usually willing to open these ports (or provide temporary gues 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), ventillation and resonably comfortable chairs
  • Sufficent powerstips or power access for laptop users.
  • One or more large projection screens with bright projectors
  • Accomidation 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: http://www.cyverse.org

Funding and Citations

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

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

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