Home
CyVerse is an NSF-funded open science workspace to easily manage all your data and research in one place. This resource provides a platform for data storage, bioinformatics tools, image analyses, and cloud services in a free, easy to use interface.
To sign up for a CyVerse account, go to their homepage at https://cyverse.org/ and click on the blue 'Create Account' box or access the new user portal at https://user.cyverse.org/signup. Follow the on-screen instructions to enter your information.
You will need a valid email address. It is highly recommended that you use an institutional email address (e.g. .edu, .org, or .gov); access to some platforms may be restricted for international and/or non-institutional users). Username must be lowercase and have at least 3 characters. First character must be a lowercase letter. Usernames may only contain lowercase letters, numbers, dashes and underscores
Once you complete the registration, check your email for an account confirmation link and follow the confirmation instructions.
You can access the DE at https://de.cyverse.org/, or after logging in and clicking on the 'Launch' button under Discovery Environment. If you are not able to access DE, you will need to request access by clicking on the 'request access' button.
Within the DE, you can access the Data Store by clicking on the "Data" icon on the left navigation bar. This will bring you to your personal folders, community 'public' folders, and folders/files shared with you. You can upload folders directly from your desktop using the upload tab, and selecting the 'browse local' drop-down option, or you can upload raw files from a url using the 'import from URL' option.
From within the Data Store, you can access your personal files, folders shared with you, and publicly available community data by selecting from the drop-down menu on the left in green. You can select individual files by checking the box beside the file name, and selecting download from the 'more actions' drop-down menu on the right in blue.
Additional methods to manage data files and transfer:
- Cyberduck is an external software tool that allows you to drag-and-drop files to and from your CyVerse data store. For installation instructions and how to connect your CyVerse account to the Cyberduck software, follow the steps in the CyVerse tutorial here.
- iCommands is a collection of commands for Linux and Mac OS operating systems that are used in the iRODS system to interact with the CyVerse Data Store. Many commands are very similar to Unix utilities. For example, to list files and directories, in Linux you use
ls, but in iCommands you useils. While iCommands are great for all transfers and for automating tasks via scripts, they are the best choice for large files (> 2 GB each) and for bulk file transfers (many small files). iCommands is a command line tool, and is operated through a terminal, which can be done using the CyVerse cloud shell detailed above. For more information on using iCommands and how to install, follow the steps in the CyVerse tutorial here.
When you are ready to analyze data, you can select from one of several hundred applications in the Discovery Environment. To access the applications view, click on the "APPs" tab on the left navigation bar, or open using the url here: https://de.cyverse.org/apps. You can view all applications available on CyVerse under the 'Browse all apps' option from the drop-down menu seen below, view apps shared with you, or apps you have developed by selecting the 'Apps Under Development' option.
Once you’ve found an app of interest, select it by clicking the checkbox in the row containing the app name. If exactly one app is selected, a Details button will appear in the upper right corner of the Apps view, just to the right of the Filter control. Clicking the Details button produces a slide-out panel containing additional information about the app (e.g., description, number of times run, etc.).
To launch an app, click on the highlighted app name, and an analysis setup window will ask you to provide input details and settings options. You can input a descriptive title for your analysis, or continue with the default created by the app. The output folder is where all files will be sent as your analysis is generating files and outputs. You can change this by selecting the browse button to the right of the output folder field.
Once your app is running, you can track progress, run time, and status by going to the analysis icon on the left navigation.
You can have up to a maximum of two analyses running simultaneously. If you get an error code when trying to launch a new application, check your analyses tab to make sure you have not exceeded your number of analyses running at a time.
To access the analysis tab, select the 'Analysis' icon on the left navigation of the DE, or directly from the url at https://de.cyverse.org/analyses. From here you can see the status of jobs in progress, cancel analyses, relaunch analyses, and view and save the parameters of previously launched analyses. You can also access all output files from a given analysis by clicking on the folder icon on the right side for any of the listed analyses, which will take you directly to the output folder.
For questions regarding your CyVerse account, getting access to the Visual and Interactive Computing Environment (VICE) or Discovery Environment (DE), please contact CyVerse directly using the following options.
***If you have any questions regarding the information contained in this guide, please contact Laura Jackson at laura.jackson@maine.edu or ARCSIM at um.arcsim@maine.edu.