Workbench
User Guide

Introduction

The DesignSafe Cyberinfrastructure provides natural hazards researchers a portal, the Research Workbench, to share natural hazards data and computational power. DesignSafe is a cloud-based environment making use of the computing resources at the Texas Advanced Computing Center (TACC) and other cloud-based applications.

This guide provides information about how to use the features and tools of the Discovery Workspace and Data Depot within the Research Workbench. These tools provide a web-based interface to all of the data and computational capabilities embedded within the DesignSafe Cyberinfrastructure.

The best way to get started will be to log in and explore. While this guide is a reference for the functionality within DesignSafe, the web interface is meant to be intuitive and user friendly.

Eligibility

The DesignSafe Cyberinfrastructure is open to all users performing open (unclassified) research in engineering resilient infrastructure in the face of natural hazards. Preference on resources is given to researchers supported by the NSF Engineering for Natural Hazards (ENH) program and those using NHERI experimental facilities. However, as resources permit, all users in these scientific fields of study are welcome to use the infrastructure, both in the United States and Internationally.

Certain functionality makes use of export controlled software or high performance computing systems. DesignSafe complies with all export control regulations under US law, and therefore use of these components of DesignSafe may be blocked for users in countries specified by the United States Department of Commerce or other appropriate authorities.

Feel free to create an account and explore!

Quick Start/Account Creation

Getting Started videos provide step-by-step details, or follow these 3 steps to quickly get access and begin exporing DesignSafe's capabilities.

  1. Login to DesignSafe
    • TACC users can log in using their TACC User Portal (TUP) credentials.
    • New users may create an account via the “Register for a TACC Account” link on the login page. You will receive an email with a link to immediately activate your account and access DesignSafe, unless you are from a Country of Concern listed by the US Department of Commerce and then we will contact you to determine your eligibility..
  2. Browse and contribute to the Data Depot, DesignSafe’s repository of public and private data
  3. Researchers can perform data analysis, run simulations, and do scientific visualization in the Discovery Workspace

Once you have provided your credentials, you will be asked to authorize the DesignSafe project to access the user profile associated with your credentials. You will only be asked to do this one time. This step allows DesignSafe to connect to the provider of your account to determine your name, email address, etc.

The final step (which you will also only be asked on your first login) is reading and accepting the DesignSafe Acceptable Use Policy, where you will be asked to use the system for legitimate research purposes.

Once you are logged on, you can proceed to access the full functionality of both the Data Depot and Discovery Workspace.

Data Depot

The Data Depot is the primary data repository for DesignSafe. The web interface to the Data Depot allows you to browse, upload, download, share and annotate data stored within the repository. Users of the system are encouraged to use the Depot not only for publication of archived results, but as a working “scratch” area for their own data and work in progress. Users may easily document and publish the data associated with their research, supporting the full data lifecycle. The Data Depot hosts both public and private data associated with a project. The Data Depot hosts both public and private data associated with a project, with the following directories:

  • My Data: Private directory for your data
  • My Projects: Group access to shared directories
  • Shared with Me: Data other users shared with me
  • Box.com: Access to my Box files for copying
  • Dropbox.com: Access to my Dropbox for copying
  • Published: Curated data/projects with DOI’s
  • Community Data: Non-curated user-contributed data

Browsing, Upload, and Download

 

Figure 1. Data Depot “My Data” screenshot

Figure 2. Upload file screenshot

 

The Data Depot provides a user interface with a familiar desktop metaphor for manipulating files. The UI for a typical “My Data” window is shown in Figure 1 above.

The “search” bar will locate files based on file names, owners, or any metadata associated with the files. Beneath the search bar, buttons are available for a number of actions -- creating folders, refreshing the screen, changing the view from a list to a grid of icons, and uploading files.

The “upload” button will open a separate form, as shown in Figure 2 above.

From the upload window, you may select files via a traditional “file manager” browser by clicking the “choose files” button, or simply drag and drop files from your desktop into the “Drop files here” section.

Below the action button is a bar that shows your position in the directory tree. Clicking in this area will allow you to navigate back up through the tree to your root directory.

Below the directory bar is the list of files and directories. Folders can be navigated simply by clicking on the name of the folders. Clicking on the name of a file will download the file. Next to each regular file and folder is an “action menu” icon. Clicking on this icon will bring up another menu of actions you can take on files, as shown in Figure 3.

The Rename, Move, Copy, Download, Preview and Remove actions all behave as one would expect. The remaining two buttons highlight some of the unique functionality of the DesignSafe cyberinfrastructure, as described below.

 

Figure 3. Action button screenshot

 

Sharing Data & Collaborating

The “Share” action button is the simplest way to share data with your collaborators. When you click this action, you can type in the user ID of any other user, and the file will be shared with them. A notification will be provided when the file is successfully shared (see “Notifications” below). Files can be shared with as many users as you choose, and you will be able to control the level of access -- you can allow other users read-only access, or read/write access to any file or folder. In the near future, you will also be able to define a group of users to share with, or to create a URL or DOI you can send to other users to share your data outside of the web interface. Sharing through the web interface changes the access control list for the file throughout the Data Depot -- this means that access is granted not only in the web applications, but also through the DesignSafe Command Line and Application Programmer Interfaces (APIs).

Other sharing methods will soon be supported in the Data Depot, including integration with popular cloud applications. In April 2016, Box.com integration will be added, followed soon by Dropbox, Amazon S3, Google Drive, and others. You will be able to sync files and folders within the Data Depot with your account on these cloud services, then share data through these mechanisms as well.

Finding Data Shared with You

When other users share data, you will find it, not surprisingly, in the “Shared with me” folder in the “My Data” area . This "Shared with me" area is organized by folders of the ID (or group/project name) of the user sharing the data with you.

Viewing and Editing Metadata

From the “Actions” menu on any file you can also select “View Metadata”. This will display any user-supplied metadata associated with the file or folder. For files you upload the metadata will typically begin empty, but you can add easily add metadata tags using the "Show/Edit Metadata" button.  Files shared publicly will also have a richer set of metadata available. Metadata is used in search and discovery, and often used by the experimental facilities to tag files. If you wish to have other users be able to find or discover your data, cite it properly, and make you famous, you are strongly encouraged to use metadata tags.

Discovery Workspace

The Discovery Workspace allows you to analyze and perform simulations on the data in the Data Depot. The Workspace will let you do things as complicated as a storm surge simulation or an interactive data visualization session, or as simple as cutting columns out of a file.

The Workspace provides a wide catalog of applications and will allow developers and users to add applications, as well as create new applications by combining existing ones into workflows. 

Discovery Workspace Applications

The Discovery Workspace currently hosts the following commonly used applications in natural hazards engineering research applications:

Data Analysis with Discovery Workspace Applications

Users may submit jobs using each application’s own customized job parameter input form (see Figure 4). The jobs run transparently using TACC’s computing and storage resources. Job status can be monitored in the right hand panel. The job’s output is placed in the archive directory within My Data or a user-designated directory.

Figure 4. Example job parameters for an ADCIRC run

Commercial Applications

The DesignSafe infrastructure includes support for commercial software. While in some cases licenses can be provided by the DesignSafe project itself, not all vendors will make licenses available for large open communities at reasonable cost. To allow broad support for as many commercial applications as possible, DesignSafe has implemented a “Bring Your Own License” (BYOL) strategy, which allows users to supply their own (or their institution’s) licenses to DesignSafe to allow access to that product integrated into the DesignSafe cloud infrastructure.

MATLAB

DesignSafe (through TACC) has negotiated with Mathworks to allow MATLAB access on TACC systems for academic research. Users submit a ticket requesting MATLAB access and are granted access upon verification they will be using MATLAB for academic research.

Notifications

Near the upper right corner of the screen next to your name is a Notifications bubble that will have a number in it and turn blue if you have unread notifications.You can also navigate to this link designsafe-ci.org/notifications. Here you will receive Site Notifications for Discovery Workspace Applications Job Statuses and File Sharing. For Finished Jobs, there is a link to view your output, and for each job state he details can be seen by clicking the button next to Raw Message. For shared files, there is a link to that file’s directory in My Data.

Managing Your Account

You can manage your account by clicking on “My account” next to your name in the upper right corner of the screen, or navigate to this link designsafe-ci.org/account/profile.

Account Profile

You may edit your personal information on this page. Please keep this information updated if you change institution, contact info, or citizenship.

Logging out

It is best to logout of DesignSafe when you are finished with your work to ensure privacy of your information and to ensure no one else uses your account in violation of the user agreement. You may logout by clicking on the down arrow next to “My account” in the upper right corner of the screen. We also recommend ensuring security by closing your browser to end all authenticated sessions.

Changing your password

You may change your password by clicking on Authentication in the lefthand menu, or by navigating to the following link designsafe-ci.org/account/authentication.

Inactive accounts

TACC security policy defines an account that has not logged in for 120 days as inactive. Use the following link to reactivate your account portal.tacc.utexas.edu/password-reset.

Notifications

You can manage your notifications settings for the portal and email by clicking on Notifications in the lefthand menu, or by navigating to the following link designsafe-ci.org/account/notifications/settings.

Help

The simplest mechanism to get additional help is to submit a support ticket. Users may submit a support ticket through the DesignSafe portal here: designsafe-ci.org/help. A staff member will follow up on your request. Help is also accessed via the global navigation on the left end of the navigation bar.

References

Policies

DesignSafe users are subject to the TACC Acceptable Use Policy and the DesignSafe Terms of Use.

 

Last update: March 9, 2016