Frequently Asked
Questions

An expanding collection of the most frequently asked questions.


FAQ Categories


Users and Accounts  

www.designsafe-ci.org/rw/support/getting-started

Q: Who can be a DesignSafe User?
A: Any natural hazards researcher that needs an environment to store, analyze, curate, publish, and discover data with a community of peers.

Q: How do I get a DesignSafe Account?
A: Fill out and submit the registration form, follow the instructions in the email you receive to confirm your account, then log into DesignSafe.

Q: Why should I get a DesignSafe Account?
A: With an account, you can:

  • Run analysis or simulations with a variety of applications on High-Performance Computing (HPC) systems in the Discovery Workspace
  • Store your data in the Data Depot
  • Collaborate and publish your work with other researchers in My Projects
  • Access data from other researchers in the Published directory

Q: How can I become more involved in DesignSafe?
A: Join our Slack team to participate in discussions and give your input on the site. All feedback is welcome and helps improve the site.


Training  

www.designsafe-ci.org/learning-center/training

Q: Does DesignSafe provide training on how to use the Data Depot and the applications in the Discovery Workspace?
A: Upcoming training opportunities are posted in the DesignSafe Learning Center, sent via email, and posted on the Slack channel. Webinars covering DesignSafe features are hosted monthly during the school year.

Q: Are training webinars recorded and available to view online?
A: Webinars on a variety of topics are recorded and made available online, and there are additional user support videos and documentation.


Data Depot  

www.designsafe-ci.org/data/browser

Q: What types of data can I upload to the Data Depot?
A: There are no restrictions on the type of data you can upload to the Data Depot. Whatever data you need to perform your research is welcomed and encouraged!

Q: How much data can I upload to the Data Depot?
A: Data storage is allocated by the gigabyte-year on a per user basis. Allocation limits are as follows:

  • Base Allocation: 50 GB – Provided to all registered users
  • Startup Allocation: up to 1 TB – For researchers in need of more than the base allocation. To receive this allocation, send a request and await approval from an internal review.
  • Research Allocation: 100 TB (negotiable) – For researchers in need of more than the startup allocation. To receive this allocation, send a request and await approval from an internal review.
  • Educational Allocation: up to 1 TB –  For teachers using DesignSafe for educational purposes. To receive this allocation, send a request and await approval from an internal review.
  • Additional Allocation: Request via XSEDE or purchase $100/TB/year

Q: How can I upload data from my computer to My Data in the Data Depot?
A: There are a few different ways to upload data from your local machine:

  • Select the Add button, then File upload to begin uploading data from your local machine. You can browse and select files or drag and drop files into the window that appears.
  • Connect to your favorite cloud storage provider. We currently support integration with Box and Dropbox. Support for Google Drive and others is coming soon.

Q: What is My Projects?
A: My Projects is a place where you can curate and publish data with other collaborators. Data models are integrated to help you easily curate your data. You do not need to be the PI to create a project, so Experimental Facilities can create projects for their users.

Q: How do I connect to Box.com, Dropbox or Google Drive?
A: You can connect to cloud storage providers in your Account Profile. We currently support integration with Box and Dropbox and will be adding support for Google Drive.

Q: How do I add Designsafe's Box app to my company's/university's whitelist?
A: This will require contacting your IT department to make sure your company/university is using a whitelist for Box apps. If they are, give them Designsafe's client id: gh3tntr70zh1lxf3po7y893rkje696zp.

Q: Where can I find the NEES Public Data that was available in the NEEShub?
A: The Published directory in the Data Depot holds the NEES Public Data. Projects published using DesignSafe will be hosted there as well. The DOIs for the NEES Public Data point to the Data Depot.


Discovery Workspace  

www.designsafe-ci.org/rw/workspace

Q: I don't see the application I need in the Discovery Workspace. How can I get my application added?
A: Submit a ticket and we will work with you to add your application to the Discovery Workspace. We can make your application available privately to you, or if it's a widely used code we can make it publicly available to all users.

Q: What computing resources are used when a job is submitted?
A: One Stampede node is requested, containing 16 cores and 32GB of memory. For more info, visit the Stampede user guide.


MATLAB  

www.designsafe-ci.org/rw/workspace

Q: Do I need to provide my own license to run MATLAB?
A: No, you don’t need to provide your own license to run MATLAB in the Discovery Workspace. Our license with MathWorks allows for academic use and you can be from any academic institution. We have a process whereby you request access to MATLAB and we then verify you are an academic user prior to adding you to the license. Simply click on MATLAB in the Discovery Workspace to start the process of requesting access.

Q: Who can use MATLAB on DesignSafe?
A: Our license with MathWorks allows for academic use and you can be from any academic institution. We have a process whereby you request access to MATLAB and we then verify you are an academic user prior to adding you to the license. Simply click on MATLAB in the Discovery Workspace to start the process of requesting access.

Q: Why won’t my MATLAB job start and it gets stuck at Staging Inputs?
A: If you are starting up with a folder that has a large number of files and/or a significant number of MB’s, the startup may take too long and time out. Try opening MATLAB with an empty or smaller folder and then once in MATLAB you can switch directories.

Q: Where did my MATLAB job output go?
A: If you do not specify a location, the default output is shown in the grayed-out text in the Job Output Archive Location field in the job submission form, which is your My Data/Archive/Jobs/YYYY-MO-DD/JobName folder.


Jupyter  

www.designsafe-ci.org/rw/workspace

Q: What is Jupyter?
A: The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. A more detailed description including a list of more than 40 supported programming languages can be found on the Jupyter website.

Q: What do people do with Jupyter?
A: Many people use Jupyter in a similar fashion as they use MATLAB to analyze and plot their data. We will be sharing example Jupyter Notebooks soon that you can copy into your My Data and customize for your research. We also provide Jupyter training.


OpenSees  

www.designsafe-ci.org/rw/workspace

Q: What research is enabled by OpenSees?
A: The Open System for Earthquake Engineering Simulation (OpenSees) is a software framework for simulating the seismic response of structural and geotechnical systems.
A more detailed description can be found on the OpenSees website.

Q: What versions of OpenSees are available on DesignSafe?
A: OpenSeesMP and OpenSeesSP are both available in the Discovery Workspace and use TACC’s HPC resources. These are recommended for longer-running jobs. OpenSees Express performs analysis using a single Tcl script and runs on a virtual machine instead of an HPC system to avoid queue time.

Q: What is OpenSees Express?
A: OpenSees Express performs analysis using a single Tcl script, and runs on a virtual machine instead of an HPC system to avoid queue time.

Q: Where did my OpenSees job output go?
A: If you do not specify a location, the default output is shown in the grayed-out text in the Job Output Archive Location field in the job submission form, which is your My Data/Archive/Jobs/YYYY-MO-DD/JobName folder.


ADCIRC  

www.designsafe-ci.org/rw/workspace

Q: What research is enabled by ADCIRC?
A: ADCIRC is a system of computer programs for solving time dependent, free surface circulation and transport problems in two and three dimensions. These programs utilize the finite element method in space allowing the use of highly flexible, unstructured grids. Typical ADCIRC applications have included:

  • prediction of storm surge and flooding
  • modeling tides and wind driven circulation
  • larval transport studies
  • near shore marine operations
  • dredging feasibility and material disposal studies

A more detailed description can be found on the ADCIRC website.

Q: Where did my ADCIRC job output go?
A: If you do not specify a location, the default output is shown in the grayed-out text in the Job Output Archive Location field in the job submission form, which is your My Data/Archive/Jobs/YYYY-MO-DD/JobName folder.

Q: Where did my ADCIRC job output go?
A: If you do not specify a location, the default output is shown in the grayed out text in the Job Output Archive Location field in the job submission form, which is your My Data/Archive/Jobs/YYYY-MO-DD/JobName folder.


OpenFOAM  

www.designsafe-ci.org/rw/workspace

Q: What research is enabled by OpenFOAM?
A: OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.
A more detailed description can be found on the OpenFOAM website.

Q: Where did my OpenFOAM job output go?
A: If you do not specify a location, the default output is shown in the grayed-out text in the Job Output Archive Location field in the job submission form, which is your My Data/Archive/Jobs/YYYY-MO-DD/JobName folder.


ParaView  

www.designsafe-ci.org/rw/workspace

Q: What data analysis and visualization capabilities are enabled by ParaView?
A: ParaView is an open-source data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques.

A more detailed description can be found on the ParaView website.

Q: Where did my ParaView job output go?
A: If you do not specify a location, the default output is shown in the grayed-out text in the Job Output Archive Location field in the job submission form, which is your My Data/Archive/Jobs/YYYY-MO-DD/JobName folder.


Experimental Facilities 

www.designsafe-ci.org/facilities/experimental

Q: What Experimental Facilities are available to the natural hazards engineering community?
A: You can explore the NSF NHERI Program Experimental Facilities on our website. Research instruments at the facilities include wind tunnels, shake tables, centrifuges, wave pools, and mobile shaker trucks.

Q: How can I learn more about the research capabilities and how to gain access to the Experimental Facilities?
A: Each facility hosts workshops to provide prospective users with the knowledge of a facility's capabilities and discuss details toward developing research proposals, such as to the NSF Engineering for Natural Hazards Program.


Citing DesignSafe 

Q: How do I cite my use of DesignSafe in my papers, presentations, and publications?
A: DesignSafe has published a marker paper that you can cite as a reference:

Rathje, E., Dawson, C. Padgett, J.E., Pinelli, J.-P., Stanzione, D., Adair, A., Arduino, P., Brandenberg, S.J., Cockerill, T., Dey, C., Esteva, M., Haan, Jr., F.L., Hanlon, M., Kareem, A., Lowes, L., Mock, S., and Mosqueda, G. 2017. “DesignSafe: A New Cyberinfrastructure for Natural Hazards Engineering,” ASCE Natural Hazards Review, doi:10.1061/(ASCE)NH.1527-6996.0000246. 


Data Curation & Publication

Q: What are the best file formats for data publications?
A: For long-term preservation purposes it is best to publish data in interoperable and open formats. For example, instead of Excel spreadsheet files -which are proprietary- it is best to convert them to CSV for publication. And, instead of Matlab files -also proprietary- it is best to publish data as simple txt (ascii) so it can be used by many different software. However, be aware that conversion may distort the data structure, so retain an original copy of any structured data (e.g. Matlab, Excel files) before attempting conversions and then check between the two for fidelity.

Q: What does DesignSafe recommend for zip files?
A: If uploaded your data as zip files, you should unzip before publishing. Zip files prevent others from directly viewing and understanding your data in the cloud. You may upload zip files to your “MyData” and unzip them using the utilities available in the workspace at: https://www.designsafe-ci.org/rw/workspace/#!/extract-0.1u1 before copying them to your project.

Q: My project has many individual files. It will be cumbersome for a user to download them one by one. What do you suggest?
A: Through the web interface, downloading a lot of individual files is cumbersome. However, DesignSafe offers a number of solutions for this issue. First, users may interact with data in the cloud, without the need to download, using Matlab scripts as well as Jupyter notebooks. In this case, users may find downloading large quantities of data to be unnecessary. If users want to download a large number of files from a project, we recommend that they use Globus, or you may consider including zip files for your data files. However, if you include zip files you should include the unzipped files in your project as well. If you wish to make your data files easy to download, it is best to aggregate small individual data files into a smaller number of large files when feasible.

Q: What type of Data projects can be published in DesignSafe?
A: At this time, we have multiple data models and you may publish project types as “Experimental”, “Simulation”, “Hybrid Simulation, ” “Field Research” and “Other”. At the moment you can publish field reconnaissance projects, reports, presentations, software and white papers in the project type “Other.”

Q: Can I organize my data files into a hierarchy of folders in DesignSafe?
A: Yes, you can create folders in DesignSafe to keep your files organized. However, DesignSafe offers methods for identifying files, including categorizing and tagging your files. Browsing through an extensive folder hierarchy on the web is slower than on your local computer, so to improve the user experience you should try to use the smallest number of nested folders necessary. Categorizing and tagging provides a method for users to identify and search your files in an efficient manner.

Q: How should I select and organize the data to be published in a project?
A: For all project types, you have the option to select a subset of the uploaded files that you wish to publish without the need to delete them.

Q: How should I describe the dataset organization in a project type “Other”?
A: In project type Other you will be able to tag individual files for ease of data understandability and reuse. However, if you publish many files and/or organize them in folders, we suggest providing a description of the organizational structure and naming convention that you use in your dataset in a “readme” file or a report. This file can simply be a text file or pdf file.

Q: Why do you require a report/readme in all of your data publications?
A: The “Experimental”, “Simulation”, “Hybrid Simulation” and “Field Research” data models provide a representation of the structure of the datasets. However, you may need to clarify the functions of your files, the meaning of their names, the way you decided to organize them, or describe other reuse characteristics of your data. Providing a report/readme file associate with your project files is an ideal way to express this information.

Q: Should I publish raw data?
A: Raw data is the data that directly comes from the recording instruments (camera, apps, sensors, scanners, etc). When raw data is corrected, calibrated, reviewed, edited or post-processed in any way for publication, it is called curated. Some researchers want to publish their raw data as well as their curated data. If this is your case, consider why it is necessary to publish both sets, and how another researcher would use it. Always clarify whether your data is raw or curated in the description or in a readme file. Before publishing use applicable methods to review the data for errors.

Q: I will publish a large collection of images. What do I need to consider?
Be selective with the images you choose to publish. Make sure they have a purpose and are illustrative of a process or a function. Use file tags to describe them. If the images include team members make sure they are comfortable with making their images public. If images include people that have been affected by the natural hazard, you should procure their authorization to make their pictures public.

Q: I have another published work that is related to the project I am now planning to publish. How can I relate them?
A: On project landing page, under Edit Project there is a “Related Work” section where you will have the option to include one or more associated projects or publications to your current project. Here, you can provide the published project title as well as a link to that project. This link can be a DOI or a URL for any content found inside or outside of DesignSafe.

Q: Which license is appropriate for my publication?
A: You can find relevant information under licensing here: https://www.designsafe-ci.org/rw/user-guides/data-publication-guidelines/.

Q: What is a DOI?
A: A Digital Object Identifier (DOI) is a unique alphanumeric string assigned by a registration agency (the International DOI Foundation) to identify content and provide a persistent link to its location on the Internet. You can find a registered resource by its DOI using the “Resolve a DOI Name” function at: http://www.doi.org/.

Q: What is the relation between a DOI and a data citation?
A: The DOI is a component of a citation for a work that is stored online. Therefore, it provides access to the permanent URL and the cited resource.

Q: I have multiple experiments/simulations/missions to publish under one project. How should I do it?
A: Projects with multiple experiments/simulations/missions can be published sequentially, so that you can focus on each publication one at a time. Or, after you publish one, if you need to continue, you may resume uploading files and you will be able to publish other experiments/simulations/missions over a larger period of time. Each of those may have different authors and will receive individual DOIs.

Q: If the project type is “Experimental”/ “Simulation”/ ”Field Research”, how can I assign relevant authors to each experiment/simulation/mission?
A: While creating experiments/simulations/missions, you will have the option to assign authors to each one. Additionally, after successful creation of the publication, you can click on “Add (Experiment/Simulation/Mission)” on the Curation Directory page and then edit the authors and their order within the corresponding experiment/simulation/mission found in the Inventory list.

Q: How can I control the order of the authors for the published project and its citation?
A: As a step in publication pipeline, under “Order Authors”, you will be able to arrange the order of authors for each publication using arrow icons on the screen. This author order will be used for the DOIs and citation.

Q: How can I provide more contextual information about my published dataset?
A: To enhance the knowledge surrounding your dataset, you can use the “Related Work” field at the project level to point to web-pages, publications, or datasets that are published within or outside DesignSafe and you consider relevant to point at in your publication. For example, you may point to a separate published project in DesignSafe or provide the title and DOI of an article that relates to your data. You may also use any of the description fields in the data model to include specific parameters or facts that you want to highlight (e.g. wind speed during a hurricane, earthquake magnitude, damage types, etc.).

Q: How can I contribute to the reuse of data?
A: By creating a complete, clean, and clearly described publication you are already inviting others to use and cite your data. Also, always cite your dataset and those of others in the reference section of your publications and papers using the citation language and DOI provided on DesignSafe, and encourage your peers and students to do the same. Datasets take a lot of work to produce; they are important research products. If and when you use social media or any presentation platform to talk about your research, always include the proper citation and DOI on your materials (ppts, abstracts, emails, etc.). And note that a researcher does not actually need to use a dataset to cite it, but rather may cite a dataset to reference something of note in the dataset (e.g., how is was collected, its uniqueness, etc.). This is similar to the process of citing other papers.

Q: How do I cite a dataset in a paper?
A: A dataset is cited using the same citation format you use for a journal article or a conference proceeding. In the reference section of your paper, use the citation language and DOI provided by DesignSafe within the published project.

Q: I reuse data from other sources in my project. How should I credit the data creators in my publication?
A: Frequently you use data from other sources in your research and sometimes you even want to re-publish it. It is always a good practice to give credit to the data creators and or make sure you can re-publish the data if you need to. Please, be aware of the following:

  1. If you cite the data, make sure there is preferably a DOI or a permanent URL in the citation so that users can get directly to the cited data. Use the Related Work box in Edit Project to include the citation/s and corresponding links.
  2. If you use external data in your analyses, you can point to it from the Referenced Data Title box as you create your analyses category.
  3. Be aware of the reused data original license conditions of usage. The license may specify if and how you can modify, distribute, and cite the reused data.
  4. If you have reused images from other sources (online, databases, publications, etc.), be aware that they may have copyrights. We recommend using the following instructions for how to cite them:

Q: How can I give credit to DesignSafe?
A: Please, include the citation of the marker paper in the references/bibliography section of your publication. This is more effective than you providing in text acknowledgements.

Rathje, E., Dawson, C. Padgett, J.E., Pinelli, J.-P., Stanzione, D., Adair, A., Arduino, P., Brandenberg, S.J., Cockerill, T., Dey, C., Esteva, M., Haan, Jr., F.L., Hanlon, M., Kareem, A., Lowes, L., Mock, S., and Mosqueda, G. 2017. “DesignSafe: A New Cyberinfrastructure for Natural Hazards Engineering,” ASCE Natural Hazards Review, doi:10.1061/(ASCE)NH.1527-6996.0000246.