Please read below for frequently asked questions (FAQ) about ADDI and AD Workbench. Can't find what you're looking for? Post in forum or email firstname.lastname@example.org.
What types of data are available?
ADDI enables access to data types including: clinical (including cognitive assessments), epigenetics, gene expression, genotype, imaging, immunoassay, placebo, proteomics, genome sequencing, and synthetic data. A variety of imaging, immunoassay, and sequencing data, such as MRI, PET, CT, qPCR, GWAS, RNA-seq ang WGS, among others, can also be found.
Datasets AD Workbench users can access focus on a number of different conditions under the dementia umbrella, including Alzheimer’s disease and mild cognitive impairment, among others.
Some datasets encompass human subjects from different clinical trial phases and intervention modalities. Additionally, a broad selection of biochemical, genetic, inflammatory, neuroimaging, and neuropsychological biomarkers can help users discover datasets specific to their research question of interest.
Why is having a workspace important?
Workspaces are free, private, collaborative analytic environments where users can manage data and perform analysis, including modeling, data cleaning, filtering, and sharing. Workspaces allow you to manage core data assets, such as database files and tables, documents, and scripts. Once uploaded, files, databases, and data files are readable and writable via both the web interface and the optional virtual desktop environment. You may also add other members of your research team to your workspace and customize their roles for optimal shareability.
How do I request a workspace?
Please submit a request for a workspace here.
How do I access data?
Please read this article that details the dataset access process.
Where do I find my requested dataset?
Please read this article that details how to access data files once a request has been approved.
Why can't I find my requested dataset in my workspace?
The dataset may take a few moments to load in your workspace. It could be necessary to refresh the page or retry after a few minutes for the files to appear in the Inbox.
How do I request a virtual machine (VM)?
As part of the workspace request form, you are able to specify whether you would like a VM installed along with your workspace. If you have already submitted your workspace request but skipped the VM installation, you can still request a VM by emailing email@example.com.
What kind of analysis can I perform with the workspace?
With your workspace, you can quickly visualize and analyze data using the point and click statistical modules. A variety of data analytics modules can help you perform data visualization, calculate descriptive statistics, and perform statistical testing and statistical modeling.
Your workspace also comes equipped with two built-in applications, Jupyter Notebook, so you can combine live code, computational output, visualizations, and explanatory text in a single document, and RStudio, an integrated development environment for the R programming language. RStudio makes using R easier, as it includes a console, code editor, tools for plotting, and other features useful for development and debugging.
What kind of data analysis tools can I find in my workspace?
Please read this article that details many of the tools accessible from within the workspace.
Additionally, if you check the box next to a .csv file, you will see the Analyze Data option on the right menu panel. Selecting Analyze Data will open the data table analytics toolkit, which includes an analytics side bar with more than 20 modules that enable quick visualization and analysis of data. You can either select the modules and then select the columns from the dataset or select the data or columns that will be used as variables in the module you want to use. Please read more here.
What kind of analyses can I perform with the virtual machine (VM)?
Once your VM is provisioned, you can use it much like a normal desktop, such as installing software or accessing your workspace files; all instructions can be found here. For security reasons, access to the internet is restricted; however, a list of the current whitelisted sites can be found here. If you would like to access other sites not found in this list, you may request these by emailing firstname.lastname@example.org.
If you have requested a data science VM, you additionally have some pre-installed common software and packages. Read more in this article.
My Windows VM cannot be accessed, it says another user is on it. What can I do?
Windows virtual machines are single user only. If multiple users require a VM at the same time within a workspace, Linux VMs should be considered, as these are multi-user. Additional VMs (Linux or Windows) can be requested by emailing email@example.com.
My workspace VM has shut down unexpectedly. Why?
Workspace VMs are set to shut down automatically at 8pm the local time for the hub each day: West US hub is PDT/PST, UK South is BST/GMT and West Europe is CET/CEST. If required, the shutdown time can be shifted or suspended (for short periods). Please email firstname.lastname@example.org if you require either of these changes.
Can I upload my own data to the workspace for analysis?
Yes, please read this article that outlines best practices and options for uploading files to the workspace.
Can I download datasets to my own local machine?
You may download files and/or datasets to your local computer or to another one of your workspaces by submitting a download/copy request through the Airlock feature. If you are a Workspace Administrator, you can instantaneously approve the request yourself by clicking the 'Approve' button. If you are a Standard User, you will not have this option, so you need to click 'Request approval' and wait until the administrator approves it. Please review the steps in this article Downloading Files from Within Your Workspace.
How do I acknowledge or cite ADDI and AD Workbench?
- To publish work created with AD Workbench, please cite the landing page as you would any website. Here is an example in APA format.
AD Workbench. (2020). Alzheimer’s Disease Data Initiative [Web site]. Retrieved from https://www.alzheimersdata.org/
- If datasets made available via AD Workbench are used during your analysis, you must cite them separately. Please contact the respective data owners for the specifics of the citation information. Data owner information can be found in the metadata section of the dataset on the FAIR portal.
- To cite tools used while working in AD Workbench, please refer to the specific tool citation guidelines. For tools included in the t-drive, please refer to the README file.
- If you are publishing a manuscript that includes your original study you are sharing with the research community via AD Workbench, here is some example wording to use in the Data Availability Statement.
The datasets generated or analyzed during the current study are accessible via the AD Workbench, [PERSISTENT DOI/WEB LINK TO DATASETS].
If you need help generating a DOI for your study, ADDI can help! Please contact email@example.com.
How do I change my phone number for login authentication?
ADDI requires 2 factor authentication to log in: a password and a phone. If your number needs to be updated, please log a ticket by emailing firstname.lastname@example.org and they will assist.
How does AD Workbench fulfill NIH's Data Management and Sharing policy?
Please review the below file to learn how ADDI and AD Workbench fulfill this policy.
Document last updated 26 April 2023.