Tau Consortium Bioinformatics Hub

Accessing the Tau Consortium Datasets Through the AD Workbench

Alzheimer’s Disease Workbench is a part of the Alzheimer’s Disease Data Initiative (ADDI). ADDI is a global team of leading academic, governmental, philanthropic, and industry organizations working together to accelerate progress towards new diagnostics, treatments and cures for Alzheimer’s disease and related dementias. Their tools empower researchers by fostering collaboration, enabling seamless access to multiple data sharing platforms, and repositories containing data from imaging, omics, clinical, and multi-modal studies.

The AD Workbench platform is free, cloud based, and allows researchers to share and access datasets, collaborative and secure workspaces, data analysis tools, and a community forum for research discussions and technical help for free.  

By creating an AD Workbench account, you can get the most out of this resource and request access to data from studies in the Tau Bioinformatics Consortium. 

The AD Discovery Portal is a publicly accessible catalog containing information pertaining to Alzheimer’s disease and related dementias such as Frontotemporal dementia or Parkinson’s disease. 

It offers a diverse collection of data (e.g. single cell sequencing, brain MRI, etc.), which includes some of our featured projects and research developed by members of the Tau Consortium. 

Fully integrated with the AD Workbench, the AD Workbench enables seamless exploration, dataset access requests, and analysis. 

Within the AD Discovery Portal, you can navigate to the catalog to explore datasets (this can be done without an account as well), filter your search, and request access to data through a form (this requires an account). Once your data access request has been approved, you can access approved datasets within an AD Workbench Workspace for analysis. 

Your AD Workbench account also gives you access to the FAIR Data Initiative. The FAIR Database and Discovery Portal are distinct but interconnected components that facilitate data sharing and analysis. FAIR stands for Findable, Accessible, Interoperable, and Reusable, representative of the four key aspects this consortium stands for. The FAIR Database is the underlying repository that stores and manages the data, ensuring it meets FAIR standards. To learn more about and have detailed instructions on FAIR Data Services and how to use them, visit https://community.addi.ad-datainitiative.org/w/faq/172/fair-data-services. 

Once you have uploaded data of your own or have been granted access to one of the available datasets, you should be able to enter your workspace. 

In a workspace, there are multiple page tabs along the top. 

  • The “Home” tab shows the workspace homepage (if configured). A workspace homepage can be configured by supplying HTML in a workspace.html file in the Files folder. 
  • The “Activity” page will display a summary of all the recent activity in the workspace (uploading or deleting files). On this page, you can also add comments or notes on any events in the workspace. 
  • The “Files” tab shows all the files in the workspace. 
  • The Database tab will show a list of the database tables and custom views available in the workspace database. 
  • The Tools tab links to the R console, built in applications like RStudio and Jupyter Notebook, and virtual machines to connect to any Windows or Linux virtual machines. 
  • The Apps tab shows built in apps, in addition to published Shiny apps. 
  • The Upload tab is where you can easily upload files and data, and generate and manage upload tokens. 
  • The Administer tab is only visible to workspace members with the Workspace Administrator Role. It provides access to the workspace Audit, showing all the auditable events that have happened in the workspace. 

AD Workbench also provides built in and external software tools to analyze data. One is the data table analytics module (found in the right-hand sidebar in a database or CSV file) to visualize and analyze the data. There are also built-in workspace tools like RStudio, Jupyter Notebook, NeuroToolKit (NTK) Analysis App, NTK Curation App, and the NTK Meta-analysis App. If these don’t suffice, you also have the option of installing additional software tools in your workspace or building your own R Shiny Apps. Additionally, you can also use scalable and heavy command-line compute analysis by installing software on a Virtual Machine.  

To answer questions about workspaces, datasets or anything related to your research, AD Data Initiative also hosts bi-weekly drop-in office hours sessions on Thursdays. Their help desk can also be reached by email at support@alzheimersdata.org.