Analysis Platforms Overview
The AD Knowledge Portal enables interoperability with several Trusted Research Environments (TREs), so you can bring Portal data into the analysis platform of your choice.
How It Works
Data in the AD Knowledge Portal is stored and governed in Synapse, which underlies the Portal. Behind the scenes, Portal files are made available to supported analysis platforms via the GA4GH DRS (Data Repository Service — a standardized way of referencing files without copying them.
How Using a TRE Supports the AD Knowledge Portal
Transferring data from our systems carries real-world costs. These expenses are covered by public funding and grants rather than individual user fees. To keep our platform running smoothly and protect access for all researchers and public members, we kindly ask everyone to be mindful of their downloading habits. Please consider working with the data in one of our interoperable TREs. Instead of downloading massive datasets locally, bring your analysis to the data! Working within a TRE saves local storage, provides powerful computing resources, ensures your compute environment is compliant with the current NIH NIST-800-171 security requirements, and eliminates egress costs.
Supported Platforms
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CAVATICA (Velsera and The Center for Data Driven Discovery in Biomedicine) — is an interactive analysis workbench with strong GA4GH support, offering compute/storage on AWS or Google Cloud, JupyterLab/RStudio, and CWL/NextFlow workflow execution. You'll find toolsets to support a diverse spectrum of researchers, from low-code to packed workflows to interactive analysis.
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Terra (Verily, Microsoft and The Broad Institute) — a cloud-based analysis workbench featuring workspaces, notebooks (Jupyter/RStudio/Galaxy), and WDL workflows. Discover, and combine data from multiple external repositories, including AD Knowledge Portal data, directly within the cloud environment.
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AD Workbench (ADDI) — is a secure, cloud-based data sharing and analytics environment; it is the interoperability layer of the AD Data Initiative technical suite and its flagship product offering.
Choosing a Platform
Each platform has different strengths depending on your analysis needs:
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|
Terra |
CAVATICA |
AD Workbench |
|---|---|---|---|
|
Best for: |
Reproducible, pipeline-based workflows (WDL) at scale |
Interactive genomics/proteomics analysis with a large public tool library |
Cross-cohort discovery and collaboration across the global AD/ADRD data ecosystem |
|
Compute Platform: |
Google Cloud |
AWS or Google Cloud (AWS recommended to avoid egress charges) |
Managed by Aridhia DRE |
|
Interactive tools: |
Jupyter, RStudio, Galaxy |
JupyterLab, RStudio, interactive Genome/Variant Browser |
Collaborative secure workspaces |
|
Workflow languages: |
WDL |
CWL, NextFlow (beta) |
N/A (workspace-based, brings your own code/models) |
|
Pre-built tools/apps: |
— |
790+ public apps (e.g., MaxQuant, Olink, FragPipe) via the CAVATICA Public Apps Gallery |
— |
|
Cost: |
Pay for your own compute (e.g., via institution or Google credit) |
Pay for your own compute |
Free |
|
Notable strength: |
Strong for large-scale, automated pipeline execution |
Strong for proteomics/transcriptomics tool ecosystem and public demo projects |
Only platform purpose-built for AD/ADRD data, with a global network of interoperable AD-focused datasets beyond just the AD Knowledge Portal |
If you're not sure which platform fits your project, reach out to us through your Service Desk ticket.
Getting Started
For any of these platforms, you'll generally need:
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An AD Knowledge Portal account, certified for data download — see Access Data.
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An existing account/workspace on your chosen analysis platform.
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To export your data: navigate to a Study Details page, select the files you want, and choose "Send All Results to Analysis Platform."
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Alternatively, if you're doing a bulk or programmatic import, you can construct a Synapse DRS URI directly for each file you need (
drs://repo-prod.prod.sagebase.org/<synID>, where<synID>is the Synapse ID of the file) and import it using your chosen platform's API or native DRS import tools, without going through the Portal UI.
Learn More – Review platform-specific Help Docs:
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CAVATICA
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Terra
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AD Workbench
Disclaimer: Sage Bionetworks may integrate with, and provide links to, compute environments as an alternative to downloading files. These integrations do not signify an endorsement of any particular environment by Sage Bionetworks or funders, nor do they alter the relationship between Sage Bionetworks, existing data contributors, project sponsors or funders, or computational providers. It is the responsibility of individual users to review and comply with the terms of data use for each compute environment, as well as for the AD Knowledge Portal.