Analysis Platforms
The integration of external analysis platforms with the ALS Knowledge Portal enables interoperability, allowing researchers to collaborate, share, and connect with data. Data from the portal can be used in two separate Trusted Research Environments (TREs) for analysis.
Enabling integration between the Portal and the CAVATICA and Terra platforms is another step toward a greater goal to provide seamless, secure access to biomedical datasets from the ALS Knowledge Portal in as many analytical and compute environments as possible.
How they fit together
Synapse: your governed data hub for data, files, tables, provenance, and more. FAIR-first and HIPAA-capable.
Terra.bio: your analysis workbench for workspaces, notebooks (Jupyter/RStudio/Galaxy), and WDL workflows. Supports account linking with Synapse and DRS-based access.
CAVATICA: your workflow and interactive environment with strong GA4GH support and native DRS import. Allows file “linking” from external repos like Synapse without copying.
Quick-Start Guide
Discover from the Portal → Analyze in CAVATICA
Identify data of interest
Complete requirements for access, as applicable
Construct Synapse DRS URIs for the files you want (Synapse DRS endpoint: drs://repo-prod.prod.sagebase.org/<synID>).
Find detailed instructions on the ELITE Portal: Send to CAVATICA
Import into CAVATICA via GA4GH DRS (UI: “Add Files → DRS” or via API for bulk). Files are aliased, i.e., they stay where they live and CAVATICA references them.
Run tasks or pipelines against the aliased, DRS-linked files
Discover from the Portal → Analyze in Terra
Identify data of interest
Complete requirements for access, as applicable
Link accounts & hand off to Terra from the Portal
Bring data into a Terra workspace via DRS (works for notebooks or workflows)
Run interactive or batch analysis by launching Jupyter, RStudio, Galaxy or run WDL pipelines