BERIL Research Navigator FAQs

Question 1

What is BERDL and how does this skill use it?

Accepted Answer

BERDL is the KBase BER Data Lakehouse, an on-prem Delta Lakehouse hosting 35 databases. This skill helps you query these databases, understand their schemas, and manage research projects using them.

Question 2

Does this skill require specific authentication?

Accepted Answer

Yes, it requires a KBASE_AUTH_TOKEN. For off-cluster use, it also requires SSH tunnels and specific environment variables which the skill helps detect and configure.

Question 3

Can this skill automate a full research project?

Accepted Answer

Yes, it guides you through Phase A (Ideation) to Phase E (Submission), including research plan creation, notebook execution, and automated report synthesis.

Question 4

What kind of data can I access through this skill?

Accepted Answer

You can access species-level pangenomes (GTDB), structural genomics, ModelSEED biochemistry, fitness scores from RB-TnSeq experiments, and environmental multi-omics.

Question 5

How does it handle research reproducibility?

Accepted Answer

It enforces a standardized directory structure, requires notebooks to be saved with outputs, and generates a structured REVIEW.md to ensure all findings are documented and reproducible.

BERIL Research Navigator

Key Features

Use Cases

BERIL Research Navigator

Key Features

Use Cases