Environment check
Skill Alim430/bioresearch-agent/skills/core/environment-check
Verify the BioResearch Agent framework installation, Python/dependency versions, network access to biomedical databases, and output-directory permissions. Use when the user asks to validate the environment, troubleshoot a failed workflow run, or before running any analysis.From its SKILL.md
npx -y skills add Alim430/bioresearch-agent --skill environment-checkAssembled from the repository path, not quoted from the project. Check it against their README if it does not work.
One thing to look at
- 1 stars1 stars. Stars are a popularity signal and not a quality one, but at this level it is likely that nobody has read this closely except its author, and you would be relying on your own review.
SKILL.md
1.2 KB, 191 tokens by cl100k_base, as published. Nobody here has run it
BioResearch Agent — Environment & Reproducibility Check
Capability
Validates that the framework is correctly installed and runnable, and that the reproducibility preconditions (dependencies, network, writable outputs) are met. This is the prerequisite skill before any literature / biomarker / causal workflow.
Run
bioresearch doctor
The check validates:
- Python version (3.9+)
- Required dependencies (pandas, numpy, scipy, matplotlib, requests, networkx)
- Demo input files present
- Network connectivity to public biomedical APIs
- Output-directory write permissions
Outputs
Console report only — no data files. Exit code 0 means ready; non-zero means a precondition
failed and should be fixed before running workflows.
Note
Skills are thin invocation wrappers. This skill dispatches to the framework's doctor command;
it makes no network calls itself.
What ships with it
Read from the repository
Just SKILL.md. No reference files, no scripts.