Bioresearch 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.
Install
$ agentstack add skill-alim430-bioresearch-agent-environment-check ✓ scanned · ✓ verified — works with Claude Code, Cursor, and more.
Security review
✓ PassedNo issues found. Passed automated security review. · v0.1.0 How review works →
- ✓ Prompt-injection patterns
- ✓ Secret / credential exfiltration
- ✓ Dangerous shell & filesystem operations
- ✓ Untrusted network calls
- ✓ Known-malicious package signatures
What it can access
- ✓ Network access No
- ✓ Filesystem access No
- ✓ Shell / process execution No
- ✓ Environment & secrets No
- ✓ Dynamic code execution No
From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.
About
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 doctorThe 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.
Source & license
This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: Alim430
- Source: Alim430/bioresearch-agent
- License: MIT
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.