📦
venue-templates
85Prepare Academic Venue Submissions
Academic submissions often fail because formatting rules vary by venue. This skill provides templates, requirements, and examples for faster preparation.
Research & Learning View
Skills biomni
📦
biomni
Content revision r1 High Risk ⚡ Contains scripts📁 Filesystem access🔑 Env variables🌐 Network access⚙️ External commands
Run Biomedical Research With Biomni
Biomedical research tasks often require many tools, datasets, and reasoning steps. This skill guides Biomni setup, task design, provider configuration, and result reporting.
Supports: Claude Codex Code(CC)
Stop for confirmation before installing.
Review the plan and obtain explicit user consent before changing files.
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Agent request
Review the Skillstore skill "biomni" from https://skillstore.io/skills/k-dense-ai-biomni.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-biomni/manifest. Verify the artifact. Stop and obtain explicit user consent before installing or changing files.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "biomni". Design a CRISPR screen for autophagy regulators in HEK293 cells.
Expected outcome:
A structured screen plan with phenotype definition, library strategy, control genes, prioritization logic, and validation assays.
Using "biomni". Interpret GWAS results for a disease trait using summary statistics.
Expected outcome:
A research summary covering significant loci, candidate causal genes, pathway enrichment themes, and follow-up analyses.
Using "biomni". Compare ADMET profiles for several candidate compounds.
Expected outcome:
A ranked assessment of absorption, distribution, metabolism, excretion, toxicity concerns, and recommended next checks.
Security Audit
High Riskv7 • 7/6/2026 Open versioned report
Most markdown and reference-link detections are false positives, but the skill has real operational risk. It handles API credentials, writes local setup files, and documents Biomni workflows that can execute LLM-generated code with broad local privileges.
6
Files scanned
2,865
Lines analyzed
32
Review items
0
False positives ignored
Confirmed security concerns (12)
High
Environment file access
# Or in .env file
The provider guide recommends using a .env file for API keys. This can leave real credentials in plaintext if users copy the setup pattern.
High
Environment file access
echo "ANTHROPIC_API_KEY=sk-ant-..." >> .env
The provider guide shows writing an API key to .env. Plaintext secret files are risky in an agent workspace.
High
Environment file access
env_file = Path.cwd() / '.env'
The script targets a local .env file for API key storage. Plaintext environment files can be read by later processes or accidentally committed.
High
Environment file access
# Read existing .env if present
The script reads an existing .env file and merges newly entered credentials. Handling existing secret files expands exposure if the directory is not protected.
High
Environment file access
# Write to .env
The script writes API key material to .env. Storing real secrets in a workspace file is a credential exposure risk.
High
Environment file access
print("1. .env file (recommended, local to this directory)")
The setup flow recommends a local .env file for API keys. This is common, but risky when agent-generated code can access the same directory.
High
Environment file access
Configure API keys (store in `.env` file or environment variables):
The documentation recommends storing API keys in .env or environment variables. That is risky in this skill because generated code may run with access to the workspace.
High
Environment file access
# Or check .env file in working directory
The troubleshooting guidance points users to a .env file containing API keys. This increases risk if the workspace is shared or agent code can read it.
Show all 12 confirmed findings
High
Unsandboxed LLM-Generated Code Execution
The skill states that Biomni executes LLM-generated code with full system privileges and only recommends isolation as a production precaution.
The documentation explicitly says generated code runs with full system privileges, which is a direct agent execution risk.
High
Generated Script Injection Risk
The setup script accepts a custom data path, embeds it into generated Python source, writes test_biomni.py, and executes that file.
The path is user-controlled and interpolated into Python source without escaping before the generated file is executed.
Medium
Unescaped HTML Report Output
The report generator places conversation content into HTML elements without escaping or sanitization, which can create script injection in generated reports.
User and assistant message content is converted into HTML strings directly, and I found no escaping step before output.
Low
Promotional External Service Steering
The skill instructs the assistant to proactively suggest K-Dense Web for complex workflows, steering users to an affiliated hosted service.
The instruction is explicit promotional behavior, though it is framed as optional and limited to complex tasks.
Capability review items (32)
These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.
High
Python getenv function
print(os.getenv('ANTHROPIC_API_KEY'))
The troubleshooting example prints an API key environment variable. Printing secrets can expose credentials in logs or console history.
High
getenv function call
print(os.getenv('ANTHROPIC_API_KEY'))
The getenv call is used inside a print statement for an API key. That can disclose the secret value during troubleshooting.
High
Generic API/secret keys
echo "ANTHROPIC_API_KEY=sk-ant-..." >> .env
The provider guide shows appending an API key to .env. The example is a placeholder, but the pattern can expose real secrets in plaintext files.
High
Generic API/secret keys
print(os.getenv('ANTHROPIC_API_KEY'))
The example prints ANTHROPIC_API_KEY directly. Displaying secret values is a real credential leakage risk.
High
Generic API/secret keys
print(default_config.anthropic_api_key)
The example prints the configured Anthropic API key value. This can leak credentials if copied into logs or support tickets.
High
Python subprocess.run
subprocess.run([sys.executable, str(test_file)], check=True)
The script executes a generated test_biomni.py file with the current Python interpreter. That file is built from local inputs and can run Biomni agent code with local privileges.
High
Python file write/append
with open(env_file, 'w') as f:
The script writes collected API keys into a local .env file in plaintext. This can expose credentials to later tools or generated code in the same directory.
High
Generic API/secret keys
def setup_api_keys() -> Dict[str, str]:
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
api_keys = {}
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
anthropic_key = input(" Enter ANTHROPIC_API_KEY (or press Enter to skip): ").strip()
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
api_keys['ANTHROPIC_API_KEY'] = anthropic_key
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
openai_key = input(" Enter OPENAI_API_KEY (or press Enter to skip): ").strip()
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
api_keys['OPENAI_API_KEY'] = openai_key
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
google_key = input(" Enter GOOGLE_API_KEY (or press Enter to skip): ").strip()
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
api_keys['GOOGLE_API_KEY'] = google_key
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
groq_key = input(" Enter GROQ_API_KEY (or press Enter to skip): ").strip()
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
api_keys['GROQ_API_KEY'] = groq_key
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
if not api_keys:
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
return api_keys
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
def save_api_keys(api_keys: Dict[str, str], method: str = 'env_file'):
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
existing_vars.update(api_keys)
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
for key, value in api_keys.items():
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
api_keys = setup_api_keys()
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
if api_keys:
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
save_api_keys(api_keys, method='shell_export')
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
save_api_keys(api_keys, method='env_file')
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
if api_keys and data_path:
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
if api_keys:
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
print(f"✓ API keys configured: {', '.join(api_keys.keys())}")
This setup workflow solicits real LLM API keys and passes them through storage or export paths. Plaintext credential handling can expose secrets to local files, logs, or generated code.
High
Generic API/secret keys
echo $ANTHROPIC_API_KEY
The troubleshooting guidance tells users to echo an API key environment variable. Printing secrets can leak credentials into terminal logs or shared screens.
Medium
Python file write/append
with open(test_file, 'w') as f:
The script writes a generated Python test file before executing it. Generated local code files increase the risk of unintended code execution.
Medium
Python file write/append
with open(example_file, 'w') as f:
The script writes an example Python file into the working directory. This is expected setup behavior but still creates executable code locally.
Risk Factors
⚡ Contains scripts (1)
📁 Filesystem access (6)
🔑 Env variables (44)
references/api_reference.md:348 references/api_reference.md:355 references/llm_providers.md:363 references/llm_providers.md:363 references/llm_providers.md:218 references/llm_providers.md:219 references/llm_providers.md:27 references/llm_providers.md:30 references/llm_providers.md:56 references/llm_providers.md:74 references/llm_providers.md:96 references/llm_providers.md:113 references/llm_providers.md:125 references/llm_providers.md:149 references/llm_providers.md:168 references/llm_providers.md:184 references/llm_providers.md:203 references/llm_providers.md:260 references/llm_providers.md:363 references/llm_providers.md:367 scripts/setup_environment.py:82 scripts/setup_environment.py:88 scripts/setup_environment.py:93 scripts/setup_environment.py:95 scripts/setup_environment.py:100 scripts/setup_environment.py:102 scripts/setup_environment.py:107 scripts/setup_environment.py:109 scripts/setup_environment.py:114 scripts/setup_environment.py:116 scripts/setup_environment.py:118 scripts/setup_environment.py:122 scripts/setup_environment.py:125 scripts/setup_environment.py:142 scripts/setup_environment.py:158 scripts/setup_environment.py:294 scripts/setup_environment.py:296 scripts/setup_environment.py:304 scripts/setup_environment.py:306 scripts/setup_environment.py:316 scripts/setup_environment.py:327 scripts/setup_environment.py:328 SKILL.md:46 SKILL.md:292
🌐 Network access (20)
references/llm_providers.md:114 references/llm_providers.md:126 references/llm_providers.md:259 references/llm_providers.md:284 scripts/generate_report.py:189 scripts/setup_environment.py:41 scripts/setup_environment.py:92 scripts/setup_environment.py:99 scripts/setup_environment.py:106 scripts/setup_environment.py:113 scripts/setup_environment.py:343 scripts/setup_environment.py:344 scripts/setup_environment.py:344 SKILL.md:272 SKILL.md:273 SKILL.md:274 SKILL.md:275 SKILL.md:276 SKILL.md:310 SKILL.md:274
⚙️ External commands (56)
scripts/generate_report.py:63 scripts/generate_report.py:69-71 scripts/generate_report.py:71-88 scripts/generate_report.py:88 scripts/setup_environment.py:25 scripts/setup_environment.py:47 scripts/setup_environment.py:67 scripts/setup_environment.py:219 SKILL.md:40-42 SKILL.md:42-44 SKILL.md:44-45 SKILL.md:45-48 SKILL.md:48-50 SKILL.md:50-54 SKILL.md:54-65 SKILL.md:65-73 SKILL.md:73-87 SKILL.md:87-90 SKILL.md:90 SKILL.md:91 SKILL.md:93-94 SKILL.md:94-97 SKILL.md:97-103 SKILL.md:103-123 SKILL.md:123-128 SKILL.md:128-136 SKILL.md:136-139 SKILL.md:139-148 SKILL.md:148-151 SKILL.md:151-162 SKILL.md:162-165 SKILL.md:165-174 SKILL.md:174-176 SKILL.md:176-187 SKILL.md:187-193 SKILL.md:193-201 SKILL.md:201-207 SKILL.md:207-221 SKILL.md:221-240 SKILL.md:240-241 SKILL.md:241-245 SKILL.md:245-254 SKILL.md:254-259 SKILL.md:259-261 SKILL.md:261-262 SKILL.md:262-263 SKILL.md:263-266 SKILL.md:266-268 SKILL.md:268-269 SKILL.md:269-283 SKILL.md:283-287 SKILL.md:287-290 SKILL.md:290-294 SKILL.md:294-297 SKILL.md:297-300 SKILL.md:300-311
Audited by: codex View Audit History →
Share & cite this report
Share the versioned assessment report, neutral badge, embed card, and citations. Skillstore reports evidence without deciding whether this Skill is safe.
Copy report link
https://skillstore.io/skills/k-dense-ai-biomni/audits/7?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_reportMarkdown badge
[](https://skillstore.io/skills/k-dense-ai-biomni?utm_source=security_passport_badge)HTML badge
<a href="https://skillstore.io/skills/k-dense-ai-biomni?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/k-dense-ai-biomni/security.svg" alt="Skillstore security assessment" loading="lazy"></a>Embed card
<iframe src="https://skillstore.io/embed/skills/k-dense-ai-biomni.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
K-Dense-AI. (2026). biomni security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-biomni/audits/7BibTeX citation
@techreport{k-dense-ai-k-dense-ai-biomni-2026,
author = {K-Dense-AI},
title = {biomni security audit report (audit version 7)},
institution = {Skillstore},
year = {2026},
number = {7},
url = {https://skillstore.io/skills/k-dense-ai-biomni/audits/7},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "biomni security audit report (audit version 7)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-06"
url: "https://skillstore.io/skills/k-dense-ai-biomni/audits/7"
identifiers:
- type: other
value: "skillstore:k-dense-ai-biomni:audit:7"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
Higher Skillstore usage
Author / source Skillstore Score Evidence Confidence Skillstore usage Updated
davila7 Recommended
davila7-biomni
Skillstore Score 38
Evidence Confidence Medium
Skillstore usage 18
Updated
2026-08-21
K-Dense-AI Current
k-dense-ai-biomni
Skillstore Score 38
Evidence Confidence Medium
Skillstore usage 11
Updated
2026-08-21
Skillstore Score
Why this score Evidence Confidence: Medium 68
Architecture
85
Maintainability
87
Content
70
Community
83
Spec Compliance
What You Can Build
Design CRISPR Screens
Plan gene knockout screens, prioritize targets, and document selection criteria for a defined phenotype.
Interpret Genomic Studies
Summarize GWAS or clinical variant results with gene mapping, pathway analysis, and evidence review.
Evaluate Drug Candidates
Frame ADMET, toxicity, target, and compound optimization tasks for Biomni-assisted investigation.
Try These Prompts
Start a Gene Query
Use Biomni to explain the function, disease links, and key evidence for [gene] in [organism]. Include source types used.
Plan a CRISPR Screen
Use Biomni to design a CRISPR knockout screen for [phenotype] in [cell type]. Include controls, prioritization rules, and expected hits.
Analyze Single-Cell Data
Use Biomni to analyze [dataset path]. Perform quality control, clustering, marker review, annotation, and condition comparison.
Run Multi-Domain Review
Use Biomni to investigate [disease]. Combine literature evidence, causal genes, candidate targets, drugs, and validation experiments.
Best Practices
- Run Biomni in a sandbox before allowing generated code execution.
- Provide clear organisms, cell types, file paths, constraints, and desired outputs.
- Validate biomedical conclusions with domain experts and primary sources.
Avoid
- Do not paste patient identifiers, private datasets, or secrets into prompts.
- Do not treat Biomni output as medical advice or final laboratory validation.
- Do not run generated code with broad credentials or unrestricted file access.
Frequently Asked Questions
What does this skill help with?
It helps structure Biomni tasks for biomedical reasoning, data analysis, provider setup, evaluation, and reporting.
Does it include the Biomni package?
No. It provides instructions and helper scripts for using the external Biomni framework.
Which AI tools can use it?
The report lists support for Claude, Codex, and Claude Code.
Can it analyze local research files?
Yes, if Biomni can access the files and required dependencies are installed.
Is it safe for sensitive data?
Use caution. The skill describes generated code execution and API key handling, so isolation is recommended.
Can outputs be used clinically?
No. Outputs require expert validation and should not replace clinical judgment or regulated review.
Developer Details
Author
K-Dense-AILicense
Apache-2.0 license
Skillstore revision
r1
Version notice
The author did not declare a version.
Repository
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/biomniRef
b8ca75d2c0a7e7102978993058777d82b8ab2610
Maintenance freshness
7/18/2026
Usage
9 downloads · 210 views
File structure
More from K-Dense-AI
View all📦
iso-13485-certification
85Prepare ISO 13485 Certification Docs
Medical device teams must create complete QMS documentation before certification audits. This skill provides templates, checklists, and gap analysis guidance for ISO 13485 readiness.
Documentation View
📦
pytdc
82Analyze therapeutic ML datasets with PyTDC
Drug discovery teams need reliable datasets and fair evaluation protocols. This skill helps Claude use PyTDC for curated therapeutic ML data, benchmark splits, metrics, and molecular oracles.
Data & Analytics View
📦
diffdock
81Run DiffDock Molecular Docking
Protein-ligand docking requires careful setup, parameter choices, and result interpretation. This skill guides DiffDock workflows for poses, confidence scores, and screening.
Research & Learning View
📦
statistical-analysis
80Analyze Research Data with Statistical Guidance
Choosing tests and reporting results can be slow and error-prone. This skill guides test selection, assumptions, effect sizes, power analysis, Bayesian options, and APA reporting.
Data & Analytics View
📦
scanpy
80Analyze Single-Cell RNA-seq with Scanpy
Single-cell RNA-seq analysis requires many linked decisions across QC, normalization, clustering, and plotting. This skill gives Claude, Codex, and Claude Code structured Scanpy workflows, reference guidance, and reusable analysis scripts.
Data & Analytics View
Related Skills
View all📦
drugbank-database
81Analyze DrugBank Data
by davila7
DrugBank data is rich but difficult to parse across XML, interactions, targets, and structures. This skill guides Claude, Codex, and Claude Code through repeatable DrugBank analysis workflows.
Research & Learning View
📦
chembl-database
80Query ChEMBL for Drug Discovery
by davila7
Drug discovery teams need reliable access to compound, target, and bioactivity records. This skill guides focused ChEMBL queries, structure searches, and result interpretation.
Research & Learning View
📦
medchem
80Filter and Prioritize Medicinal Chemistry Libraries
by davila7
Large compound libraries are difficult to assess consistently with multiple medicinal chemistry criteria. This skill combines established filters, alerts, constraints, and reports.
Research & Learning View
📦
gene-database
79Query NCBI Gene Data
by davila7
Gene lookup often requires several NCBI endpoints and careful query formatting. This skill gives Claude, Codex, and Claude Code reusable workflows for gene search, retrieval, and batch annotation.
Research & Learning View
📦
deepchem
79Build Molecular ML Workflows with DeepChem
by davila7
Molecular machine learning requires specialized data handling, featurization, splitting, and model selection. This skill provides DeepChem guidance, reference workflows, and runnable training scripts.
Research & Learning View
📦
torchdrug
76Build TorchDrug Drug Discovery Workflows
by davila7
Drug discovery teams need reliable choices among molecular datasets, graph models, and evaluation methods. This skill provides focused TorchDrug guidance for complete research workflows.
Research & Learning View