Neoantigen Predictor

Generate NIH Biosketch documents compliant with the 2022 OMB-approved.

Install

openclaw skills install neoantigen-predictor

NIH Biosketch Builder

ID: 101
Version: 1.0.0
NIH Format: 2022 OMB-approved version

When to Use

Use this skill when the task is to Generate NIH Biosketch documents compliant with the 2022 OMB-approved.
Use this skill for academic writing tasks that require explicit assumptions, bounded scope, and a reproducible output format.
Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.

Key Features

Scope-focused workflow aligned to: Generate NIH Biosketch documents compliant with the 2022 OMB-approved.
Packaged executable path(s): scripts/main.py.
Reference material available in references/ for task-specific guidance.
Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

Python 3.8+
python-docx
requests (for PubMed API)

Install dependencies:

pip install python-docx requests

Example Usage

See ## Usage above for related details.

cd "20260318/scientific-skills/Academic Writing/nih-biosketch-builder"
python -m py_compile scripts/main.py
python scripts/main.py --help

Example run plan:

Confirm the user input, output path, and any required config values.
Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
Run python scripts/main.py with the validated inputs.
Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

See ## Workflow above for related details.

Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
Primary implementation surface: scripts/main.py.
Reference guidance: references/ contains supporting rules, prompts, or checklists.
Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py
python scripts/main.py --help

Workflow

Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Functions

Automatically generate NIH Biosketch documents in the 2022 format for NIH grant applications.

NIH Biosketch Format Requirements (2022 Version)

Required Sections

Personal Statement - Personal statement (max 1 page)
Positions and Honors - Positions and honors
Contributions to Science - Scientific contributions (max 4 items)
Research Support - Research support (optional)

Format Specifications

Page count: No more than 5 pages
Fonts: Arial, Helvetica, Palatino Linotype, or Georgia, ≥11pt
Margins: ≥0.5 inches
Line spacing: Single or double

Usage

Command Line

python skills/nih-biosketch-builder/scripts/main.py --input data.json --output biosketch.docx

Input Data Format (JSON)

{
  "personal_info": {
    "name": "Zhang San",
    "position": "Associate Professor",
    "department": "Department of Biology",
    "organization": "University of Example",
    "email": "zhang.san@example.edu"
  },
  "personal_statement": "Your personal statement text here...",
  "positions_and_honors": [
    {"year": "2020-present", "position": "Associate Professor", "institution": "University of Example"}
  ],
  "contributions": [
    {
      "title": "Breakthrough in Cancer Research",
      "description": "Detailed description of contribution...",
      "publications": ["PMID:12345678", "DOI:10.1000/example"]
    }
  ],
  "research_support": [
    {"title": "R01 Grant", "agency": "NIH", "period": "2021-2026", "amount": "$1,500,000"}
  ]
}

SCI Paper Auto-import


# Automatically retrieve paper information via PMID
python skills/nih-biosketch-builder/scripts/main.py --import-pubmed "12345678,23456789" --output publications.json

# Auto-fill into biosketch
python skills/nih-biosketch-builder/scripts/main.py --input data.json --auto-import-pubmed --output biosketch.docx

Output Format

Generate DOCX file in NIH official template format, ready to use for grant applications.

References

NIH Biosketch Format Instructions
SciENcv - NIH official tool

Risk Assessment

Risk Indicator	Assessment	Level
Code Execution	Python scripts with tools	High
Network Access	External API calls	High
File System Access	Read/write data	Medium
Instruction Tampering	Standard prompt guidelines	Low
Data Exposure	Data handled securely	Medium

Security Checklist

Prerequisites

No additional Python packages required.

Evaluation Criteria

Success Metrics

Successfully executes main functionality
Output meets quality standards
Handles edge cases gracefully
Performance is acceptable

Test Cases

Basic Functionality: Standard input → Expected output
Edge Case: Invalid input → Graceful error handling
Performance: Large dataset → Acceptable processing time

Lifecycle Status

Current Stage: Draft
Next Review Date: 2026-03-06
Known Issues: None
Planned Improvements:
- Performance optimization
- Additional feature support

Output Requirements

Every final response should make these items explicit when they are relevant:

Objective or requested deliverable
Inputs used and assumptions introduced
Workflow or decision path
Core result, recommendation, or artifact
Constraints, risks, caveats, or validation needs
Unresolved items and next-step checks

Error Handling

If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of nih-biosketch-builder and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

nih-biosketch-builder only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

References

references/audit-reference.md - Supported scope, audit commands, and fallback boundaries

Response Template

Use the following fixed structure for non-trivial requests:

Objective
Inputs Received
Assumptions
Workflow
Deliverable
Risks and Limits
Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.