ARRIVE Guideline Architect

Overview

AI-powered protocol design tool that creates publication-ready animal research protocols compliant with ARRIVE 2.0 guidelines (Animal Research: Reporting of In Vivo Experiments). Generates structured documentation for ethical review, transparent reporting, and reproducible science.

Key Capabilities:

• - Protocol Generation: Complete ARRIVE 2.0 compliant study protocols
• Sample Size Calculator: Statistical power analysis with justification
• Compliance Checker: Validate existing protocols against ARRIVE standards
• Randomization Schemes: Generate and document allocation strategies
• Ethics Support: IACUC protocol templates and animal welfare documentation
• Reporting Templates: Manuscript preparation with required elements

When to Use

✅ Use this skill when:

• - Designing new animal studies requiring ethical approval
• Preparing IACUC (Institutional Animal Care and Use Committee) applications
• Writing manuscripts for journals requiring ARRIVE compliance (PLOS, Nature, etc.)
• Validating existing protocols for transparency and completeness
• Training researchers on animal research best practices
• Planning multi-site studies requiring standardized protocols
• Reviewing protocols for grant applications

❌ Do NOT use when:

• - Human clinical trials → Use INLINECODE0
• In vitro studies (cell culture only) → No ARRIVE requirements apply
• Field studies on wild animals → Use specialized wildlife research guidelines
• Veterinary clinical cases → Use veterinary case report standards
• Systematic reviews/meta-analyses → Use PRISMA guidelines

Integration:

• - Upstream: sample-size-power-calculator (statistical design)
• Downstream: iacuc-protocol-drafter (ethics submission), manuscript-prep-assistant (publication)

Core Capabilities

1. ARRIVE 2.0 Protocol Builder

Generate complete protocols covering all Essential 10 items:

CODEBLOCK0

Generates:

1. 1. Study Design: Experimental groups, timelines, endpoints
2. Sample Size: Power calculations with justification
3. Inclusion/Exclusion: Animal selection criteria
4. Randomization: Allocation method (software/hardware)
5. Blinding: Who, when, how blinding implemented
6. Outcome Measures: Primary, secondary, exploratory endpoints
7. Statistical Methods: Analysis plan, software, significance level
8. Experimental Animals: Species, strain, sex, age, weight, source
9. Experimental Procedures: Detailed methods with timing
10. Results Reporting: Data presentation templates

2. Sample Size Calculator

Statistical power analysis with ARRIVE-compliant justification:

CODEBLOCK1

Features:

• - Effect Size Selection: Cohen's d, odds ratio, hazard ratio
• Multiple Comparisons: Bonferroni, FDR corrections
• Dropout Adjustment: Account for expected attrition
• Justification Text: Auto-generate sample size rationale
• Power Curves: Generate power calculations for various sample sizes

3. Compliance Validator

Check existing protocols against ARRIVE 2.0:

CODEBLOCK2

Output:
CODEBLOCK3

Validation Levels:

• - Essential 10: Required for all publications
• Recommended Set: Required by top-tier journals
• Journal-Specific: Custom checks for specific publishers

4. Randomization & Blinding Generator

Create allocation schemes with documentation:

CODEBLOCK4

Methods Supported:

• - Simple randomization
• Block randomization (fixed/random block sizes)
• Stratified randomization (by sex, age, baseline)
• Covariate-adaptive minimization

Common Patterns

Pattern 1: Drug Efficacy Study

Template for therapeutic intervention studies:

CODEBLOCK5

Key Considerations:

• - Include positive control for assay validation
• Multiple doses to establish dose-response
• Power calculation based on expected effect size
• Sample size accounts for disease variability

Pattern 2: Toxicology Study

Template for safety assessment:

CODEBLOCK6

Key Considerations:

• - Dose selection based on MTD (maximum tolerated dose)
• Recovery groups for reversibility assessment
• Comprehensive clinical pathology panels
• Histopathology on all high-dose and control animals

Pattern 3: Behavioral Study

Template for neuroscience/behavioral research:

CODEBLOCK7

Key Considerations:

• - Counterbalance test order (learning effects)
• Blind video analysis to prevent bias
• Standardized testing environment (lighting, noise)
• Experimenter training and reliability testing

Pattern 4: Surgical Model Study

Template for procedure-based research:

CODEBLOCK8

Key Considerations:

• - Detailed surgical protocol with timing
• Comprehensive perioperative care
• Clear humane endpoints (refinement)
• Sham surgery controls for procedure effects
• Pain management per IACUC guidelines

Complete Workflow Example

From study concept to IACUC submission:

CODEBLOCK9

Output Files:
CODEBLOCK10

Quality Checklist

Pre-Study:

• - [ ] CRITICAL: IACUC approval obtained before starting
• [ ] Sample size adequately powered (≥80%)
• [ ] Randomization method documented and reproducible
• [ ] Blinding plan clear for all assessors
• [ ] Humane endpoints defined with clear criteria
• [ ] Inclusion/exclusion criteria prespecified

During Study:

• - [ ] Randomization followed without deviations
• [ ] Blinding maintained (unblinding only for safety)
• [ ] All animals accounted for (CONSORT-style flow diagram)
• [ ] Adverse events documented and reported to IACUC
• [ ] Sample collection at predetermined timepoints

Reporting:

• - [ ] All Essential 10 items addressed in manuscript
• [ ] CONSORT-style flow diagram for animal studies
• [ ] Raw data available (or sharing statement)
• [ ] Conflict of interest disclosed
• [ ] Funding sources acknowledged

Common Pitfalls

Design Issues:

• - ❌ Inadequate controls → Cannot distinguish treatment from confounding effects

• - ❌ Convenience sampling → Selection bias

• - ❌ Unblinded assessment → Observer bias

Sample Size Issues:

• - ❌ No power calculation → Underpowered study, false negatives

• - ❌ Ignoring dropout → Final sample too small

Reporting Issues:

• - ❌ Selective outcome reporting → Publication bias

• - ❌ Missing animal numbers → Transparency concerns

References

Available in references/ directory:

• - arrive_2.0_guidelines.md - Official ARRIVE 2.0 checklist and explanations
• INLINECODE6 - Statistical methods for animal studies
• INLINECODE7 - Mouse, rat, zebrafish considerations
• INLINECODE8 - Requirements by publisher (Nature, Science, Cell)
• INLINECODE9 - Analysis approaches for common designs
• INLINECODE10 - Ethics committee application templates
• INLINECODE11 - Published compliant protocols as examples

Scripts

Located in scripts/ directory:

• - main.py - Protocol generation CLI
• INLINECODE14 - Core protocol builder
• INLINECODE15 - Power analysis calculator
• INLINECODE16 - Allocation scheme generator
• INLINECODE17 - ARRIVE compliance checker
• INLINECODE18 - Interactive checklist tool
• INLINECODE19 - Multi-format output (PDF, Word, Markdown)

Limitations

• - Template-Based: Generates standard protocols; highly specialized studies may need customization
• No Statistical Analysis: Calculates sample size but does not perform analysis
• No Real-Time Monitoring: Protocol generation only; does not track actual experiments
• Species Coverage: Optimized for mice and rats; other species may need adaptation
• Regulatory Variation: IACUC requirements vary by institution; may need local customization

Parameters

Usage Modes:

• - Automation Mode (Recommended for CI/CD): Use --input with JSON configuration file
• Interactive Mode: Use --interactive for guided setup via prompts

Example - Automation Mode:
CODEBLOCK11

Example - Interactive Mode:
CODEBLOCK12