Research Assistant Template

A cloneable project template that transforms VS Code + GitHub Copilot into a domain-specific Research Assistant (RA) for computational researchers.

What Is This?

This is not a standalone tool or extension. It's a project template containing context files, slash commands, and configuration that guide VS Code's GitHub Copilot to behave as a specialized research assistant.

Clone this template for each new research project. The RA will:

• Guide you through research phases (planning → development → analysis → writing)
• Help write manuscript sections from your actual code and data
• Ensure reproducibility through proper documentation and DVC pipelines
• Track tasks and action items from meetings
• Conduct regular reviews to keep you on track

Quick Start

# Clone the template
git clone https://github.com/[username]/research-assistant-template my-new-project
cd my-new-project

# Remove template's git history
rm -rf .git
git init

# Open in VS Code
code .

Then open GitHub Copilot Chat and type:

/next

The RA will guide you through setup.

Core Philosophy

"Feed the Beast" - The RA is only as good as the context you give it.

This template provides:

• Context files that tell the RA about your project and preferences
• Slash commands that define specific workflows
• Templates for manuscript sections, figure captions, and reviews
• Phase gates that prevent skipping critical reproducibility steps

Key Features

🎯 Phase-Based Guidance

Projects progress through: SETUP → PLANNING → DEVELOPMENT → ANALYSIS → WRITING → REVIEW

The RA tracks where you are and won't let you skip critical steps.

📝 Manuscript Integration

Write your methods section as you code. Generate results from figures. Draft background from literature reviews.

🔍 Literature Research

Deep research with verified citations. No hallucinated references.

📋 Task Management

Extract action items from meeting transcripts. Route to tasks.md or GitHub Issues based on complexity.

📊 Regular Reviews

Weekly project check-ins. Monthly alignment checks. Quarterly mission reviews.

Commands

Command	Purpose
/next	Start here. Get suggested next steps based on project state.
/deep_research [topic]	Literature search with verified citations
/write_background	Draft background section from literature
/write_methods	Generate methods from documented scripts
/write_results	Draft results from figures and captions
/review_script [path]	Check code documentation quality
/weekly_review	Weekly progress review
/monthly_review	Monthly alignment check
/quarterly_review	Quarterly mission review
/plan_week	Create focused weekly plan
/transcribe [file]	Transcribe meeting audio
/summarize_meeting [file]	Extract action items from transcript

Directory Structure

├── .ra/                               # RA tool framework
│   ├── copilot-instructions.md        # RA brain and personality
│   ├── commands/                      # Slash command definitions
│   └── tools/                         # RA utilities (transcribe.py, etc.)
├── .research/
│   ├── project_telos.md               # Your project's aims and state
│   ├── phase_checklist.md             # Progress tracking
│   ├── literature/                    # Research outputs with citations
│   ├── meetings/                      # Meeting recordings and transcripts
│   │   ├── audio/                     # Audio files (.m4a, .mp3, .wav)
│   │   └── transcripts/               # Transcript markdown files
│   └── logs/                          # Activity and review logs
├── data/
│   ├── raw/                           # Immutable source data
│   ├── processed/                     # Derived data
│   └── .sensitive/                    # Excluded from AI (IRB data, etc.)
├── scripts/                           # Your analysis code
├── manuscript/
│   ├── background.md
│   ├── methods.md
│   ├── results.md
│   ├── discussion.md
│   └── figures/                       # Figures with caption files
├── meetings/                          # Audio files and transcripts
├── dvc.yaml                           # Reproducible pipeline
├── params.yaml                        # Pipeline parameters
├── tasks.md                           # Quick todos
└── researcher_telos_template.md       # Your profile (moves to ~/.researchAssistant/)

Two-Tier Context

RA Framework (.ra/):

• copilot-instructions.md - RA brain and personality
• commands/ - Slash command definitions
• tools/ - RA utilities (transcribe.py, etc.)
• Committed to git - gets cloned with every project
• Readable by Copilot - Copilot needs these to function as RA
• Don't modify - part of the framework you're cloning

User-level (~/.researchAssistant/):

• researcher_telos.md - Your preferences, productivity patterns, strengths
• Persists across all projects
• Set up once, used everywhere

Project-level (.research/):

• project_telos.md - This project's aims, phase, goals
• phase_checklist.md - Progress through research phases
• Specific to each project

Privacy

Sensitive data can be placed in data/.sensitive/. This directory is:

• Listed in .copilotignore - AI cannot read these files
• Listed in .gitignore - Files are not committed

Requirements

• VS Code with GitHub Copilot enabled
• Python 3.10+ (or R, if preferred)
• DVC for pipeline management
• Git for version control

Contributing

This template is designed to be forked and customized. If you develop useful commands or improvements, please consider contributing back.

License

MIT License - Use freely for your research.

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Inspired by the "Feed the Beast" philosophy and Telos-based context management.