Table of Contents

Overview: Why GitHub Copilot Enterprise at VA?

• GitHub Copilot Enterprise is an premium AI-powered digital assistant approved for VA use. This guide walks you through step-by-step setup and advanced usage, specifically for healthcare professionals at Edward Hines Jr. VA Hospital.
• Agent Mode vs. Standard ChatGPT or AI:
  • Directly create, edit, and manage files on your computer (not just text)
  • Read and analyze existing documents (Word, Excel, PDFs)
  • Fetch real-time information from the internet
  • Automate complex, multi-step processes
  • Remember your work patterns and adapt to your VA role
  • Integrate with VA systems while maintaining compliance

Prerequisites

• ✅ Valid VA.gov email address (personal emails will not work for Copilot Enterprise licensing)
• ✅ Access to OneDrive or a VA network drive for file storage and backups
• ✅ Basic Windows navigation skills: File Explorer, right-clicking, etc.

Phase 1: GitHub Account & Enterprise Access (Required)

Step 1: Create a New GitHub Account

1. Go to: github.com/signup (Do not use a personal GitHub account)
2. Fill in details:
   • Email: Use your VA.gov address ONLY
   • Password: Minimum 15 characters, or 8+ with number and lowercase letter
   • Username: Professional, alphanumeric/hyphens only (no hyphens at start/end; visible to VA users)
3. Verify your account: Complete email and any other verification steps
• If your username is taken, try adding your VA ID or department
• Use a password manager—GitHub's requirements are strict
• Email verification may take a few minutes

Step 2: Request VA Enterprise Access

1. Go to: https://vaww.oit.va.gov/services/github/#signup (internal VA site)
2. In "Individual Access" section, fill the form:
   • First and last name
   • VA.gov email address
   • GitHub username you just created
3. Submit and wait for confirmation email (usually 24-36 hours)

Step 3: Verify Enterprise Access

1. Wait for approval from Step 2
2. Go to github.com/settings/copilot/features
3. Look for message: You are assigned a seat as part of a GitHub Copilot Enterprise subscription managed by department-of-veterans-affairs
4. Test Copilot web interface: github.com/copilot

Phase 2: Development Environment Setup

• Why do this optional (but recommended) step? VS Code + Copilot Agent unlocks advanced features:
  • Direct file and folder manipulation
  • Multi-step automations
  • Workspace awareness, context, and persistent settings
  • Preconfigurable prompt files and instructionals

Step 4: Install Visual Studio Code

1. Download from code.visualstudio.com/download
   • Choose "Windows User Installer" (64-bit x64 is standard for VA)
2. Run installer (no OIT/Administrator permissions needed)
3. When prompted for options:
   • Accept Microsoft License
   • Check "Add to PATH"
   • Check "Create desktop icon"
   • Check both "Open with Code" context menu options
4. Open VS Code after install (don’t install extensions yet!)

Step 5: Create Workspace Directory

1. Open VS Code, go to FILE → OPEN FOLDER
2. Choose storage location:
   • OneDrive (recommended): C:\Users\%USERNAME%\OneDrive\GitHub_Workspace\
   • Local: C:\Users\%USERNAME%\Desktop\GitHub_Workspace\
   • Network: S:\YourTeam\GitHub_Workspace\
3. Right-click, create new folder: GitHub_Workspace, select it and click OK

Step 6: Add Work Folders

1. In VS Code: FILE → ADD FOLDER TO WORKSPACE
2. Add folders you use often:
   • Desktop
   • Documents
   • Personal/Team/Project drives
3. Add each folder individually; they will appear in the Explorer panel

Step 7: Save Workspace Configuration

1. Go to FILE → SAVE WORKSPACE AS
2. Save as GitHub_Workspace.code-workspace in your GitHub_Workspace folder
3. Check that the file was created (a few KB, JSON config)

Step 8: Create Desktop Shortcut

1. Open File Explorer to GitHub_Workspace
2. Right-click GitHub_Workspace.code-workspace → Send to > Desktop (Create Shortcut)
3. (Optional) Rename the shortcut (e.g., "GitHub Copilot Workspace") and change icon if desired (right-click → Properties)
4. Daily workflow: Always use this shortcut to open VS Code with your workspace context.

Phase 3: Copilot Configuration & Optimization

• Purpose: Personalize Copilot to your workflow, preferences, and VA context.
• Key Benefits: Smarter automations, better document formatting, persistent settings, and time savings every day.

Step 10: Initial Copilot Setup

1. Open Copilot Chat with Ctrl+Alt+I (sign in if prompted)
2. Copilot Modes:
   • ASK Mode: Simple Q&A, limited file access, good for "how do I..." questions
   • AGENT Mode: Full workspace/file access, can automate tasks, create/edit files, run multi-step processes
3. Choose LLM Model: Click the "model selector" in chat to access different AI LLM's optimized for specific kinds of tasks:
   Available LLM Models with your new VA GitHub License vs Civilian Editions:

   Model	Provider	VA Access	Key Strengths	Best For
   GPT-4.1	OpenAI	✅ Enterprise	Enhanced reasoning, coding, complex tasks	Detailed analysis, multi-step automations
   Claude Sonnet 4	Anthropic	✅ Enterprise	Document analysis, ethical reasoning	Clinical content, compliance tasks
   GPT 5	OpenAI	✅ Enterprise	Next-gen reasoning, multimodal excellence	Advanced research, complex problem solving
   o4-mini	OpenAI	✅ Enterprise	Efficient reasoning, rapid responses	Quick tasks, maintaining accuracy
   Claude Opus 4	Anthropic	✅ Enterprise	Complex reasoning, long-form content	Comprehensive reports, documentation
   Claude Sonnet 3.7 Thinking	Anthropic	✅ Enterprise	Shows thought process, advanced reasoning	Troubleshooting, step-by-step solutions
   Gemini 2.0 Flash	Google	✅ Enterprise	Fastest speed, multimodal capabilities	Quick analysis, image/document processing
   Perplexity Sonar Large	Perplexity	❌ Civilian Only	Real-time web search, current information	Research with live data, fact-checking
   ChatGPT (Civilian)	OpenAI	❌ Civilian Only	General conversation, basic tasks	Personal use, no enterprise features
   Llama 3.1	Meta/Facebook	❌ Civilian Only	Open source, customizable	Custom implementations, research
   Grok-3	X (Twitter)	❌ Civilian Only	Real-time X/Twitter integration	Social media analysis, current events
   Amazon Nova	Amazon	❌ Civilian Only	AWS integration, cloud services	Cloud automation, AWS workflows
   Microsoft Phi-3	Microsoft	❌ Civilian Only	Lightweight, efficient processing	Edge computing, mobile devices
   Alibaba Qwen 3	Alibaba	❌ Civilian Only	Multilingual capabilities, Chinese focus	International content, language translation

   Quick Selection Guide: When using GitHub Copilot in "Agent Mode", you should use "GPT-4.1" for coding, use "Claude Sonnet 4" for writing & speech, use "Claude Opus 4" for advanced reasoning, logic, and analysis/reports, use "o4-mini" for speed. When using GitHub Copilot in "Ask Mode", you can take advantage of the premium flagship LLM's like "GPT-5" and "Claude Opus 4.1" for the most compelex and demanding tasks. Just be aware of the premium token costs that are taken out of your monthly allowance for premium model usage.
   
   
4. Test it out: Try "What can you help me with?" or "What files do you see in my workspace?". gent Mode's advanced capabilities: Create/edit files, analyze documents, automate reports, generate code/scripts, integrate with other tools, remember your preferences, and more!

Step 11: Configure Personal Settings

1. Copy and paste the prompt from the next slide into Copilot Chat.
2. Answer Copilot's follow-up questions (work type, file types, daily tasks, etc.)
3. Review proposed changes to your settings/configuration; approve or modify as needed.
4. Ask Copilot for clarification on any settings you don't understand.

Step 13: Personalize Your Copilot

1. Provide personal context:
   My name is [Your Name] My job title is [Your Title] I work at [Your VA Facility/Department] My primary responsibilities include: [List 3-5 responsibilities]
2. Set VA branding preferences:
   Please #fetch the official VA.gov styles, colors, fonts, and visual themes. Use these parameters when generating any future content, documents, presentations, or web pages. Always apply VA branding consistently to maintain professional appearance.
3. Define your automation needs: Discuss your daily, weekly, or monthly repetitive tasks, data sources, forms/templates, and communication patterns.
4. Establish security protocols:
   Always remind me about PHI/PII compliance when working with any healthcare or personal data. Never suggest including sensitive information in any outputs. Alert me if any requested task might involve compliance concerns.
5. Create task templates: Ask Copilot to create reusable templates (emails, reports, agendas, documentation, etc.).

Phase 4: Practical Applications for VA Healthcare Work

• These real-world examples show how Copilot Agent Mode transforms daily operations at Edward Hines Jr. VA Hospital.
• Each task here is achievable with the guidance in this setup guide.

Clinical Documentation & Patient Care

Our cardiology department needs updated heart failure guidelines. Please:
1. #fetch the latest AHA/ACC heart failure guidelines from official sources
2. #fetch the current VA/DoD clinical practice guidelines for heart failure
3. Compare the two documents and identify key differences
4. Create a summary document highlighting what's changed since our last update
5. Generate a staff memo explaining the updates with implementation timeline
6. Create a quick reference card for nurses with the new protocols
7. Update our existing heart failure patient education handout
8. Save all documents with proper VA formatting and today's date
9. Create a tracking spreadsheet for staff training completion

Patient Education Material Generation

Create comprehensive patient education materials for our newly diagnosed Type 2 diabetes patients:

1. Generate a welcome packet including:
   - Simple explanation of diabetes (6th grade reading level)
   - Hines VA diabetes clinic contact information and hours
   - Local pharmacy locations that accept VA prescriptions
   - Community resources for diabetic supplies

2. Create interactive tools:
   - Blood sugar tracking spreadsheet with color coding
   - Medication schedule template
   - Grocery shopping guide for diabetic-friendly foods
   - Exercise plan template for veterans with mobility limitations

3. Generate digital versions:
   - Email-friendly format for MyHealtheVet messaging
   - Large print versions
   - Spanish language translations
   - Audio script for vision-impaired patients

4. Create staff resources:
   - Teaching checklist for nurses
   - Common patient questions with evidence-based answers
   - Referral criteria for diabetes educator consultations

Clinical Quality Improvement Projects

Help me complete our quarterly infection control report for the medical ward:

1. Analyze the infection data spreadsheet I'll upload:
   - Calculate infection rates by unit and month
   - Identify trends and outliers
   - Compare to national benchmarks

2. Create visualizations:
   - Infection rate trends over 12 months
   - Heat map showing which units need attention
   - Before/after charts for interventions

3. Generate the quarterly report:
   - Executive summary for leadership
   - Detailed analysis for infection control committee
   - Action plan with recommendations
   - Staff presentation slides

4. Create follow-up tools:
   - Monitoring checklist for nursing staff
   - Audit forms for compliance verification
   - Training materials for new interventions

Apply all VA infection control guidelines and ensure HIPAA compliance throughout.

Administrative Automation

After uploading our staff meeting audio file, please:
1. Transcribe the full audio to text
2. Summarize key discussion points and decisions
3. Extract all assigned action items and responsible staff
4. Generate a follow-up email draft for attendees
5. Create a task tracking spreadsheet with due dates
6. Apply VA branding and confidentiality notices to all documents

Research & Data Analysis

I need a draft abstract for our recent heart failure outcomes study:
1. Analyze the Excel data I upload (demographics, interventions, outcomes)
2. Summarize key findings and statistical results
3. Create an abstract in AMA format (250 words max)
4. List 3-5 references in AMA style, pulled from PubMed or VA Library
5. Generate a PowerPoint with 3 summary slides for leadership

Training & Professional Development

Create a new staff orientation checklist for the medical ward:
1. List required training modules and deadlines
2. Add links to VA Talent Management System (TMS) and required policies
3. Include space for supervisor sign-off and completion dates
4. Format as a fillable PDF and a printable checklist
5. Generate reminder emails for incomplete items

Emergency Preparedness & Crisis Management

Help me run a code blue disaster drill:
1. Generate a scenario script for the drill
2. Create a step-by-step facilitator guide
3. Produce participant evaluation forms
4. Analyze completed forms for improvement areas
5. Summarize results for the Quality Improvement committee

The Bottom Line: Why Agent Mode Changes Everything

• Agent mode bridges knowledge, automation, and compliance for VA teams.
• It saves time, reduces burnout, and enables everyone to work at the top of their license.
• With the right setup and prompts, Copilot becomes an always-on, VA-customized digital assistant.

Prompt Templates – Administrative Automation

• Task/Project Tracker:
  Create a project tracker spreadsheet for all ongoing QI projects in our department. Include columns for project name, leader, start/end dates, current status, and key milestones.
• VA-Formatted Email:
  Draft a VA-branded email to staff about updated infection control protocols. Include summary of changes, required actions, and links to resources. Apply official VA signature block.
• Staff Scheduling:
  Generate a monthly staff schedule for our nursing unit, ensuring proper coverage for all shifts, compliance with union rules, and minimizing overtime. Output as Excel and PDF.

Prompt Templates – Data Analysis

• Data Clean-Up:
  Analyze the attached spreadsheet for missing values, duplicates, and outliers. Generate a cleaned version and a summary report of corrections.
• VA Performance Dashboard:
  Create an interactive dashboard using PowerBI to visualize patient satisfaction scores by unit and quarter for the past year, highlighting any trends or areas needing attention.

Prompt Templates – Documentation & Communication

• Clinical Note Draft:
  Generate a first-draft progress note for a patient with CHF, using the following structured template: HPI, Physical Exam, Assessment, Plan. Format for CPRS import.
• Committee Minutes:
  Summarize the attached meeting transcript into formal minutes, including attendees, decisions, action items, and deadlines. Use VA template style.

Prompt Templates – Creative & Educational

• Patient Handout:
  Create a handout for veterans on managing hypertension. Use clear, plain language, VA logos, and cite only official VA or CDC references.
• Staff Training Quiz:
  Write a 10-question multiple-choice quiz on new VA privacy policies. Include answer key and explanations, and format for online learning modules.

Importable Copilot Template Files (Ready to Use)

• copilot-instructions.md –
  Template for workspace/project-specific Copilot instructions. Sets standards, folder structure, automation, and best practices for VA Power Platform projects. Use to bootstrap or customize Copilot for a new VA project workspace.
• COPILOT_BRIEFING.md –
  Rich context file for Copilot sessions. Includes developer profile, VA compliance rules, template organization, workflow requirements, and briefing prompts. Use to ensure Copilot understands your org, automation style, and security needs.
• tasks.json –
  VS Code Tasks configuration file. Enables one-click execution of productivity reports, workspace cleanup, PowerApp actions, SQL exports, file organization, syntax checks, and version tracking. Import into .vscode/tasks.json to standardize automation for all users.
• Add-LicenseHeaders.ps1 –
  Automatically inserts VA-compliant license headers in PowerShell, SQL, JS, CSS, and HTML files. Supports dry-run mode, skips files with existing headers, and maintains logs. Ensures attribution and compliance in all source files.
• Clean-Workspace.ps1 –
  Safely removes temp, log, and archive files; old backups; and workspace clutter. Supports quick, standard, deep, and archive cleanup levels, plus dry-run and interactive modes. Maintains a secure and neat workspace.
• Generate-ProductivityReport.ps1 –
  Generates detailed productivity reports from workspace and Git activity, including VA-specific work effort estimates. Supports custom date ranges and multiple output formats. Ready for supervisor or compliance reporting.
• Validate-Syntax.ps1 –
  Checks configuration files (YAML, JSON, XML, MSAPP) for syntax errors. Can auto-fix simple mistakes and logs all results. Use before deploying configs or committing changes.
• Validate-WorkspaceSetup.ps1 –
  Validates full workspace setup (folders, files, VS Code config, Git, Power Platform CLI). Optionally auto-fixes missing directories and checks PowerShell script syntax. Outputs a report for onboarding and compliance.

How to use: Open the ./copilot-instructions/prompts/ or ./copilot-instructions/ folder in VS Code, then copy or run the desired template in your own workspace. Each file contains usage notes or documentation.

Tip: These templates are designed for a Power Platform developer in Clinical Informatics at Hines VA, but are very easilyadaptable for any VA project. You can even tell your new Copilot Agent to update these templates to for you, to customize your needs.

Troubleshooting: Common Issues and Solutions

• Copilot Not Responding: Check internet, GitHub login in VS Code, restart VS Code, clear cache (Ctrl+Shift+P → "Developer: Clear Cache and Reload")
• No Enterprise Features: Confirm VA org membership, wait full 36 hours, contact DevOpsTeam@va.gov
• Extensions Not Working: Restart VS Code, check compatibility, disable conflicts, reinstall as needed
• Workspace Not Loading: Check file location, permissions, recreate workspace if needed, verify referenced folders exist
• Performance Issues: Close unused folders, limit file monitoring in large dirs, increase memory allocation, check for resource-intensive extensions