Vibe Coding for Clinicians, Researchers, and Educators
A beginner-friendly handbook for physicians who want to build useful clinical, research, and teaching tools with AI coding assistants without pretending to be software engineers.
Audience
Beginner physician-builders
Best first use
Education, research, and workflow prototypes
1 - Start here
What vibe coding means for physicians
Vibe coding means building software by describing what you want in natural language, letting an AI coding assistant draft the code, testing the result, and refining it through conversation. You are not handing over clinical judgment. You are using AI as a fast junior developer while you remain the clinical architect.
Your advantage
You know the messy workflow, the edge cases, the language clinicians use, and what would actually be useful in clinic, in the bronchoscopy suite, or in a fellow course.
The assistant advantage
It can scaffold code, explain unfamiliar libraries, write tests, refactor files, and help debug without tiring of the iteration loop.
The non-negotiable
You decide whether the result is accurate, safe, maintainable, and appropriate for the intended educational, research, or workflow setting.
Good first uses
- Educational apps: board review, anatomy teaching, EBUS station practice, procedural checklists, simulation modules.
- Research tools: REDCap helpers, screening logs, CSV parsers, abstract dashboards, literature extraction workflows.
- Workflow prototypes: note templates, registry extraction mockups, CPT coding demos, QA dashboards.
Not a shortcut for
- Sending protected health information to unapproved tools.
- Replacing institutional IT, security review, IRB, compliance, or FDA review when those apply.
- Shipping clinical decision support without validation.
2 - Why this matters
IP tools are often too niche for industry
Interventional pulmonology has problems that are obvious to physicians but too narrow for many commercial roadmaps: registry capture from procedure notes, board-style teaching tools, procedure simulators, anatomy modules, literature assistants, and workflows that understand EBUS-TBNA, cryobiopsy, navigational bronchoscopy, pleural procedures, valves, rigid bronchoscopy, and stent surveillance.
Turn notes into structure
Extract EBUS station, needle passes, adequacy, ROSE, complications, specimens, CPT hints, and registry fields from synoptic text.
Build the course you wanted
Create interactive bronchoscopy anatomy, TNM staging practice, EBUS knobology, board review cases, simulation labs, and feedback loops.
Lower the friction
Screen abstracts, classify cases, generate tables, build dashboards, track enrollment, and standardize data collection.
Prototype cautiously
Educational calculators, guideline summaries, and checklists can be useful, but patient-specific recommendations need validation and governance.
3 - Core loop
The physician-builder workflow
- 1Describe the clinical problemState the user, setting, input, output, and success criteria. "Build an EBUS station quiz for fellows" is better than "make an app."
- 2Plan before codingUse a chat assistant to turn the idea into requirements, a feature list, a data model, and first-version scope.
- 3Generate small piecesAsk for one component, one script, or one route at a time. Large prompts are fine for planning; small prompts are better for reliable implementation.
- 4Run and testUse the IDE terminal. Copy exact error messages back to the assistant. Ask for reproducible checks, not just another attempt.
- 5Refine with domain expertiseCorrect medical language, workflows, and edge cases. Ask AI to critique the product, not just write code.
- 6Commit, review, and shareUse GitHub as project memory. Save checkpoints, create issues, get review, and deploy only when the risk level is appropriate.
AI as workbench builder
When a visual task is hard to describe, ask AI to create a temporary editor. Example: a hotspot placement page where you drag controls into position, copy JSON, and then delete the temporary tool after integration.
Show, do not only describe
For spatial bugs, layouts, 3D anatomy, ultrasound geometry, or UI problems, screenshots and target images converge faster than paragraphs.
Make invisible state visible
Ask for debug panels, timestamps, axes, centroids, labels, and logs. Many bugs stay hidden because you cannot see the state the code is using.
4 - Tool stack chooser
Which tools should a beginner physician use?
Do not start by learning every tool. Pick the stack that matches the current goal.
| Goal | Best starter stack | Why | First project |
|---|---|---|---|
| Learn the workflow | Chat assistant + Google Colab | No local setup. Good for Python, data, and concept learning. | Parse 20 synthetic CT reports into a CSV. |
| Build a research dashboard | Python + Streamlit + GitHub | Fast path from a data table to an interactive app. | Bronchoscopy complication dashboard from a de-identified CSV. |
| Build a teaching app | VS Code, Cursor, or Windsurf + React/Vite | Best for interactive UI, quizzes, anatomy diagrams, and mobile-responsive teaching tools. | EBUS station flashcards with a 20-question quiz. |
| Maintain a real codebase | VS Code + Copilot, Cursor, or Codex | Good balance of manual control, codebase context, chat, and version control. | Refactor an existing app and add tests. |
| Delegate multi-file work | Codex, Claude Code, or Copilot coding agent | Agents can inspect the repo, edit files, run commands, and summarize changes. | Add a new TNM staging module to an existing course app. |
Three tiers of AI coding tools
Chat-based assistants
ChatGPT, Claude, and similar tools are useful for planning, explaining code, drafting prompts, summarizing errors, and small snippets.
IDE-integrated assistants
GitHub Copilot in VS Code, Cursor, and Windsurf are strongest when the assistant can see the files you are editing.
Agentic coding tools
Codex, Claude Code, and coding agents are best for multi-file changes, tests, pull requests, and codebase exploration.
5 - IDE basics
What an IDE is, and why clinicians should care
An IDE is an integrated development environment: a workspace where you view files, edit code, run commands, manage Git, and debug errors. Think of it as the software workbench that keeps the editor, terminal, source control, and AI assistant in one place.
VS Code
Free, widely used, and supported by a large extension ecosystem, GitHub Copilot, terminals, notebooks, and many language plugins.
Open resourceCursor
An AI-native editor designed around agents and codebase context. Useful when you want coordinated edits across a project.
Open resourceWindsurf
An AI coding editor focused on agentic development, flow, browser context, terminal commands, and iterative app building.
Open resourceJupyter / Colab
Notebook environments are excellent for research data, Python, statistics, and teaching. They are a great first scripting surface.
Open resourceThe five IDE areas beginners should learn
- 1File explorerShows project folders and files. Ask AI to explain the folder structure.
- 2EditorWhere files open. Comments can become prompts, such as "// Build a quiz component that loads questions from quizData.json".
- 3TerminalWhere commands run, such as npm run dev, python app.py, or git status.
- 4Source control panelShows what changed. Review this before every commit.
- 5AI chat / agent panelWhere you describe tasks, review errors, and request scoped changes.
6 - GitHub basics
GitHub for physicians: the minimum you need
Git tracks changes. GitHub stores those changes online, supports collaboration, and can host simple websites. Beginners can start with GitHub Desktop before relying on terminal commands.
| Term | Plain-English meaning | Medical analogy |
|---|---|---|
| Repository / repo | A project folder with history. | A case chart plus all revisions. |
| Commit | A saved checkpoint with a message. | Procedure note signed at a point in time. |
| Branch | A safe copy for trying changes. | A simulation run before changing the real workflow. |
| Pull request | A proposed set of changes for review. | Peer review before deployment. |
| Issue | A to-do item, bug, or feature request. | Clinic task list or research tracker. |
| README | The project front page and instructions. | Protocol summary. |
| .gitignore | A list of files Git should never track. | Do not include PHI, secrets, exports, or temp files. |
The beginner GitHub workflow
- 1Create a private repositoryUse a short name, add a README, and add a license only when you are ready to share.
- 2Clone it locallyUse GitHub Desktop or the terminal. Open the folder in VS Code, Cursor, or Windsurf.
- 3Build one featureAdd one page, one parser, one component, or one test.
- 4Review changed filesRead the diff. Ask the AI to explain anything you do not understand.
- 5Commit with a useful messageExample: Add EBUS station quiz with JSON question data.
- 6Push to GitHubNow the checkpoint exists online and can be reviewed, deployed, or continued elsewhere.
# See what changed
git status
# Save all changed files into the next checkpoint
git add .
# Create the checkpoint
git commit -m "Add EBUS station quiz"
# Upload to GitHub
git push
# Create a safe branch for a new feature
git checkout -b add-tnm-module7 - Agentic coding
How to use coding agents safely
Agents are different from chatbots. A chatbot answers. An agent can inspect files, edit files, run commands, and sometimes create pull requests. That power is why agents are useful and why guardrails matter.
Use an agent when
- The project is already in GitHub or otherwise backed up.
- You can describe a clear goal and success test.
- The change spans multiple files.
- You want tests, documentation, or refactoring.
- You can review the diff before accepting changes.
The safest agent workflow
- 1Start from a clean Git stateRun git status. Commit or stash current work.
- 2Create a branchExample: git checkout -b add-tnm-staging-module.
- 3Ask for a plan before editsTell the agent: Inspect the repo and propose a plan. Do not edit yet.
- 4Approve a small scopePrefer one feature. Avoid rebuilding the entire app in one pass.
- 5Run tests or buildRequire npm run build, pytest, or whatever applies.
- 6Review the diff and summaryAsk for changed files, risks, assumptions, and manual test steps.
You are working in my GitHub repo for an educational interventional pulmonology app.
Goal: Add a TNM staging teaching module for pulmonary fellows.
Rules:
- Do not use or create any patient-identifiable data.
- Do not make changes until you inspect the repo and propose a short plan.
- Keep the first version small: reference cards, a simple staging builder, and 3 cases.
- Use existing styling and navigation patterns.
- Add or update tests if the project already has tests.
- Run the build command and report whether it passes.
- At the end, summarize changed files, assumptions, risks, and manual test steps.
Start by inspecting README.md, package.json, and the src folder. Then propose a plan.| Agent | Good use | How to think about it | Beginner guardrail |
|---|---|---|---|
| Codex | Cloud, CLI, IDE, and app coding tasks; repo inspection; bug fixes; feature implementation. | Delegate a well-scoped task and review the output. | Ask for plan -> branch -> tests -> diff summary. |
| Claude Code | Terminal and IDE workflows, repo-level reasoning, refactoring, explanations, and careful review. | A coding collaborator living in the development environment. | Use permission prompts and review shell commands. |
| GitHub Copilot coding agent | Issue-driven tasks and pull-request style workflows inside the GitHub and Copilot ecosystem. | Turn a detailed issue into a proposed change. | Write detailed issues and review PRs like manuscripts. |
| Cursor / Windsurf agents | Interactive IDE-based building with live codebase context and visual feedback. | Build while watching the app run. | Keep tasks small and watch the changed-files list. |
8 - Prompt library
Copy-ready prompts for clinicians
The goal is not perfect wording. The goal is enough context for the assistant to make good decisions.
C - Context
Clinical domain, user, setting, and why it matters.
L - Layout
How you want the response or app structured.
E - Examples
Sample inputs, outputs, reports, cases, screenshots, or user stories.
A - Accuracy
Standards, units, guideline references, validation expectations.
R - Requirements
Constraints: privacy, accessibility, file formats, tests, deployment, and edge cases.
I am a pulmonary/critical care physician building a beginner project with AI coding tools.
Clinical problem:
[Describe the problem]
Users:
[Medical students / fellows / research coordinator / attending / quality team]
Setting:
[Education only / research data / clinical workflow prototype]
Inputs:
[CSV, text notes, images, REDCap export, synthetic cases]
Outputs:
[Dashboard, quiz, parser output, report, PDF, table]
Constraints:
- Use de-identified or synthetic data only.
- Beginner-friendly stack.
- First version should be small and buildable in one weekend.
Please create:
1. A one-paragraph project summary.
2. MVP feature list.
3. Future feature backlog.
4. Recommended tech stack.
5. Data model.
6. Step-by-step build plan.
7. Risks and safety review checklist.I am getting this error while running my app:
[Paste exact error]
Context:
- Tool/editor: [VS Code / Cursor / Claude Code / Codex]
- Command I ran: [npm run dev / python app.py / pytest]
- File I think is involved: [filename]
- What I expected: [expected behavior]
- What happened: [actual behavior]
Please:
1. Explain the error in beginner-friendly terms.
2. Identify the likely cause.
3. Give the smallest safe fix.
4. Tell me exactly which file to edit.
5. Suggest a test to confirm it is fixed.This is a visual/spatial problem and text iteration is not converging.
Please build a temporary workbench page that lets me manually adjust the values.
Requirements:
- Show the target image or object.
- Let me drag, resize, and nudge the hotspots, labels, or points.
- Show live coordinates and dimensions.
- Include a Copy JSON button.
- Store the temporary page in a clearly named route: /debug-hotspot-editor.
- Do not integrate into production yet.
After I paste the final JSON, help me wire it into the production component and remove the debug page.Build a React + Vite teaching app for EBUS nodal stations.
Audience: pulmonary fellows.
Purpose: rapid visual review before simulation lab.
Features:
1. Landing page with learning objectives.
2. Interactive station map with clickable stations 2R, 2L, 4R, 4L, 7, 10R/L, 11R/L.
3. Flashcard mode.
4. 15-question quiz with immediate feedback.
5. Case mode with 3 realistic staging cases.
6. Content stored in JSON files for easy editing.
7. Mobile-responsive layout.
8. Accessibility: keyboard navigation and alt text.
9. Disclaimer: educational use only.
Use synthetic cases only. Create the folder structure and starter components.9 - Starter projects
Beginner projects that teach useful skills
| Project | Skills learned | Stack | Safety level |
|---|---|---|---|
| Procedure checklist generator | Forms, conditional display, printable summaries. | React/Vite or Streamlit. | Low if educational and no PHI. |
| EBUS station flashcards | JSON content, UI components, quiz state. | React/Vite + GitHub Pages. | Low. |
| Synthetic CT report nodule parser | Regex, natural language parsing, CSV export. | Python + Streamlit. | Low with synthetic data. |
| Board review question bank | Data modeling, search/filter, scoring, spaced repetition. | React or Next.js. | Low. |
| REDCap data dictionary generator | CSV schemas, validation rules, research workflow. | Python. | Medium; coordinate with the research team. |
| Literature RAG assistant | Embeddings, document ingestion, retrieval, citation display. | Python + vector database + LLM API. | Medium to high depending on use. |
| Clinical decision support prototype | Guideline logic, validation, audit trails, governance. | Usually more than a beginner stack. | High; involve IT, compliance, and regulatory experts early. |
10 - Safety and governance
Build responsibly
Healthcare software has a different risk profile than a hobby app. Treat safety as a design requirement, not a final checklist.
PHI is not prompt material
Use synthetic or properly de-identified data. If a vendor handles PHI for a covered entity, business associate obligations may apply.
Secrets stay out of GitHub
Never commit API keys, passwords, tokens, database URLs, exports, or patient files. Use environment variables and secret managers.
Clinical output must be checked
Recommendations, registry values, coding suggestions, staging, risk scores, and triage flags need expert review and validation.
Know when it becomes device-like
Software that supports diagnosis or treatment may enter FDA clinical decision support or SaMD territory. Get institutional guidance early.
Pre-share checklist
- No patient names, dates, MRNs, accession numbers, locations, faces, voice, or identifiers.
- No secrets in code, screenshots, logs, notebooks, or GitHub history.
- README explains purpose, limitations, install steps, and data policy.
- Clinical content reviewed by a domain expert.
- Educational disclaimer or research disclaimer included.
- Build or test command passes.
- Repo visibility set intentionally: private for early work, public only when safe.
- Institutional IT, IRB, compliance, or CMIO involved when appropriate.
.env
.env.*
*.key
*.pem
*.csv
*.xlsx
*.dcm
*.nii
*.nii.gz
patient_data/
exports/
logs/
node_modules/
__pycache__/
.DS_Store11 - Learning pathway
A 30-day beginner plan for physicians
| Week | Goal | What to do | Deliverable |
|---|---|---|---|
| Week 1 | Understand the loop | Plan 3 small project ideas. Learn GitHub vocabulary. Run one Colab notebook. | One project specification. |
| Week 2 | Build a small script | Use Python to parse or summarize synthetic data. Ask AI to explain every line. Save to GitHub. | A working script or notebook. |
| Week 3 | Build a simple app | Use Streamlit or React/Vite to make a quiz, checklist, or dashboard. Commit daily. | A local app that runs. |
| Week 4 | Review and share | Ask AI and colleagues to critique. Add README, disclaimer, tests, and a simple sharing plan. | A shareable link or private demo. |
12 - Useful links
Curated links for clinician-builders
AI coding assistants and IDEs
GitHub, hosting, and deployment
Data apps, notebooks, and research tools
Medical imaging and educational assets
Healthcare AI safety and governance
13 - Glossary
Plain-English glossary
| Term | Meaning |
|---|---|
| App | A software tool people can use: website, dashboard, mobile app, calculator, notebook, or script. |
| CLI | Command-line interface. A text box where you run commands. |
| Component | A reusable piece of a web app, like a quiz card, navigation bar, or anatomy panel. |
| Dependency | A package your project relies on. |
| Environment variable | A private setting used for secrets like API keys. Do not hard-code secrets in files. |
| Framework | A structured way to build software, such as React, Next.js, Streamlit, or Django. |
| JSON | A structured text format for data. Excellent for quiz questions, case data, and configuration. |
| Linting | Automated checking for code style and common mistakes. |
| MCP | Model Context Protocol, a way for AI tools to connect to external tools and data sources. Use carefully. |
| Package manager | Tool that installs dependencies, such as npm for JavaScript or uv/pip for Python. |
| Pull request | A proposed change set for review before merging into the main project. |
| RAG | Retrieval-augmented generation: an AI system that retrieves relevant documents before answering. |
| Static site | A website made of HTML, CSS, and JavaScript files that can be hosted simply. |
| Test | Code that checks whether your code behaves as expected. |