Nicholas Johnson — Personal Website

Personal portfolio website for Nicholas Johnson, a Neuroscience student at George Mason University with a concentration in Computational Neuroscience.

Live site: nicholas-johnson-website.vercel.app | Tool: nicholas-johnson-website.vercel.app/tool | NEUR 327: nicholas-johnson-website.vercel.app/neur327 | HH Simulator: nicholas-johnson-website.vercel.app/hodgkin-huxley

Resume (PDF, always on GitHub): Nicholas_Johnson_Resume.pdf

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Source Code

api/index.py — Python (Flask Backend)

The entire backend. Serves all pages and proxies the analysis service for structured research paper breakdowns.

api/templates/index.html — HTML / CSS / JavaScript (Portfolio Page)

The main portfolio page with hero section, interactive 3D neuron animation rendered on HTML5 Canvas, project cards, and contact information.

api/templates/tool.html — HTML / CSS / JavaScript (Scientific Article Tool)

Research paper analysis tool. Paste text or upload a PDF to get a structured 15-section breakdown. Streams responses in real time and renders formatted output with markdown.

api/templates/neur327.html — HTML / CSS / JavaScript (NEUR 327 Presentation)

Interactive 20-slide presentation on BiPOLES (Bidirectional Pair of Opsins for Light-induced Excitation and Silencing) for Cellular Neuroscience (NEUR 327). Features keyboard/click navigation, editable content fields, and optional Firebase real-time team sync.

api/templates/hodgkin-huxley.html — HTML / CSS / JavaScript (Hodgkin-Huxley Simulator)

Interactive Hodgkin-Huxley neuron simulator. Full 1952 equations, RK4 integration, current clamp and voltage clamp modes, Nernst-computed reversal potentials, adjustable conductances and ion concentrations.

requirements.txt — Python Dependencies

vercel.json — Deployment Configuration

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Overview

A Flask-powered portfolio featuring an interactive 3D neuron animation (action potential propagation rendered on HTML5 Canvas), project cards, contact information, and a Scientific Article Tool that produces structured 15-section breakdowns of research papers.

Flask Routes (api/index.py)

Route	Method	Description
/	GET	Serves the portfolio home page
/tool	GET	Serves the Scientific Article Tool
/neur327	GET	Serves the NEUR 327 BiPOLES presentation
/hodgkin-huxley	GET	Serves the Hodgkin-Huxley neuron simulator
/api/gemini	POST	Proxies analysis requests with SSE streaming

The analysis proxy keeps credentials secure on the server — frontend users never see or need them.

Portfolio Page — index.html

• Hero section — Name, university, degree, and bio on the left; interactive 3D neuron animation on the right. The neuron is rendered in JavaScript on a <canvas> element with perspective projection, depth sorting, click-and-drag rotation, and action potential cycling.
• Projects — Card grid linking to project pages.
• Contact — Email, GitHub, and LinkedIn links.

NEUR 327 Presentation — neur327.html

• BiPOLES — 20-slide interactive presentation on Bidirectional Pair of Opsins for Light-induced Excitation and Silencing.
• Keyboard navigation — Arrow keys and click to advance/retreat slides.
• Editable fields — Content-editable sections for collaborative group work.
• Firebase sync — Optional real-time team editing via Firebase Realtime Database.

Hodgkin-Huxley Simulator — hodgkin-huxley.html

• Full HH model — Membrane potential and ionic currents from the 1952 Hodgkin-Huxley equations.
• RK4 integration — 4th-order Runge-Kutta with 0.01 ms time step.
• Current clamp — Single pulse, pulse train, or step current injection.
• Voltage clamp — Command voltage steps with clamp current display.
• Nernst potentials — E_Na and E_K computed from user-adjustable ion concentrations.
• Adjustable conductances — g_Na, g_K, g_L, C_m with real-time updates.

Scientific Article Tool — tool.html

• Structured analysis — Paste text or upload a PDF of any research paper to get a 15-section breakdown. Handles full-length papers.
• 15-section structured output — TL;DR, problem, background, hypothesis, study design, methods, data, results, statistics, key figures, author interpretation, limitations, implications, future directions, and verdict.
• Real-time streaming with live cursor and markdown rendering (bold, italic, bullet points, numbered lists).

Deployment

Hosted on Vercel using the Python serverless runtime.

Environment Variable	Description
GEMINI_API_KEY	API key for the analysis service (server-side only)

npm i -g vercel
vercel --prod

Technologies

Technology	Role
Python / Flask	Backend server and API proxy
HTML5 Canvas	3D neuron animation with perspective projection
Vanilla JavaScript	All frontend logic — no frameworks
CSS Custom Properties	Design system with dark theme
PDF.js	Client-side PDF text extraction
Vercel	Python serverless hosting

Author

Nicholas Johnson