CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

This is a modern portfolio website for Anthony Fullam (fullam.net), a Senior Bioinformatics Software Engineer at EMBL. Built with Jekyll and customized Minimal Mistakes remote theme, the site showcases bioinformatics research, tools, publications, and professional experience. Hosted on GitHub Pages with a single-page scrolling design.

Development Commands

Local Development

# Install dependencies (requires Ruby and Bundler)
bundle install

# Serve the site locally with live reload
bundle exec jekyll serve

# Serve with drafts visible
bundle exec jekyll serve --drafts

# Build the site (output to _site/)
bundle exec jekyll build

Deployment

The site is deployed automatically via GitHub Pages when changes are pushed to the main branch. No manual deployment steps are required.

Site Architecture

Configuration

• _config.yml: Main Jekyll configuration containing site metadata, theme settings, author information, social links, and analytics (Google Analytics ID: G-N2BC96R915)
• remote_theme: Uses customized mmistakes/minimal-mistakes theme with extensive SCSS overrides

Layout & Design

• Single-page scrolling portfolio with sections: Hero, Featured Work, Publications, Skills, Experience
• Dark theme with bioinformatics-inspired color palette (blues, greens, purples)
• Custom layouts: _layouts/portfolio.html - Full-width sections with minimal navigation
• Custom components: _includes/ directory contains modular sections (hero, projects, publications, skills, timeline)
• Custom styling: _sass/custom/ directory with component-specific SCSS files
• Interactive features: Smooth scrolling, typing animation, counter animations, filterable publications

Data Structure

• _data/publications.yml: Research publications with metadata (title, journal, year, citations, links, tags)
• _data/projects.yml: Featured projects (GUNC, proGenomes, SPIRE, VIRE) with impact metrics
• _data/skills.yml: Technical expertise organized by category (Bioinformatics, Software Dev, Infrastructure)
• _data/timeline.yml: Professional experience with highlights and tech stacks
• _data/navigation.yml: Section navigation links

Assets

• assets/css/main.scss: Master stylesheet importing Minimal Mistakes + custom styles
• assets/js/: JavaScript files for interactivity (smooth-scroll.js, portfolio-interactions.js)
• assets/images/: Images and project screenshots

Key Features

• Modern portfolio design: Impact-focused, not CV-style
• Interactive publications: Filterable by type, searchable, with citation metrics
• Animated elements: Typing effect, counter animations, scroll-triggered fade-ins
• Particle background: Canvas-based animation in hero section
• Responsive design: Mobile-optimized with adaptive layouts
• SEO optimized: Meta tags, structured data, sitemap
• Analytics: Google Analytics integration

Jekyll Plugins

• jekyll-sitemap
• jekyll-feed
• jemoji
• jekyll-include-cache

Content Management

Updating Publications

Edit _data/publications.yml to add or update publications:

• Add to featured: array for prominent display
• Include: title, authors, journal, year, citations, DOI, links, tags
• Tags enable filtering: genomics, metagenomics, database, tools, etc.
• Set first_author: true for first-author publications

Updating Projects

Edit _data/projects.yml to add or modify featured projects:

• Include: name, tagline, description, impact metrics, tech_stack, links
• Set featured: true and featured_order for display priority
• Add project images to assets/images/projects/

Updating Skills

Edit _data/skills.yml to modify technical expertise:

• Organized by categories: Bioinformatics, Software Development, Data Science, Infrastructure
• Each skill includes: name, level (expert/advanced/intermediate), description, tools/frameworks
• Visual indicators automatically generated from level field

Updating Experience

Edit _data/timeline.yml to add or modify positions:

• Include: title, organization, location, dates, type (industry/academic)
• Add highlights array for key achievements
• List relevant technologies in tech array

Styling and Customization

Color Scheme

Colors defined in _sass/custom/variables.scss:

• Primary: $primary-bio-blue (#4A90E2)
• Secondary: $secondary-green (#7ED321)
• Accent: $accent-purple (#BD10E0)
• Backgrounds: $dark-bg, $darker-bg, $card-bg

Component Styles

Each section has dedicated SCSS in _sass/custom/:

• hero.scss - Hero section with typing animation
• projects.scss - Featured projects cards
• publications.scss - Publications grid and filters
• skills.scss - Skills matrix layout
• timeline.scss - Professional experience timeline

JavaScript Customization

Interactive features in assets/js/:

• smooth-scroll.js - Section navigation and scroll behavior
• portfolio-interactions.js - Animations, filters, counters, particles

Development Notes

• Site uses Minimal Mistakes as base theme with extensive customization
• Custom layouts override default theme behavior
• Jekyll Liquid templates in _includes/ for modular components
• All data-driven content stored in _data/ directory for easy updates
• GitHub Pages automatically rebuilds on push to main branch