Initial BIO-CODES website

Jekyll-based static site for bio-codes.github.io with:
- Hero, Challenge/Solution/Impact, ISCC explanation with SVG flow diagram
- Features grid, Tools showcase, Platform integrations
- Dark mode, responsive design, scroll-based nav highlighting
- GitHub Actions workflow for Pages deployment
- Data-driven content via _data/ YAML files

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: etzm

.github/workflows/jekyll.yml

@@ -0,0 +1,47 @@
+name: Deploy Jekyll site to Pages
+
+on:
+  push:
+    branches: ["main"]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.3"
+          bundler-cache: true
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v5
+      - name: Build with Jekyll
+        run: bundle exec jekyll build
+        env:
+          JEKYLL_ENV: production
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -0,0 +1,10 @@
+_site/
+.sass-cache/
+.jekyll-cache/
+.jekyll-metadata
+vendor/
+.DS_Store
+.claude/
+node_modules/
+*.swp
+*.swo

Gemfile

@@ -0,0 +1,9 @@
+source "https://rubygems.org"
+
+gem "jekyll", "~> 4.3"
+gem "webrick"
+
+group :jekyll_plugins do
+  gem "jekyll-seo-tag"
+  gem "jekyll-sitemap"
+end

Gemfile.lock

@@ -0,0 +1,241 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.8.9)
+      public_suffix (>= 2.0.2, < 8.0)
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+    concurrent-ruby (1.3.6)
+    csv (3.3.5)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    eventmachine (1.2.7)
+    ffi (1.17.3)
+    ffi (1.17.3-aarch64-linux-gnu)
+    ffi (1.17.3-aarch64-linux-musl)
+    ffi (1.17.3-arm-linux-gnu)
+    ffi (1.17.3-arm-linux-musl)
+    ffi (1.17.3-arm64-darwin)
+    ffi (1.17.3-x86-linux-gnu)
+    ffi (1.17.3-x86-linux-musl)
+    ffi (1.17.3-x86_64-darwin)
+    ffi (1.17.3-x86_64-linux-gnu)
+    ffi (1.17.3-x86_64-linux-musl)
+    forwardable-extended (2.6.0)
+    google-protobuf (4.34.0)
+      bigdecimal
+      rake (~> 13.3)
+    google-protobuf (4.34.0-aarch64-linux-gnu)
+      bigdecimal
+      rake (~> 13.3)
+    google-protobuf (4.34.0-aarch64-linux-musl)
+      bigdecimal
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+    google-protobuf (4.34.0-x86_64-linux-musl)
+      bigdecimal
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+      concurrent-ruby (~> 1.0)
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+      json (~> 2.6)
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+      pathutil (~> 0.9)
+      rouge (>= 3.0, < 5.0)
+      safe_yaml (~> 1.0)
+      terminal-table (>= 1.8, < 4.0)
+      webrick (~> 1.7)
+    jekyll-sass-converter (3.1.0)
+      sass-embedded (~> 1.75)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-sitemap (1.4.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
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+      rexml (>= 3.4.4)
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.4)
+    listen (3.10.0)
+      logger
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.7.0)
+    mercenary (0.4.0)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (7.0.5)
+    rake (13.3.1)
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+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
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+    sass-embedded (1.97.3)
+      google-protobuf (~> 4.31)
+      rake (>= 13)
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+      unicode-display_width (>= 1.1.1, < 3)
+    unicode-display_width (2.6.0)
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+
+PLATFORMS
+  aarch64-linux-android
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+  aarch64-linux-musl
+  arm-linux-androideabi
+  arm-linux-gnu
+  arm-linux-gnueabihf
+  arm-linux-musl
+  arm-linux-musleabihf
+  arm64-darwin
+  riscv64-linux-android
+  riscv64-linux-gnu
+  riscv64-linux-musl
+  ruby
+  x86-linux-gnu
+  x86-linux-musl
+  x86_64-darwin
+  x86_64-linux-android
+  x86_64-linux-gnu
+  x86_64-linux-musl
+
+DEPENDENCIES
+  jekyll (~> 4.3)
+  jekyll-seo-tag
+  jekyll-sitemap
+  webrick
+
+CHECKSUMS
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+  terminal-table (3.0.2) sha256=f951b6af5f3e00203fb290a669e0a85c5dd5b051b3b023392ccfd67ba5abae91
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+
+BUNDLED WITH
+  4.0.6

_config.yml

@@ -0,0 +1,31 @@
+# Site settings
+title: "BIO-CODES"
+description: "Content-Based Identifiers for Bioimaging Data — ISO 24138 ISCC implementation for scientific imaging"
+url: "https://bio-codes.github.io"
+baseurl: ""
+
+# Project
+tagline: "Content-Based Identifiers for Bioimaging Data"
+
+# Build settings
+markdown: kramdown
+permalink: pretty
+
+# Exclude from build
+exclude:
+  - Gemfile
+  - Gemfile.lock
+  - README.md
+  - .DS_Store
+  - vendor
+  - .claude
+  - files
+  - Logos
+  - Copy
+  - iscc-flow-diagram-v3.html
+  - node_modules
+
+# Plugins
+plugins:
+  - jekyll-seo-tag
+  - jekyll-sitemap

_data/challenge.yml

@@ -0,0 +1,56 @@
+# _data/challenge.yml
+# ─────────────────────────────────────────────────────────────────
+# The three-column Challenge / Solution / Scientific Impact cards.
+# Each card has an icon, heading, and a list of bullet items.
+# Items support optional `strong` for the bold lead-in phrase.
+# ─────────────────────────────────────────────────────────────────
+
+section_title: "Enhancing AI-Readiness of Bioimaging Data<br/>with Content-Based Identifiers"
+
+cards:
+  - id: challenge
+    icon: "⚠"
+    heading: Challenge
+    items:
+      - strong: "Growing volume of data:"
+        text: >
+          Bio(imaging) data exist at different states — raw, repository,
+          publications — with no shared identity across them.
+      - strong: "No Audit Trail:"
+        text: >
+          Challenges to verify data integrity or detect manipulation
+          after the fact.
+      - strong: "Lost Provenance:"
+        text: >
+          Published figures are disconnected from raw data and the
+          processing steps that produced them.
+
+  - id: solution
+    icon: "💡"
+    heading: Solution
+    items:
+      - strong: "International Standard Content Code (ISCC ISO 24138)."
+        text: >
+          Open and open-source. Interoperable content identification &
+          fingerprinting system. Computed directly from the asset itself —
+          can never be removed or decoupled from the data.
+      - strong: "Anyone can compute ISCCs"
+        text: >
+          from available data — independently and without any central authority.
+          Use the ISCC Generator at iscc.io/resources.
+        url: https://iscc.io/resources/
+      - strong: "Generating, signing, and timestamping ISCCs"
+        text: >
+          creates persistent identifiers to securely reference and link
+          data in repositories with images in papers.
+
+  - id: impact
+    icon: "🔬"
+    heading: Scientific Impact
+    items:
+      - strong: "Cryptographic figure data verification"
+        text: "via the ISCC audit trail."
+      - strong: "Improved data integrity, transparency, and reusability."
+        text: ""
+      - strong: "Enhanced AI-readiness"
+        text: "of bioimaging datasets for trusted AI applications."