Redesign homepage, add navbar, restructure navigation

_quarto.yml

@@ -3,8 +3,24 @@ project:
   output-dir: docs
 
 website:
-  title: "iSamples"  
+  title: "iSamples"
   favicon: assets/isamplesfavicon.ico
+  navbar:
+    logo: assets/isampleslogopetal.png
+    left:
+      - href: index.qmd
+        text: Home
+      - href: tutorials/progressive_globe.qmd
+        text: Interactive Explorer
+      - href: tutorials/index.qmd
+        text: Tutorials
+      - href: about.qmd
+        text: About
+    right:
+      - icon: github
+        href: https://github.com/isamplesorg
+      - icon: slack
+        href: https://isamples.slack.com/
   sidebar:
     style: "docked"
     search: true
@@ -17,50 +33,53 @@ website:
       - icon: twitter
         href: https://twitter.com/isamplesorg
     contents:
-      - href: index_alt.qmd
-        text: Alt Home Page
-        aria-label: "Goals of the iSamples project"
-      - href: about.qmd
-        text: Goals
-        aria-label: "Goals of the iSamples project"
-      - href: people.qmd
-        text: People
-        aria-label: "People of the iSamples project"
+      - href: index.qmd
+        text: Home
+      - text: "Interactive Explorer"
+        href: tutorials/progressive_globe.qmd
+        aria-label: "Explore 6.7M samples on an interactive globe"
+      - section: "Tutorials"
+        contents:
+        - text: "Overview"
+          href: tutorials/index.qmd
+        - text: "Deep-Dive Analysis"
+          href: tutorials/zenodo_isamples_analysis.qmd
+        - text: "3D Globe Visualization"
+          href: tutorials/parquet_cesium_isamples_wide.qmd
+        - text: "Progressive Globe (H3 + Samples)"
+          href: tutorials/progressive_globe.qmd
+        - text: "Interactive Explorer"
+          href: tutorials/isamples_explorer.qmd
+        - text: "Technical: Narrow vs Wide"
+          href: tutorials/narrow_vs_wide_performance.qmd
+      - section: "About"
+        contents:
+        - href: about.qmd
+          text: Goals
+        - href: people.qmd
+          text: People
       - section: "Information Architecture"
         contents:
           - design/index.qmd
           - design/requirements.md
           - text: Metadata Model
             href: "https://isamplesorg.github.io/metadata/"
           - models/index.qmd
-      - section: "Outputs"
+      - section: "Published Research"
         contents:
+        - text: Publications
+          href: pubs.qmd
         - text: 2020 SPNHC conference talk (video)
           href: https://youtu.be/eRUw5NMksFo?t=105
         - text: iSamples metadata model talk (slides, PDF)
           href: assets/2022-11_iSamplesMetadata.pdf
-        - text: Publications
-          href: pubs.qmd
+      - section: "Resources"
+        contents:
         - text: Zenodo community
           href: https://zenodo.org/communities/isamples
         - icon: github
           text: Github repositories
           href: "https://github.com/isamplesorg/"
-      - text: "Interactive Explorer"
-        href: tutorials/isamples_explorer.qmd
-        aria-label: "Search and explore 6.7M samples"
-      - section: "Tutorials"
-        contents:
-        - text: "Overview"
-          href: tutorials/index.qmd
-        - text: "Deep-Dive Analysis"
-          href: tutorials/zenodo_isamples_analysis.qmd
-        - text: "3D Globe Visualization"
-          href: tutorials/parquet_cesium_isamples_wide.qmd
-        - text: "Progressive Globe (H3 + Samples)"
-          href: tutorials/progressive_globe.qmd
-        - text: "Technical: Narrow vs Wide"
-          href: tutorials/narrow_vs_wide_performance.qmd
 
   repo-url: https://github.com/isamplesorg/isamplesorg.github.io
   repo-actions: [edit, issue]

index.qmd

@@ -1,20 +1,71 @@
 ---
 title: "Internet of Samples: iSamples"
-subtitle: "Toward an Interdisciplinary Cyberinfrastructure for Material Samples [![](https://img.shields.io/badge/NSF-2004839-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=2004839)"
+subtitle: "Toward an Interdisciplinary Cyberinfrastructure for Material Samples"
 number-sections: false
+toc: false
+sidebar: false
+page-layout: full
 ---
 
-The Internet of Samples (iSamples) is a multi-disciplinary and multi-institutional project funded by the National Science Foundation to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications.
+::: {.column-page}
 
-# Current Data Access: Geoparquet-Based Approach
+[![Explore 6.7 million samples on an interactive globe](assets/isamples_planet.jpg){fig-alt="Globe showing iSamples data points from 4 scientific repositories" width="100%"}](/tutorials/progressive_globe.html "Explore the interactive globe")
 
-**Note**: iSamples Central is currently unavailable. The project now uses **geoparquet files** for efficient, browser-based data access and analysis:
+:::
 
-📊    **[Interactive Tutorials](/tutorials/)** - Modern browser-based analysis with DuckDB-WASM
-<br/>
-🗺️ &nbsp;&nbsp; **Comprehensive Coverage** - Complete datasets from SESAR, OpenContext, GEOME, and Smithsonian
-<br/>
-🚀 &nbsp;&nbsp; **High Performance** - Fast, efficient data access with minimal memory usage
-<br/>
-🌐 &nbsp;&nbsp; **Universal Access** - Works in any modern browser without software installation
+::: {.callout-note appearance="minimal"}
+**6.7 million** physical samples | **4** repositories (SESAR, OpenContext, GEOME, Smithsonian) | **90+** countries | **Zero installation** — runs in your browser
+:::
 
+## Showcase: Real Samples from the Collection {.unnumbered}
+
+::: {layout-ncol=4 layout-valign="center"}
+
+[![](assets/IGSN_10.58052_DIA0000YL.png){group="showcase" fig-alt="Diamond sample"}](https://doi.org/10.58052/DIA0000YL "Diamond, collected 2019-06-11, Brazil")
+
+[![](assets/IGSN_10.58052_IEGIL000C.png){group="showcase" fig-alt="Fossil coral sample"}](https://doi.org/10.58052/IEGIL000C "Fossil coral, from 10000 BCE, Cayman Islands")
+
+[![](assets/ark_65665_337856f1a655e4ad78b1ef10a16dfb6e3.png){group="showcase" fig-alt="Fish specimen"}](https://n2t.net/ark:65665/337856f1a655e4ad78b1ef10a16dfb6e3 "Paracirrhites arcatus, collected 2006-03-10, French Polynesia")
+
+[![](assets/ark_28722_r2p24_vdm_19600211.png){group="showcase" fig-alt="Red-figure askoi"}](https://n2t.net/ark:28722/r2p24/vdm_19600211 "Red-figure askoi, late-4th to early-3rd century BCE, Murlo, Italy")
+
+:::
+
+::: {.callout-tip collapse="true"}
+## What is iSamples?
+
+The Internet of Samples (iSamples) is a multi-disciplinary and multi-institutional project funded by the **National Science Foundation** to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications.
+
+iSamples integrates data from four major scientific repositories:
+
+- **[SESAR](https://www.geosamples.org/)** — Earth science samples (rocks, minerals, sediments, soils)
+- **[OpenContext](https://opencontext.org/)** — Archaeological and cultural heritage materials
+- **[GEOME](https://geome-db.org/)** — Genomic and biological specimens
+- **[Smithsonian](https://collections.nmnh.si.edu/)** — Natural history museum collections
+:::
+
+::: {.callout-tip collapse="true"}
+## How can I access it?
+
+The project uses **geoparquet files + DuckDB-WASM** for efficient, browser-based data access and analysis — no server required.
+
+- **iSamples Full Dataset**: ~280 MB wide format, 6.7M samples
+- **Available via**: Cloudflare R2 with HTTP range requests
+- **Interactive tools**: [Progressive Globe](/tutorials/progressive_globe.html) for visual exploration, [Interactive Explorer](/tutorials/isamples_explorer.html) for search and filtering
+
+All analysis happens in your browser. Only the data you need is downloaded — typically less than 1 MB for initial exploration.
+:::
+
+::: {.callout-tip collapse="true"}
+## Why browser-based?
+
+- **Universal access** — No installation, works in any modern browser
+- **Fast analysis** — 5-10x faster than downloading full datasets
+- **Memory efficient** — Analyze 300MB datasets using less than 100MB browser memory
+- **Minimal transfer** — Only download the columns and rows you need
+- **Reproducible** — Share a URL and anyone can see exactly what you see
+:::
+
+---
+
+[![](assets/moorea_cover.jpg){width="100%" group="showcase" fig-alt="iSamples data visualization from Moorea"}](https://youtu.be/JzNadmklzNs "Watch the iSamples data visualization video")