VEuPathDB · bobular · Oct 18, 2025 · Oct 18, 2025 · Oct 18, 2025 · Oct 18, 2025
diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,8 @@ tmp/
 node_modules/
 dist/
 data/
+!comparison/data/
+
 *~
 
 .yarn

diff --git a/CLAUDE-ai-provider-comparison.md b/CLAUDE-ai-provider-comparison.md
diff --git a/comparison/config/sites.json b/comparison/config/sites.json
@@ -0,0 +1,65 @@
+{
+  "public_site": {
+    "name": "VectorBase",
+    "base_url": "https://vectorbase.org/vectorbase"
+  },
+  "_analysis_model": {
+    "model_string": "claude-sonnet-4-5-20250929",
+    "name": "claude4_5",
+    "model": "Claude Sonnet 4.5",
+    "platform": "anthropic"
+  },
+  "__analysis_model": {
+    "model_string": "claude-sonnet-4-20250514",
+    "name": "claude4",
+    "model": "Claude Sonnet 4",
+    "platform": "anthropic"
+  },
+  "analysis_model": {
+    "model_string": "gpt-5-2025-08-07",
+    "name": "gpt5",
+    "model": "GPT-5 (minimal reasoning)",
+    "platform": "openai"
+  },
+  "sites": [
+    {
+      "name": "claude4_5",
+      "hostname": "bmaccallum.vectorbase.org",
+      "appPath": "vectorbase.bmaccallum",
+      "model": "Claude Sonnet 4.5",
+      "skip": true,
+      "disableGenePageLinks": true
+    },
+    {
+      "name": "claude4_5thinking",
+      "hostname": "bmaccallum.vectorbase.org",
+      "appPath": "vectorbase.bmaccallum",
+      "model": "Claude Sonnet 4.5 Thinking",
+      "skip": false,
+      "disableGenePageLinks": false
+    },
+    {
+      "name": "claude4",
+      "hostname": "bmaccallum.vectorbase.org",
+      "appPath": "vectorbase.bmaccallum",
+      "model": "Claude Sonnet 4",
+      "skip": true
+    },
+    {
+      "name": "gpt5",
+      "hostname": "bmaccallum-b.vectorbase.org",
+      "appPath": "vectorbase.bmaccallum-b",
+      "model": "GPT-5",
+      "skip": false
+    },
+    {
+      "name": "gpt4o",
+      "hostname": "qa.vectorbase.org",
+      "appPath": "vectorbase.b69",
+      "model": "GPT-4o",
+      "skip": true
+    }
+  ],
+  "endpoint": "/service/record-types/gene/searches/single_record_question_GeneRecordClasses_GeneRecordClass/reports/aiExpression",
+  "projectId": "VectorBase"
+}
diff --git a/comparison/data/.gitignore b/comparison/data/.gitignore
@@ -0,0 +1,10 @@
+# Ignore most intermediate data files
+summaries/
+comparisons/
+condensed/
+*.json
+*.zip
+
+# But DO check in the final aggregate reports (~20MB)
+# These are the final research outputs worth preserving
+!aggregate-reports/
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diff --git a/comparison/data/aggregate-reports/claude4/html-summaries/AGAP012703-gpt4o.html b/comparison/data/aggregate-reports/claude4/html-summaries/AGAP012703-gpt4o.html
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diff --git a/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-claude4.html b/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-claude4.html
diff --git a/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-claude4_5.html b/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-claude4_5.html
diff --git a/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-claude4_5thinking.html b/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-claude4_5thinking.html
diff --git a/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-gpt4o.html b/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-gpt4o.html
diff --git a/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-gpt5.html b/comparison/data/aggregate-reports/claude4/html-summaries/AGAP013543-gpt5.html
diff --git a/comparison/data/aggregate-reports/claude4/index.html b/comparison/data/aggregate-reports/claude4/index.html
@@ -0,0 +1,76 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <title>Model Comparison Reports - Claude Sonnet 4</title>
+  <script src="https://cdn.tailwindcss.com"></script>
+</head>
+<body class="bg-gray-100 min-h-screen py-8">
+  <div class="container mx-auto px-4 max-w-6xl">
+    <div class="bg-white shadow-md rounded-lg p-6 mb-6">
+      <h1 class="text-3xl font-bold text-gray-800 mb-2">
+        VEuPathDB AI Gene Expression Summaries
+      </h1>
+      <p class="text-gray-600">
+        <span class="font-semibold">Analysis by:</span> Claude Sonnet 4
+      </p>
+    </div>
+
+    <div class="bg-white shadow-md rounded-lg p-6 mb-6">
+      <h2 class="text-2xl font-bold text-gray-800 mb-4">Model Comparison Matrix</h2>
+      <div class="bg-blue-50 border-l-4 border-blue-400 p-3 mb-4">
+        <p class="text-sm text-gray-700">
+          <span class="font-semibold">How to read this matrix:</span> Each cell shows links to comparison reports
+          for the corresponding model pair. The matrix shows only the upper triangle since comparisons are symmetric.
+          Click <strong>HTML</strong> for the formatted report or <strong>JSON</strong> for the raw data.
+        </p>
+      </div>
+
+    <div class="overflow-x-auto">
+      <table class="min-w-full bg-white shadow-md rounded-lg">
+        <thead>
+          <tr class="bg-gray-100 border-b border-gray-300">
+            <th class="px-4 py-3 text-left text-sm font-semibold text-gray-700">Model</th>
+            <th class="px-4 py-3 text-center text-sm font-semibold text-gray-700">claude4</th><th class="px-4 py-3 text-center text-sm font-semibold text-gray-700">claude4_5</th><th class="px-4 py-3 text-center text-sm font-semibold text-gray-700">claude4_5thinking</th><th class="px-4 py-3 text-center text-sm font-semibold text-gray-700">gpt4o</th><th class="px-4 py-3 text-center text-sm font-semibold text-gray-700">gpt5</th>
+          </tr>
+        </thead>
+        <tbody>
+
+      <tr class="border-t border-gray-200">
+        <th class="px-4 py-3 text-left text-sm font-semibold text-gray-700 bg-gray-50">claude4</th>
+        <td class="px-4 py-3 bg-gray-200 text-center text-gray-400">—</td><td class="px-4 py-3 text-center text-sm"><a href="claude4-claude4_5-report.html" class="text-blue-600 hover:text-blue-800 font-medium">HTML</a> / <a href="claude4-claude4_5-report.json" class="text-gray-600 hover:text-gray-800 font-medium">JSON</a></td><td class="px-4 py-3 text-center text-gray-400 text-sm">—</td><td class="px-4 py-3 text-center text-sm"><a href="claude4-gpt4o-report.html" class="text-blue-600 hover:text-blue-800 font-medium">HTML</a> / <a href="claude4-gpt4o-report.json" class="text-gray-600 hover:text-gray-800 font-medium">JSON</a></td><td class="px-4 py-3 text-center text-sm"><a href="claude4-gpt5-report.html" class="text-blue-600 hover:text-blue-800 font-medium">HTML</a> / <a href="claude4-gpt5-report.json" class="text-gray-600 hover:text-gray-800 font-medium">JSON</a></td>
+      </tr>
+
+      <tr class="border-t border-gray-200">
+        <th class="px-4 py-3 text-left text-sm font-semibold text-gray-700 bg-gray-50">claude4_5</th>
+        <td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-200 text-center text-gray-400">—</td><td class="px-4 py-3 text-center text-sm"><a href="claude4_5-claude4_5thinking-report.html" class="text-blue-600 hover:text-blue-800 font-medium">HTML</a> / <a href="claude4_5-claude4_5thinking-report.json" class="text-gray-600 hover:text-gray-800 font-medium">JSON</a></td><td class="px-4 py-3 text-center text-sm"><a href="claude4_5-gpt4o-report.html" class="text-blue-600 hover:text-blue-800 font-medium">HTML</a> / <a href="claude4_5-gpt4o-report.json" class="text-gray-600 hover:text-gray-800 font-medium">JSON</a></td><td class="px-4 py-3 text-center text-sm"><a href="claude4_5-gpt5-report.html" class="text-blue-600 hover:text-blue-800 font-medium">HTML</a> / <a href="claude4_5-gpt5-report.json" class="text-gray-600 hover:text-gray-800 font-medium">JSON</a></td>
+      </tr>
+
+      <tr class="border-t border-gray-200">
+        <th class="px-4 py-3 text-left text-sm font-semibold text-gray-700 bg-gray-50">claude4_5thinking</th>
+        <td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-200 text-center text-gray-400">—</td><td class="px-4 py-3 text-center text-gray-400 text-sm">—</td><td class="px-4 py-3 text-center text-sm"><a href="claude4_5thinking-gpt5-report.html" class="text-blue-600 hover:text-blue-800 font-medium">HTML</a> / <a href="claude4_5thinking-gpt5-report.json" class="text-gray-600 hover:text-gray-800 font-medium">JSON</a></td>
+      </tr>
+
+      <tr class="border-t border-gray-200">
+        <th class="px-4 py-3 text-left text-sm font-semibold text-gray-700 bg-gray-50">gpt4o</th>
+        <td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-200 text-center text-gray-400">—</td><td class="px-4 py-3 text-center text-sm"><a href="gpt4o-gpt5-report.html" class="text-blue-600 hover:text-blue-800 font-medium">HTML</a> / <a href="gpt4o-gpt5-report.json" class="text-gray-600 hover:text-gray-800 font-medium">JSON</a></td>
+      </tr>
+
+      <tr class="border-t border-gray-200">
+        <th class="px-4 py-3 text-left text-sm font-semibold text-gray-700 bg-gray-50">gpt5</th>
+        <td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-50"></td><td class="px-4 py-3 bg-gray-200 text-center text-gray-400">—</td>
+      </tr>
+
+        </tbody>
+      </table>
+    </div>
+
+    </div>
+
+    <footer class="text-center text-gray-500 text-sm mt-8">
+      Generated on 11/11/2025, 4:28:23 PM
+    </footer>
+  </div>
+</body>
+</html>
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,6 +3,8 @@ tmp/ @@
     node_modules/
     dist/
     data/
+    !comparison/data/
     *~
     .yarn
@@ Expand Down @@