feat: add AI-assisted research tools module

README.md

@@ -1,2 +1,6 @@
 # deepevents.ai
 deepevents.ai main codebase
+
+## Modules
+
+- [`ai-assisted-research-tools`](./ai-assisted-research-tools) - runnable prototype for AI paper summaries, peer review diagnostics, and citation recommendations for scientific manuscripts.

ai-assisted-research-tools/README.md

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+# AI-Assisted Research Tools
+
+This module is a self-contained implementation for SCIBASE.AI issue #13. It provides a runnable MVP for three AI-assisted research workflows: paper summarization, peer review diagnostics, and citation recommendation.
+
+## What It Covers
+
+- AI Paper Summarizer
+  - Abstract, executive, and layperson summary modes.
+  - Domain-aware keyword extraction and manuscript profiling.
+  - Key findings, implications, and recommended next steps.
+- AI Peer Review Aid
+  - Diagnostic report for similarity, grammar/clarity, statistical reporting, and compliance gaps.
+  - Domain templates for biology, physics, and social science.
+  - Checklist output for ethics, consent, data availability, uncertainty, and related statements.
+- AI Citation Tool
+  - Context-aware citation retrieval from a local open-corpus fixture.
+  - APA, MLA, and Nature formatting.
+  - Similar-paper suggestions and manuscript insertion snippets.
+- Browser demo and JSON API
+  - Static dashboard for reviewers.
+  - No external services, keys, seed funding, or paid APIs required.
+
+## Run Locally
+
+```bash
+cd ai-assisted-research-tools
+npm test
+npm start
+```
+
+Then open `http://localhost:4128`.
+
+## API Surface
+
+- `GET /api/dashboard` returns the full manuscript profile, all summary modes, peer review report, and citation recommendations.
+- `GET /api/summarize?mode=abstract|executive|layperson` returns one summary mode.
+- `GET /api/review` returns the diagnostic peer review report.
+- `GET /api/citations?style=APA|MLA|Nature` returns formatted citation recommendations.
+
+## Requirement Mapping
+
+- Concise summaries of repositories, preprints, or uploaded PDFs: implemented as manuscript section summarization in `src/research-ai.js`.
+- Abstract, executive, and layperson modes: implemented by `summarizePaper`.
+- Domain-aware output: implemented through keyword extraction, domain inference, and review templates.
+- Key findings, implications, and next steps: returned by `summarizePaper`.
+- Peer review diagnostic reports: implemented by `peerReviewAid`.
+- Plagiarism/similarity, grammar/clarity, statistical, and compliance checks: implemented by dedicated detector functions in `src/research-ai.js`.
+- Custom templates for biology, physics, and social science: configured in `src/data/open-corpus.js`.
+- Citation recommendations from open corpora: implemented by `recommendCitations` using a local Semantic Scholar/arXiv/PubMed-style corpus fixture.
+- APA, MLA, and Nature citation formatting: implemented by `formatCitation`.
+- Similar papers widget and insert text: returned by `recommendCitations` and rendered in the browser dashboard.
+
+## Verification
+
+```bash
+npm test
+node src/server.js
+```
+
+Optional smoke checks:
+
+```bash
+curl -s http://localhost:4128/api/dashboard
+curl -s "http://localhost:4128/api/summarize?mode=layperson"
+curl -s "http://localhost:4128/api/citations?style=Nature"
+```
+
+Demo artifacts are committed under `docs/demo/`, including `dashboard.png`, `ai-assisted-research-tools.svg`, and `ai-assisted-research-tools-demo.mp4`.

ai-assisted-research-tools/docs/demo-script.md

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+# Demo Script
+
+1. Run `npm test` to verify summarization, peer review, citation, and dashboard logic.
+2. Run `npm start` and open `http://localhost:4128`.
+3. Switch between Abstract, Executive, and Layperson summary modes.
+4. Review the diagnostic report for similarity, statistics, compliance, and clarity findings.
+5. Change the citation style selector and verify formatted APA, MLA, or Nature references.
+6. Use the citation insert text shown on each recommendation as the manuscript insertion preview.

ai-assisted-research-tools/package.json

@@ -0,0 +1,14 @@
+{
+  "name": "@scibase/ai-assisted-research-tools",
+  "version": "0.1.0",
+  "private": true,
+  "description": "Self-contained AI-assisted research tooling prototype for SCIBASE.AI issue #13.",
+  "type": "module",
+  "scripts": {
+    "start": "node src/server.js",
+    "test": "node --test test/*.test.js"
+  },
+  "engines": {
+    "node": ">=20"
+  }
+}

ai-assisted-research-tools/public/app.js

@@ -0,0 +1,98 @@
+let dashboard;
+
+const elements = {
+  title: document.querySelector("#title"),
+  profile: document.querySelector("#profile"),
+  highlighted: document.querySelector("#highlighted"),
+  score: document.querySelector("#score"),
+  summary: document.querySelector("#summary"),
+  findings: document.querySelector("#findings"),
+  nextSteps: document.querySelector("#nextSteps"),
+  template: document.querySelector("#template"),
+  issues: document.querySelector("#issues"),
+  citations: document.querySelector("#citations"),
+  style: document.querySelector("#style")
+};
+
+async function loadDashboard() {
+  dashboard = await fetchJson("/api/dashboard");
+  elements.title.textContent = dashboard.profile.title;
+  elements.profile.innerHTML = profileItem("Domain", dashboard.profile.domain) + profileItem("Words", dashboard.profile.wordCount) + profileItem("Keywords", dashboard.profile.keywords.slice(0, 5).join(", "));
+  elements.highlighted.textContent = dashboard.citations.highlightedText;
+  elements.score.textContent = dashboard.review.score;
+  renderSummary("abstract");
+  renderReview();
+  renderCitations(dashboard.citations);
+}
+
+function renderSummary(mode) {
+  const summary = dashboard.summaries[mode];
+  elements.summary.textContent = summary.summary;
+  elements.findings.innerHTML = summary.keyFindings.map((item) => `<li>${escapeHtml(item)}</li>`).join("");
+  elements.nextSteps.innerHTML = summary.nextSteps.map((item) => `<li>${escapeHtml(item)}</li>`).join("");
+}
+
+function renderReview() {
+  elements.template.textContent = dashboard.review.template;
+  elements.issues.innerHTML = dashboard.review.issues
+    .map(
+      (issue) => `
+        <article class="issue ${issue.severity}">
+          <div>
+            <span>${issue.type}</span>
+            <strong>${issue.severity}</strong>
+          </div>
+          <p>${escapeHtml(issue.message)}</p>
+          <small>${escapeHtml(issue.evidence)}</small>
+        </article>
+      `
+    )
+    .join("");
+}
+
+function renderCitations(citationPayload) {
+  elements.citations.innerHTML = citationPayload.recommendations
+    .map(
+      (paper) => `
+        <article class="citation">
+          <div>
+            <strong>${escapeHtml(paper.title)}</strong>
+            <span>${paper.score.toFixed(2)}</span>
+          </div>
+          <p>${escapeHtml(paper.reason)}</p>
+          <code>${escapeHtml(paper.formatted)}</code>
+          <button data-insert="${escapeHtml(paper.insertText)}">${escapeHtml(paper.insertText)}</button>
+        </article>
+      `
+    )
+    .join("");
+}
+
+function profileItem(label, value) {
+  return `<div><span>${label}</span><strong>${escapeHtml(String(value))}</strong></div>`;
+}
+
+async function fetchJson(path) {
+  const response = await fetch(path);
+  if (!response.ok) throw new Error(`Request failed: ${response.status}`);
+  return response.json();
+}
+
+function escapeHtml(value) {
+  return value.replace(/[&<>"']/g, (char) => ({ "&": "&amp;", "<": "&lt;", ">": "&gt;", '"': "&quot;", "'": "&#039;" })[char]);
+}
+
+document.querySelectorAll("[data-mode]").forEach((button) => {
+  button.addEventListener("click", () => {
+    document.querySelectorAll("[data-mode]").forEach((item) => item.classList.toggle("active", item === button));
+    renderSummary(button.dataset.mode);
+  });
+});
+
+elements.style.addEventListener("change", async () => {
+  renderCitations(await fetchJson(`/api/citations?style=${encodeURIComponent(elements.style.value)}`));
+});
+
+loadDashboard().catch((error) => {
+  document.body.innerHTML = `<pre>${escapeHtml(error.stack || error.message)}</pre>`;
+});

ai-assisted-research-tools/public/index.html

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+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>SCIBASE AI-Assisted Research Tools</title>
+    <link rel="stylesheet" href="/styles.css" />
+  </head>
+  <body>
+    <main class="shell">
+      <header class="topbar">
+        <div>
+          <p class="eyebrow">SCIBASE.AI / issue #13</p>
+          <h1>AI-Assisted Research Tools</h1>
+        </div>
+        <div class="score" aria-label="review quality score">
+          <span id="score">--</span>
+          <small>review score</small>
+        </div>
+      </header>
+
+      <section class="workspace">
+        <aside class="panel manuscript">
+          <p class="label">Manuscript</p>
+          <h2 id="title">Loading manuscript...</h2>
+          <div id="profile" class="profile-grid"></div>
+          <div class="highlight">
+            <p class="label">Highlighted text</p>
+            <p id="highlighted"></p>
+          </div>
+        </aside>
+
+        <section class="panel summaries">
+          <div class="section-heading">
+            <div>
+              <p class="label">AI Paper Summarizer</p>
+              <h2>Domain-aware summaries</h2>
+            </div>
+            <div class="segmented" role="tablist" aria-label="summary modes">
+              <button class="active" data-mode="abstract">Abstract</button>
+              <button data-mode="executive">Executive</button>
+              <button data-mode="layperson">Layperson</button>
+            </div>
+          </div>
+          <p id="summary" class="summary-text"></p>
+          <div class="columns">
+            <div>
+              <p class="label">Key findings</p>
+              <ul id="findings"></ul>
+            </div>
+            <div>
+              <p class="label">Next steps</p>
+              <ul id="nextSteps"></ul>
+            </div>
+          </div>
+        </section>
+
+        <section class="panel review">
+          <div class="section-heading">
+            <div>
+              <p class="label">AI Peer Review Aid</p>
+              <h2>Diagnostic manuscript report</h2>
+            </div>
+            <span id="template" class="tag"></span>
+          </div>
+          <div id="issues" class="issue-list"></div>
+        </section>
+
+        <section class="panel citations">
+          <div class="section-heading">
+            <div>
+              <p class="label">AI Citation Tool</p>
+              <h2>Recommendations and insert text</h2>
+            </div>
+            <select id="style" aria-label="citation style">
+              <option>Nature</option>
+              <option>APA</option>
+              <option>MLA</option>
+            </select>
+          </div>
+          <div id="citations" class="citation-list"></div>
+        </section>
+      </section>
+    </main>
+    <script src="/app.js" type="module"></script>
+  </body>
+</html>