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+++ b/README.md
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# 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.
diff --git a/ai-assisted-research-tools/README.md b/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`.
diff --git a/ai-assisted-research-tools/docs/demo-script.md b/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.
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+
diff --git a/ai-assisted-research-tools/docs/demo/dashboard.png b/ai-assisted-research-tools/docs/demo/dashboard.png
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diff --git a/ai-assisted-research-tools/package.json b/ai-assisted-research-tools/package.json
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+{
+ "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"
+ }
+}
diff --git a/ai-assisted-research-tools/public/app.js b/ai-assisted-research-tools/public/app.js
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+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) => `${escapeHtml(item)}`).join("");
+ elements.nextSteps.innerHTML = summary.nextSteps.map((item) => `${escapeHtml(item)}`).join("");
+}
+
+function renderReview() {
+ elements.template.textContent = dashboard.review.template;
+ elements.issues.innerHTML = dashboard.review.issues
+ .map(
+ (issue) => `
+
+
+ ${issue.type}
+ ${issue.severity}
+
+ ${escapeHtml(issue.message)}
+ ${escapeHtml(issue.evidence)}
+
+ `
+ )
+ .join("");
+}
+
+function renderCitations(citationPayload) {
+ elements.citations.innerHTML = citationPayload.recommendations
+ .map(
+ (paper) => `
+
+
+ ${escapeHtml(paper.title)}
+ ${paper.score.toFixed(2)}
+
+ ${escapeHtml(paper.reason)}
+ ${escapeHtml(paper.formatted)}
+
+
+ `
+ )
+ .join("");
+}
+
+function profileItem(label, value) {
+ return `${label}${escapeHtml(String(value))}
`;
+}
+
+async function fetchJson(path) {
+ const response = await fetch(path);
+ if (!response.ok) throw new Error(`Request failed: ${response.status}`);
+ return response.json();
+}
+
+function escapeHtml(value) {
+ return value.replace(/[&<>"']/g, (char) => ({ "&": "&", "<": "<", ">": ">", '"': """, "'": "'" })[char]);
+}
+
+document.querySelectorAll("[data-mode]").forEach((button) => {
+ button.addEventListener("click", () => {
+ document.querySelectorAll("[data-mode]").forEach((item) => item.classList.toggle("active", item === button));
+ renderSummary(button.dataset.mode);
+ });
+});
+
+elements.style.addEventListener("change", async () => {
+ renderCitations(await fetchJson(`/api/citations?style=${encodeURIComponent(elements.style.value)}`));
+});
+
+loadDashboard().catch((error) => {
+ document.body.innerHTML = `${escapeHtml(error.stack || error.message)}`;
+});
diff --git a/ai-assisted-research-tools/public/index.html b/ai-assisted-research-tools/public/index.html
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+
+
+
+
+
+ SCIBASE AI-Assisted Research Tools
+
+
+
+
+
+
+
SCIBASE.AI / issue #13
+
AI-Assisted Research Tools
+
+ --
+ review score
+
+
+
+
+
+
+
+
+
+
AI Paper Summarizer
+
Domain-aware summaries
+
+
+
+
+
+
+
+
+
AI Peer Review Aid
+
Diagnostic manuscript report
+
+
+
+
+
AI Citation Tool
+
Recommendations and insert text
+
+
+