Add research reproducibility intelligence suite

research-reproducibility-intelligence/README.md

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+# Research Reproducibility Intelligence
+
+Self-contained AI-powered research assistant suite milestone for [SCIBASE.AI issue #16](https://github.com/SCIBASE-AI/SCIBASE.AI/issues/16).
+
+This module turns a scientific project packet into a deterministic assistant report covering auto peer-review, reproducibility checks, and research-gap discovery. It is designed for easy review: no API keys, no external services, no package install required beyond Node.js.
+
+## What It Adds
+
+- Auto peer-review report with manuscript structure checks, clarity findings, statistical reporting signals, and claim-to-evidence alignment.
+- Reproducibility report with artifact fingerprinting, pinned dependency checks, runnable file detection, data dictionary/source data checks, and a runbook.
+- Sandbox execution plan and evidence validation for notebooks/scripts, including disabled-network policy, resource limits, output hashes, execution logs, and reported-output consistency checks.
+- Linked prior reproducibility attempts, sorted by current artifact fingerprint match and recency.
+- Research-gap feed that ranks corpus items by relevance, replication gap, limitation signals, and novelty.
+- Workflow orchestration that converts findings into staged, owner-assigned, evidence-hashed actions.
+- Combined assistant packet with readiness score, orchestration status, and next-action queue.
+- Sample project fixture, tests, requirement mapping, CLI demo, and short demo GIF.
+
+## Run
+
+```bash
+cd research-reproducibility-intelligence
+npm run check
+npm test
+npm run demo
+```
+
+Expected demo shape:
+
+```json
+{
+  "project": "Longitudinal microbiome shifts after coastal flooding",
+  "readinessScore": 71,
+  "peerReviewScore": 62,
+  "reproducibilityStatus": "reproducible",
+  "sandboxSummary": {
+    "plannedRuns": 1,
+    "observedRuns": 1,
+    "cleanRuns": 1,
+    "consistentOutputs": 1,
+    "missingRuns": 0
+  },
+  "workflowBlocked": true,
+  "workflowRiskScore": 88,
+  "topWorkflowAction": {
+    "id": "review-1",
+    "stage": "peer-review",
+    "status": "blocking",
+    "owner": "Dr. Chen"
+  },
+  "linkedAttempt": {
+    "id": "attempt-2026-04-dry-run",
+    "matchesCurrentArtifacts": true
+  },
+  "topResearchGap": {
+    "paperId": "paper-1",
+    "priority": 0.8
+  }
+}
+```
+
+## Demo Artifact
+
+See [docs/demo.gif](docs/demo.gif) for a short visual walkthrough. The SVG source is included at [docs/demo.svg](docs/demo.svg).
+
+## Files
+
+- `src/research-assistant.js` - deterministic assistant engine.
+- `data/sample-project.json` - reviewable project/corpus fixture.
+- `test/research-assistant.test.js` - Node assertion tests.
+- `scripts/demo.js` - CLI demo.
+- `docs/issue-16-requirement-map.md` - maps implementation to bounty requirements.
+
+## AI-Assisted Disclosure
+
+This contribution was produced with AI assistance and manually verified with the local commands above.

research-reproducibility-intelligence/data/sample-project.json

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+{
+  "id": "proj-microbiome-2026",
+  "title": "Longitudinal microbiome shifts after coastal flooding",
+  "domain": "environmental health",
+  "interests": ["microbiome", "coastal flooding", "public health", "replication"],
+  "manuscript": {
+    "abstract": "We study microbiome shifts after coastal flooding using repeated household samples. The analysis suggests water intrusion changes bacterial diversity and may affect respiratory outcomes.",
+    "methods": "Households were sampled monthly. DNA sequencing was performed and results were normalized by read depth. The current manuscript clearly shows that flooding changes all exposed communities in a way that is obviously relevant to public health but the text still needs more direct evidence links.",
+    "results": "Observed diversity increased in exposed homes and returned toward baseline after remediation. The estimated effect size was larger in homes with persistent moisture.",
+    "limitations": "The pilot cohort is small and future work should replicate findings across more regions."
+  },
+  "claims": [
+    {
+      "id": "claim-1",
+      "text": "Flood exposure increases microbial diversity in sampled homes."
+    },
+    {
+      "id": "claim-2",
+      "text": "Hospital admissions declined after a regional policy intervention."
+    }
+  ],
+  "results": [
+    {
+      "id": "result-1",
+      "summary": "Microbial diversity increased in exposed homes after flooding and moved toward baseline after remediation."
+    },
+    {
+      "id": "result-2",
+      "summary": "Persistent moisture was associated with a larger estimated effect size."
+    }
+  ],
+  "files": [
+    { "name": "README.md" },
+    { "name": "analysis.ipynb" },
+    { "name": "data_dictionary.md" },
+    { "name": "samples.csv" },
+    { "name": "requirements.txt" }
+  ],
+  "dependencies": [
+    { "name": "python", "version": "3.12.3" },
+    { "name": "pandas", "version": "2.2.2" },
+    { "name": "scipy", "version": "1.13.0" }
+  ],
+  "sandboxPolicy": {
+    "image": "python:3.12-slim",
+    "network": "disabled",
+    "cpu": "2",
+    "memory": "4g",
+    "timeoutSeconds": 1800
+  },
+  "executionEvidence": [
+    {
+      "targetId": "run-13846284",
+      "exitCode": 0,
+      "durationSeconds": 142,
+      "outputHashes": ["sha256:diversity-summary-2026", "sha256:moisture-effect-2026"],
+      "logUrl": "https://example.org/reproducibility/proj-microbiome-2026/logs/analysis-ipynb",
+      "generatedArtifacts": ["diversity-summary.csv", "moisture-effect.json"],
+      "reportedArtifacts": ["diversity-summary.csv", "moisture-effect.json"]
+    }
+  ],
+  "workflowPreferences": {
+    "reviewOwner": "Dr. Chen",
+    "reproducibilityOwner": "Replication Desk",
+    "strategyOwner": "Research Strategy",
+    "publicationOwner": "Corresponding Author",
+    "deadline": "2026-05-28"
+  },
+  "reproducibilityAttempts": [
+    {
+      "id": "attempt-2026-04-dry-run",
+      "date": "2026-04-18",
+      "status": "successful",
+      "url": "https://example.org/reproducibility/proj-microbiome-2026/attempt-2026-04-dry-run",
+      "artifactFingerprint": "d584da823d10eaa1",
+      "notes": "Clean-room rerun reproduced reported diversity trends and stored execution logs."
+    },
+    {
+      "id": "attempt-2026-03-pilot",
+      "date": "2026-03-12",
+      "status": "partial",
+      "url": "https://example.org/reproducibility/proj-microbiome-2026/attempt-2026-03-pilot",
+      "artifactFingerprint": "legacy-artifacts",
+      "notes": "Earlier attempt predated dependency pinning and did not include all source data."
+    }
+  ],
+  "corpus": [
+    {
+      "id": "paper-1",
+      "title": "Microbial exposure after hurricane flooding",
+      "abstract": "A pilot study of household microbial exposure after hurricane flooding. Limitations include small sample size and unresolved replication across regions.",
+      "keywords": ["microbiome", "flooding", "indoor exposure"],
+      "replications": 0
+    },
+    {
+      "id": "paper-2",
+      "title": "Respiratory health after household remediation",
+      "abstract": "Remediation studies report mixed respiratory health outcomes and call for future work that links environmental sampling to clinical endpoints.",
+      "keywords": ["respiratory", "remediation", "public health"],
+      "replications": 1
+    },
+    {
+      "id": "paper-3",
+      "title": "Open protocols for environmental sequencing",
+      "abstract": "Protocol standardization improves reproducibility in environmental sequencing projects.",
+      "keywords": ["sequencing", "reproducibility", "protocol"],
+      "replications": 4
+    }
+  ]
+}

research-reproducibility-intelligence/docs/issue-16-requirement-map.md

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+# Issue #16 Requirement Map
+
+This module is a deterministic milestone for SCIBASE issue #16, AI-Powered Research Assistant Suite. It provides local, reviewable implementations of the three requested capabilities without external APIs or model keys.
+
+| Issue requirement | Implementation |
+| --- | --- |
+| Auto peer review reports | `buildPeerReviewReport()` checks manuscript structure, clarity risks, statistical reporting signals, and claim-to-evidence alignment. |
+| Reproducibility checker | `buildReproducibilityReport()` evaluates README/runbook presence, pinned dependencies, runnable artifacts, data dictionary, source data, sandbox execution plans, sandbox run evidence, reported-output consistency, and produces a reproducibility runbook. |
+| Auto-executes project code and notebooks in sandbox environments | `buildSandboxExecutionPlan()` creates disabled-network sandbox targets for notebooks/scripts with resource limits, read-only project mounts, writable output mounts, expected result IDs, and executable commands. `evaluateSandboxEvidence()` validates exit codes, output hashes, log URLs, generated artifacts, reported artifacts, clean-run counts, and missing-run counts. |
+| Research gap finder | `buildResearchGapFeed()` scans a corpus fixture for relevance, low replication count, limitation language, and novelty signals, then ranks opportunities. |
+| Real-time insights and workflow automation | `buildWorkflowOrchestration()` turns review, reproducibility, and gap signals into staged actions with owners, blockers, dependencies, risk score, deadline, and evidence hashes. |
+| Integrated assistant packet | `buildAssistantPacket()` combines review, reproducibility, gap discovery, workflow orchestration, one readiness score, and a prioritized action queue. |
+| Reviewer-friendly local demo | `npm run demo` prints the assistant packet summary for `data/sample-project.json`. |
+| Verification | `npm run check` and `npm test` run with Node built-ins only. |
+
+## Design Notes
+
+- The scoring is transparent and deterministic, which makes it suitable for review and regression testing.
+- The module is isolated under `research-reproducibility-intelligence/`.
+- It is intentionally credential-free. A future production integration can replace deterministic scoring with model-backed adapters while keeping the same report shape.

research-reproducibility-intelligence/package.json

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+{
+  "name": "scibase-research-reproducibility-intelligence",
+  "version": "0.1.0",
+  "private": true,
+  "description": "Deterministic AI-powered research assistant suite milestone for SCIBASE issue #16.",
+  "type": "commonjs",
+  "scripts": {
+    "check": "node --check src/research-assistant.js && node --check scripts/demo.js && node --check test/research-assistant.test.js",
+    "demo": "node scripts/demo.js",
+    "test": "node test/research-assistant.test.js"
+  }
+}

research-reproducibility-intelligence/scripts/demo.js

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+"use strict";
+
+const sampleProject = require("../data/sample-project.json");
+const { buildAssistantPacket } = require("../src/research-assistant");
+
+const packet = buildAssistantPacket(sampleProject);
+
+console.log(
+  JSON.stringify(
+    {
+      project: packet.project.title,
+      readinessScore: packet.readinessScore,
+      peerReviewScore: packet.peerReview.score,
+      reproducibilityStatus: packet.reproducibility.status,
+      sandboxTarget: packet.reproducibility.sandboxPlan.targets[0],
+      sandboxSummary: packet.reproducibility.sandboxEvidence.summary,
+      workflowBlocked: packet.workflow.blocked,
+      workflowRiskScore: packet.workflow.riskScore,
+      topWorkflowAction: packet.workflow.actions[0],
+      linkedAttempt: packet.reproducibility.linkedAttempts[0],
+      topResearchGap: packet.researchGaps[0],
+      nextActions: packet.nextActions.slice(0, 5),
+    },
+    null,
+    2,
+  ),
+);