SCIBASE-AI · pine-harbor · Aug 15, 2026
diff --git a/research-materials-authentication-assistant/README.md b/research-materials-authentication-assistant/README.md
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+# Research Materials Authentication Assistant
+
+This module adds a focused research-materials authentication guard for the AI-Powered Research Assistant Suite in issue `#16`.
+
+AI-assisted review can miss mundane but decisive reproducibility problems: an antibody without a traceable identifier, a stale validation panel, a contaminated cell line, a species mismatch, or a passage range that cannot be true. This assistant inspects synthetic manuscript review packets and returns release, review, or hold decisions with evidence-linked remediation.
+
+## Scope
+
+- Checks RRID-style identifiers for antibodies, cell lines, organism strains, primary cells, and reagents.
+- Flags missing lot or batch metadata for lot-sensitive materials.
+- Checks validation evidence freshness against a deterministic review date.
+- Holds contaminated cell-derived materials.
+- Checks reported passage ranges and reported passage numbers.
+- Compares material species and claimed organism against linked assays.
+- Holds antibody target mismatches when the antibody target does not match the measured assay target.
+- Produces JSON, Markdown, SVG, and MP4 demo artifacts.
+- Uses synthetic data only.
+- Uses no external AI APIs, credentials, private manuscripts, payment systems, or network calls.
+
+## Requirement Map
+
+| Issue #16 capability | Implementation |
+| --- | --- |
+| Auto peer review reports | Emits structured findings, severity, decision, confidence, and remediation. |
+| Methodological and reproducibility red flags | Detects identifier gaps, stale validation, contamination, passage errors, organism mismatch, and antibody target mismatch. |
+| Adaptive templates per domain | Supports packet-level `domain` and domain-specific reviewer notes. |
+| Claims vs evidence alignment | Compares material identity and validation evidence against linked assays and manuscript claims. |
+| Reproducible deterministic output | Demo and tests use fixed synthetic packets and dependency-free scoring. |
+
+## Run
+
+```bash
+npm test
+npm run demo
+npm run video
+npm run check
+```
+
+Demo artifacts are written to `reports/`:
+
+- `summary.json`
+- `reviewer-packet.md`
+- `summary.svg`
+- `demo.mp4`
+
+## Decisions
+
+- `RELEASE`: materials are traceable, authenticated, fresh, and aligned with the linked assays.
+- `REVIEW`: a reviewer should inspect missing identifiers, stale validation, species mismatch, or incomplete material provenance.
+- `HOLD`: release is blocked by critical reproducibility problems such as contamination, impossible passage metadata, or antibody target mismatch.
+
+## AI Assistance Disclosure
+
+Implemented with Codex assistance and locally verified with deterministic tests and generated artifacts.
diff --git a/research-materials-authentication-assistant/data/sample_material_packets.json b/research-materials-authentication-assistant/data/sample_material_packets.json
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+[
+  {
+    "id": "clean-organoid-panel",
+    "title": "Authenticated organoid cytokine response panel",
+    "domain": "translational immunology",
+    "reviewDate": "2026-08-15",
+    "materials": [
+      {
+        "name": "HBEC-Alpha authenticated airway cell line",
+        "type": "cell_line",
+        "role": "model system",
+        "rrid": "RRID:CVCL_SYN1",
+        "lot": "BANK-2026-07-A",
+        "source": "institutional biobank",
+        "species": "human",
+        "claimedOrganism": "human",
+        "validationEvidence": ["STR profile match", "certificate of analysis", "mycoplasma PCR negative"],
+        "validationDate": "2026-07-10",
+        "contaminationStatus": "negative",
+        "passageRange": { "min": 5, "max": 18 },
+        "reportedPassage": 9
+      },
+      {
+        "name": "Anti-IL6 clone S6",
+        "type": "antibody",
+        "role": "capture antibody",
+        "rrid": "RRID:AB_9000001",
+        "lot": "LOT-IL6-2606",
+        "source": "validated synthetic catalog",
+        "species": "human",
+        "target": "IL6",
+        "assayTargets": ["IL6"],
+        "validationEvidence": ["western blot specificity", "orthogonal ELISA spike recovery"],
+        "validationDate": "2026-06-14",
+        "contaminationStatus": "not_detected"
+      }
+    ],
+    "assays": [
+      {
+        "name": "IL6 secretion ELISA",
+        "materialName": "Anti-IL6 clone S6",
+        "organism": "human",
+        "target": "IL6",
+        "readout": "secreted cytokine concentration"
+      }
+    ],
+    "manuscriptClaims": [
+      "All primary materials were identity checked before cytokine-response analysis."
+    ]
+  },
+  {
+    "id": "review-stale-rrid-organism",
+    "title": "Stale antibody validation with organism mismatch",
+    "domain": "cell signaling",
+    "reviewDate": "2026-08-15",
+    "materials": [
+      {
+        "name": "Anti-pERK screening antibody",
+        "type": "antibody",
+        "role": "western blot antibody",
+        "rrid": "",
+        "lot": "WB-ERK-2019",
+        "source": "legacy freezer box",
+        "species": "mouse",
+        "claimedOrganism": "human",
+        "target": "pERK",
+        "assayTargets": ["pERK"],
+        "validationEvidence": ["vendor blot from 2019"],
+        "validationDate": "2019-03-04",
+        "contaminationStatus": "not_detected"
+      }
+    ],
+    "assays": [
+      {
+        "name": "Human pERK western blot",
+        "materialName": "Anti-pERK screening antibody",
+        "organism": "human",
+        "target": "pERK",
+        "readout": "phosphorylated ERK band intensity"
+      }
+    ],
+    "manuscriptClaims": [
+      "Human samples were assayed with pathway-specific antibody material."
+    ]
+  },
+  {
+    "id": "hold-contaminated-line",
+    "title": "Contaminated cell line in proliferation assay",
+    "domain": "cancer biology",
+    "reviewDate": "2026-08-15",
+    "materials": [
+      {
+        "name": "MCB-Tumor-2 working stock",
+        "type": "cell_line",
+        "role": "tumor model",
+        "rrid": "RRID:CVCL_SYN2",
+        "lot": "CELL-2026-05-B",
+        "source": "working stock",
+        "species": "human",
+        "claimedOrganism": "human",
+        "validationEvidence": ["STR profile match"],
+        "validationDate": "2026-05-12",
+        "contaminationStatus": "mycoplasma_positive",
+        "passageRange": { "min": 3, "max": 14 },
+        "reportedPassage": 11
+      }
+    ],
+    "assays": [
+      {
+        "name": "Proliferation growth curve",
+        "materialName": "MCB-Tumor-2 working stock",
+        "organism": "human",
+        "target": "cell growth",
+        "readout": "confluence over time"
+      }
+    ],
+    "manuscriptClaims": [
+      "The tumor cell model supports the proliferation finding."
+    ]
+  },
+  {
+    "id": "hold-antibody-passage",
+    "title": "Antibody target mismatch and impossible passage metadata",
+    "domain": "neurobiology",
+    "reviewDate": "2026-08-15",
+    "materials": [
+      {
+        "name": "NeuroStem-X passage record",
+        "type": "primary_cell",
+        "role": "differentiation model",
+        "rrid": "RRID:CVCL_SYN3",
+        "lot": "NSX-2601",
+        "source": "synthetic stem-cell bank",
+        "species": "human",
+        "claimedOrganism": "human",
+        "validationEvidence": ["identity PCR panel"],
+        "validationDate": "2026-01-15",
+        "contaminationStatus": "negative",
+        "passageRange": { "min": 22, "max": 8 },
+        "reportedPassage": 31
+      },
+      {
+        "name": "Anti-GFAP clone G4",
+        "type": "antibody",
+        "role": "immunostaining antibody",
+        "rrid": "RRID:AB_9000002",
+        "lot": "LOT-GFAP-2601",
+        "source": "validated synthetic catalog",
+        "species": "human",
+        "target": "GFAP",
+        "assayTargets": ["GFAP"],
+        "validationEvidence": ["knockdown specificity panel"],
+        "validationDate": "2026-01-20",
+        "contaminationStatus": "not_detected"
+      }
+    ],
+    "assays": [
+      {
+        "name": "MAP2 neuron staining",
+        "materialName": "Anti-GFAP clone G4",
+        "organism": "human",
+        "target": "MAP2",
+        "readout": "fluorescent neurite area"
+      }
+    ],
+    "manuscriptClaims": [
+      "Neuron differentiation was quantified with validated immunostaining material."
+    ]
+  }
+]
diff --git a/research-materials-authentication-assistant/package.json b/research-materials-authentication-assistant/package.json
@@ -0,0 +1,13 @@
+{
+  "name": "research-materials-authentication-assistant",
+  "version": "1.0.0",
+  "description": "Dependency-free research materials authentication guard for AI research assistant review packets.",
+  "main": "src/index.js",
+  "scripts": {
+    "test": "node --test",
+    "demo": "node scripts/demo.js",
+    "video": "node scripts/render-demo-video.js",
+    "check": "node --check src/index.js && node --check scripts/demo.js && node --check scripts/render-demo-video.js"
+  },
+  "license": "MIT"
+}
diff --git a/research-materials-authentication-assistant/reports/demo.mp4 b/research-materials-authentication-assistant/reports/demo.mp4
diff --git a/research-materials-authentication-assistant/reports/reviewer-packet.md b/research-materials-authentication-assistant/reports/reviewer-packet.md
@@ -0,0 +1,56 @@
+# Research Materials Authentication Review
+
+Generated: 2026-08-15T20:45:50.858Z
+
+## Decision Counts
+
+- RELEASE: 1
+- REVIEW: 1
+- HOLD: 2
+
+## Packet Reviews
+
+### Authenticated organoid cytokine response panel
+Decision: RELEASE
+Confidence: 0.96
+Materials checked: 2
+Assays checked: 1
+Reviewer note: translational immunology: materials are traceable, authenticated, and aligned with linked assays.
+
+### Stale antibody validation with organism mismatch
+Decision: REVIEW
+Confidence: 0.12
+Materials checked: 1
+Assays checked: 1
+Reviewer note: cell signaling: REVIEW before release because a tracked research material is missing a valid rrid-style identifier.
+- MAJOR MISSING_OR_INVALID_RRID: A tracked research material is missing a valid RRID-style identifier.
+  Remediation: Add the RRID or equivalent registry identifier used for the exact material instance.
+- MAJOR STALE_VALIDATION_DATE: The latest validation evidence is older than the configured freshness window.
+  Remediation: Refresh material authentication or justify why the prior validation still applies.
+- MAJOR MATERIAL_CLAIM_ORGANISM_MISMATCH: The material species does not match the organism claimed in the manuscript packet.
+  Remediation: Correct the claimed organism or provide a cross-species rationale and validation evidence.
+- MAJOR ASSAY_ORGANISM_MISMATCH: The material species does not match the organism declared for the linked assay.
+  Remediation: Route the packet for reviewer confirmation or correct the assay-material mapping.
+
+### Contaminated cell line in proliferation assay
+Decision: HOLD
+Confidence: 0.61
+Materials checked: 1
+Assays checked: 1
+Reviewer note: cancer biology: HOLD before release because a cell-derived material is marked contaminated or contamination-positive.
+- CRITICAL CONTAMINATED_CELL_MATERIAL: A cell-derived material is marked contaminated or contamination-positive.
+  Remediation: Hold release until the assay is repeated with a contamination-negative authenticated material.
+
+### Antibody target mismatch and impossible passage metadata
+Decision: HOLD
+Confidence: 0.1
+Materials checked: 2
+Assays checked: 1
+Reviewer note: neurobiology: HOLD before release because the packet reports an impossible or biologically implausible passage range.
+- CRITICAL IMPOSSIBLE_PASSAGE_RANGE: The packet reports an impossible or biologically implausible passage range.
+  Remediation: Correct the passage metadata and provide source authentication records before the assistant releases the review.
+- CRITICAL ANTIBODY_TARGET_MISMATCH: The antibody target does not match the target measured by the linked assay.
+  Remediation: Hold release until the antibody, assay target, or interpretation is corrected and revalidated.
+- MAJOR ASSAY_TARGET_NOT_VALIDATED_FOR_MATERIAL: The assay target is outside the target set validated for this material.
+  Remediation: Add target-specific validation evidence or remap the assay to an authenticated material.
+