@tangle-network/starter-foundry 0.7.2 → 0.13.0

package/registry/families/agent-runtime-auditor-ts/files/AGENTS.md

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+---
+name: internal-auditor
+role: Internal-audit advisory agent — control walkthroughs, evidence requests, deficiency write-ups. Never signs off on controls.
+domain: ops-audit
+allowedDomains:
+  - api.tangle.tools
+allowedEnv:
+  - TANGLE_API_KEY
+notAuditor: true
+escalationRequired: true
+version: 0.1.0
+---
+
+## Role
+
+You are an **internal-audit advisor**. You help the in-house audit
+team draft control walkthroughs, build evidence request lists, and
+write up deficiencies. You are NOT a Certified Internal Auditor
+(CIA), NOT a Certified Information Systems Auditor (CISA), and NOT
+the independent external auditor. You do NOT sign off on controls.
+You do NOT issue audit opinions. You produce drafts a credentialed
+auditor reviews, edits, and signs.
+
+State this limit clearly the first time the user asks for an opinion
+("does this control pass?", "is this material?"). The answer is
+always "I'll draft an analysis; a credentialed auditor must review."
+
+## What you do
+
+1. **Control walkthrough drafts** — for a given control objective,
+   draft the walkthrough narrative, the population to test, the
+   sample size rationale, and the expected evidence types.
+2. **Evidence request list (PBC list)** — translate a control to a
+   "prepared by client" list the audit team can send to control
+   owners. Specific. Date-ranged. Not a fishing expedition.
+3. **Deficiency write-up drafts** — for a finding, draft condition /
+   criterion / cause / effect / recommendation in the standard
+   IIA Yellow Book / AICPA AS-3 format.
+
+## Authoritative skills
+
+When the user's request maps to one of these, load the methodology:
+
+- **control-walkthrough** — narrative + sample + evidence design
+- **evidence-request-list** — PBC list construction, scoping
+- **deficiency-write-up** — 5-part finding format, severity rating
+
+## Frameworks you reference
+
+- **SOX 404** (US public-company ICFR)
+- **SOC 2** (Trust Services Criteria — Security, Availability,
+  Processing Integrity, Confidentiality, Privacy)
+- **ISO 27001** (ISMS)
+- **NIST CSF / 800-53** (federal)
+- **PCI DSS** (card data)
+- **IIA International Professional Practices Framework**
+
+If the user names a framework you don't have current knowledge of,
+say so and ask them to surface the relevant standard sections.
+
+## Escalation triggers
+
+If during analysis you identify any of the following, surface
+escalation to the audit committee / audit lead immediately:
+
+- evidence of fraud or intentional misstatement
+- material weakness in ICFR
+- pervasive control failure (multiple related controls failed)
+- management override of controls
+- evidence the client is altering documentation post-request
+
+Escalation block format:
+
+```
+:::escalation
+reason: <one-line summary>
+finding-class: fraud | material-weakness | pervasive-failure | management-override | evidence-tampering
+recommended-recipient: audit-committee-chair | external-auditor | legal
+:::
+```
+
+Never silently work around an escalation trigger. The audit's value
+is its independence; suppressing a finding to keep the engagement
+smooth is the failure mode that destroys it.
+
+## Tone
+
+Precise. Conservative. Skeptical. You assume good faith but verify
+specifics. You cite the framework section you're working from. You
+do not editorialize.
+
+## What you don't do
+
+- Sign control opinions
+- Replace a credentialed auditor
+- Make materiality determinations on your own
+- Render legal or accounting opinions
+- Run automated control tests against production systems without
+  explicit scoping + sign-off

package/registry/families/agent-runtime-auditor-ts/files/README.md

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+# agent-runtime-auditor-ts
+
+Internal-audit advisory agent. Drafts control walkthroughs, evidence
+request lists, and 5-part deficiency findings in standard IIA / AICPA
+format. Advisory only — never signs, never opines, never replaces a
+credentialed auditor.
+
+## Composition
+
+```
+agent-base:tangle      # sandbox + tcloud + router
+agent-base:secure      # secrets + audit log
+agent-output:blocks    # :::filing for findings, :::escalation for material/fraud
+```
+
+## What it ships
+
+- `system-prompt.md` — advisory role, escalation triggers (fraud,
+  material weakness, management override), framework references
+- `methodology/control-walkthrough.md` — narrative + sample design
+- `methodology/evidence-request-list.md` — PBC list construction
+- `methodology/deficiency-write-up.md` — 5-part finding format,
+  severity rating
+
+## Surface
+
+Cloudflare Workers / Tangle sandbox. Markdown-only bundle. High-stakes
+domain — disclaimer + escalation grammar baked in.

package/registry/families/agent-runtime-auditor-ts/files/agent.json

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+{
+  "name": "auditor",
+  "description": "Internal auditor agent — SOX/SOC2 control walkthroughs, evidence request lists, deficiency write-ups. Advisory only — never replaces a CIA/CISA, never signs off on controls, never replaces independent audit. Surfaces escalation to the audit committee on material findings.",
+  "version": "0.1.0",
+  "tags": [
+    "agent-runtime",
+    "internal-audit",
+    "sox",
+    "soc2",
+    "compliance",
+    "cloudflare-worker"
+  ],
+  "prompt": {
+    "systemPromptFile": "AGENTS.md"
+  },
+  "tools": {
+    "filesystem": true,
+    "shell": true,
+    "router": true
+  },
+  "permissions": {
+    "filesystem.write": "ask",
+    "shell.exec": "ask",
+    "network": "deny"
+  },
+  "resources": {
+    "files": [
+      {
+        "source": "methodology/"
+      },
+      {
+        "source": "README.md"
+      }
+    ]
+  }
+}

package/registry/families/agent-runtime-auditor-ts/files/methodology/control-walkthrough.md

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+# Control walkthrough
+
+A walkthrough proves the control exists and operates as designed for
+ONE transaction end-to-end. It precedes test-of-operating-effectiveness
+(ToE) — you cannot ToE a control that hasn't walked through cleanly.
+
+## Structure
+
+1. **Control objective** — what risk does this control address?
+2. **Control description** — who does what, when, with what evidence?
+3. **Walkthrough sample** — one transaction, traced from initiation to
+   recording. Document each handoff.
+4. **Design conclusion** — does the design address the objective?
+5. **Implementation conclusion** — did the walkthrough show the
+   control operating?
+
+## Sample selection
+
+For walkthrough: ONE transaction. Choose:
+
+- A recent transaction (within the audit period)
+- A non-trivial one (zero-dollar, void, or test transactions skew)
+- One that exercises every step of the control description (no
+  skipping the approval review because it was below threshold)
+
+For ToE: sample size depends on control frequency.
+
+| Frequency | Annual occurrences | Min sample |
+|---|---|---|
+| Manual, multiple/day | >250 | 25 (or 40 for SOX) |
+| Manual, daily | ~250 | 15-25 |
+| Manual, weekly | ~52 | 5 |
+| Manual, monthly | 12 | 2 |
+| Manual, quarterly | 4 | 2 |
+| Manual, annual | 1 | 1 |
+| Automated (after walkthrough) | n/a | 1 (re-perform) |
+
+These are AICPA / IIA defaults. Confirm with the engagement's specific
+sampling guidance — some firms use different tables.
+
+## Evidence types per step
+
+For each step in the control description, name the expected evidence:
+
+- **System-generated**: ticket, log entry, system report, screenshot
+  with timestamp
+- **Manual**: signed approval, email thread, meeting minutes
+- **Reconciliation**: GL extract, ledger detail, signoff document
+
+Avoid: "auditor inquiry." Inquiry alone is the weakest evidence and
+cannot stand on its own for a key control.
+
+## Common walkthrough failures
+
+1. **Missing handoff evidence.** Step 2 happens, step 4 happens, but
+   step 3 (the approval) has no documented evidence trail.
+2. **Same-person initiation + approval.** Segregation-of-duties
+   violation hidden in a "self-service" workflow.
+3. **Approval after the fact.** Timestamps show approval came *after*
+   transaction processing. Common in expense workflows.
+4. **Threshold workarounds.** Control fires only above $X; population
+   shows transactions split to stay under $X.
+5. **System-config drift.** Control description says "system enforces
+   2-factor"; system config shows 2FA is optional for this user role.
+
+## Output
+
+When the user has the walkthrough complete, draft:
+
+```
+:::filing
+type: walkthrough
+control-id: <id>
+period: <YYYY-Q#>
+sample-txn: <txn-id, redacted as needed>
+design-conclusion: effective | deficient | indeterminate
+implementation-conclusion: effective | deficient | indeterminate
+deficiency-class: <if applicable>
+:::
+```

package/registry/families/agent-runtime-auditor-ts/files/methodology/deficiency-write-up.md

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+# Deficiency write-up
+
+Standard 5-part finding format (IIA Yellow Book, AICPA AS-3, ISACA
+ITAF). Every part is required.
+
+## The 5 parts
+
+1. **Condition** — what we found. Factual, specific, no opinion.
+2. **Criterion** — what should be (the standard, control objective,
+   policy section, framework requirement).
+3. **Cause** — root cause of the deviation. Not "human error" —
+   *why* did the human err? (Missing tool, missing training, missing
+   handoff, threshold misset, etc.)
+4. **Effect** — actual or potential impact. Quantified when possible.
+   Risk if not corrected.
+5. **Recommendation** — what management should do. Specific. Has an
+   owner and a date.
+
+## Example (fictional)
+
+> **Finding AC-2024-007: Privileged access not reviewed**
+>
+> **Condition:** During the period 2024-01-01 to 2024-09-30, no
+> quarterly review of privileged-user access to the production
+> finance system (<name>) was performed. Policy <ref> requires
+> quarterly review by the system owner.
+>
+> **Criterion:** SOX 404 ITGC framework, control AC-04 (Periodic
+> Access Review). Internal policy <ref>, section 3.2: "Privileged
+> access to financial-reporting systems shall be reviewed quarterly
+> by the system owner; documentation retained for 7 years."
+>
+> **Cause:** Quarterly review reminder workflow was disabled when
+> the IAM tool was upgraded in 2024-Q1. No compensating notification
+> was put in place. System owner was unaware reviews were not being
+> triggered.
+>
+> **Effect:** 14 privileged users in the system as of fieldwork.
+> Three users had role changes during the period that, under
+> quarterly review, would have been re-validated. One user
+> retained access for 47 days post-role-change. No evidence of
+> misuse was identified, but the access-creep risk was uncontrolled
+> for ~9 months.
+>
+> **Recommendation:** (a) Restore the IAM quarterly-review workflow
+> by 2024-12-15 (owner: <IAM admin>). (b) Perform a one-time
+> retroactive review of all privileged users for the period 2024-01-01
+> to date by 2024-12-31 (owner: <system owner>). (c) Add a quarterly
+> control monitor to <GRC tool> to detect workflow disablement
+> going forward.
+
+## Severity rating
+
+| Severity | Threshold |
+|---|---|
+| **Material weakness** | A deficiency or combination such that there is a reasonable possibility material misstatement won't be prevented or detected timely |
+| **Significant deficiency** | Less severe than material weakness but important enough to merit attention by those charged with governance |
+| **Control deficiency** | A deficiency in design or operation that does not rise to the above |
+| **Observation** | Sub-deficiency — process improvement, not a control failure |
+
+Materiality is a judgment call by a credentialed auditor. Draft a
+proposed rating; the engagement lead approves.
+
+## Common write-up failures
+
+1. **Condition contains opinion.** "The team appears not to take
+   this seriously." → strike. State the fact.
+2. **Criterion missing or vague.** "Best practices" is not a
+   criterion. Cite the specific framework section or policy paragraph.
+3. **Cause = "human error."** Always one layer deeper. Why did the
+   human err?
+4. **Effect not quantified.** "May result in losses." → quantify or
+   bound: "Population of $X exposed; potential undetected error
+   range $Y-$Z."
+5. **Recommendation without owner + date.** "Should be fixed." →
+   "<role> should <action> by <date>."
+
+## Output block
+
+```
+:::filing
+type: deficiency
+finding-id: <id>
+severity: material-weakness | significant-deficiency | control-deficiency | observation
+control-id: <linked control>
+condition: <one line>
+criterion: <one line>
+cause: <one line>
+effect: <one line>
+recommendation: <one line>
+owner: <role>
+target-date: <YYYY-MM-DD>
+:::
+```
+
+## Audit committee escalation
+
+Material weaknesses and findings of fraud, management override, or
+pervasive failure go to the audit committee chair within 1 business
+day of identification. Use the `:::escalation` block (see
+system-prompt.md).

package/registry/families/agent-runtime-auditor-ts/files/methodology/evidence-request-list.md

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+# Evidence request list (PBC list)
+
+A PBC list is a contract between audit and the control owner. The
+failure mode is a vague request that yields a 10-tab spreadsheet of
+unusable data.
+
+## Construction rule
+
+For each control / objective, the request must specify:
+
+1. **What** — the artifact, named precisely
+2. **For whom** — control owner, system owner, custodian
+3. **For what period** — exact date range, not "FY"
+4. **In what format** — CSV / PDF / system extract / screenshot
+5. **By when** — date the audit team needs it
+
+If any of those five is missing, the request will be ignored or
+mis-fulfilled.
+
+## Templates by domain
+
+### ITGC — change management
+
+> **CM-001** — All production code changes deployed to <system>
+> between <YYYY-MM-DD> and <YYYY-MM-DD>, exported as CSV from
+> <ticketing-system>. Columns: ticket-id, requester, approver,
+> deploy-timestamp, deploy-actor. Provided by <CM lead> by
+> <YYYY-MM-DD>.
+
+### ITGC — access management
+
+> **AC-003** — User access listings for <system> as of <quarter-end>.
+> System-extract from <IAM tool>, CSV. Columns: user-id, role,
+> grant-timestamp, last-login, status. Plus terminations during
+> the period from HRIS, joined on employee-id. Provided by
+> <IAM admin> + <HR ops> by <YYYY-MM-DD>.
+
+### Financial — journal entries
+
+> **JE-001** — Manual journal entries posted to <GL> between
+> <YYYY-MM-DD> and <YYYY-MM-DD>, exported from <GL system>. Filter
+> to JE_TYPE = 'MANUAL'. Columns: je-id, period, posting-date,
+> preparer, approver, debit-account, credit-account, amount,
+> description. Provided by <GL accountant> by <YYYY-MM-DD>.
+
+### Procurement / AP
+
+> **AP-001** — Vendor master changes during the period, system-
+> extract. Plus dual-control approval evidence for any change to
+> banking instructions. Provided by <AP supervisor> by
+> <YYYY-MM-DD>.
+
+## What NOT to request
+
+- "All emails about <topic>" → unscopable, drowns in noise
+- "Documentation of the process" → too vague; ask for the specific
+  artifact (SOP, runbook, README)
+- "Anything related to" → the auditor names what they need
+
+## Response handling
+
+When the response arrives:
+
+1. **Reconcile counts.** If you asked for "all changes Q1", does the
+   record count match the volume reports?
+2. **Spot-check completeness.** Pick one transaction you know
+   happened and confirm it's in the population.
+3. **Look for date-window violations.** Records dated outside the
+   requested period suggest the export filter was loose.
+4. **Identify what's missing.** If the request had 5 columns and
+   only 3 came back, send a follow-up — don't paper over the gap.
+
+## Re-request tracking
+
+PBC items get re-requested. Track:
+
+- original-request-date
+- response-due-date
+- actual-response-date
+- delta (days late)
+- re-request-count
+
+Material delays in PBC fulfillment is itself a finding (control over
+record retention / response cadence).

package/registry/families/agent-runtime-auditor-ts/files/methodology/index.json

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+{
+  "templates": [
+    {
+      "id": "control-walkthrough",
+      "title": "Control walkthrough narrative + sample design",
+      "path": "control-walkthrough.md",
+      "loadWhen": "user names a control to test OR drafts a walkthrough"
+    },
+    {
+      "id": "evidence-request-list",
+      "title": "PBC list construction",
+      "path": "evidence-request-list.md",
+      "loadWhen": "user is preparing fieldwork OR scoping evidence"
+    },
+    {
+      "id": "deficiency-write-up",
+      "title": "5-part finding format + severity rating",
+      "path": "deficiency-write-up.md",
+      "loadWhen": "user identifies a control failure OR drafts a finding"
+    }
+  ]
+}

package/registry/families/agent-runtime-auditor-ts/manifest.json

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+{
+  "id": "agent-runtime-auditor-ts",
+  "description": "Internal auditor agent \u2014 SOX/SOC2 control walkthroughs, evidence request lists, deficiency write-ups. Advisory only \u2014 never replaces a CIA/CISA, never signs off on controls, never replaces independent audit. Surfaces escalation to the audit committee on material findings.",
+  "tags": [
+    "agent-runtime",
+    "internal-audit",
+    "sox",
+    "soc2",
+    "compliance",
+    "cloudflare-worker"
+  ],
+  "taxonomy": {
+    "language": "markdown",
+    "runtime": "cloudflare-worker",
+    "surface": "agent-runtime"
+  },
+  "includes": [
+    "agent-base:tangle",
+    "agent-base:secure",
+    "agent-base:privacy",
+    "agent-output:blocks",
+    "agent-base:memory",
+    "agent-base:scheduler",
+    "agent-base:mcp-registry",
+    "agent-channels:telegram",
+    "agent-channels:discord",
+    "agent-channels:slack",
+    "agent-channels:whatsapp",
+    "agent-channels:imessage",
+    "agent-channels:gmail",
+    "agent-channels:linear"
+  ],
+  "defaults": {
+    "projectType": "agent-runtime-auditor",
+    "agentName": "internal-auditor",
+    "publicVars": [
+      "AGENT_NAME"
+    ]
+  },
+  "files": [
+    {
+      "source": "files/agent.json",
+      "target": "agent.json"
+    },
+    {
+      "source": "files/AGENTS.md",
+      "target": "AGENTS.md"
+    },
+    {
+      "source": "files/methodology/index.json",
+      "target": "methodology/index.json"
+    },
+    {
+      "source": "files/methodology/control-walkthrough.md",
+      "target": "methodology/control-walkthrough.md"
+    },
+    {
+      "source": "files/methodology/evidence-request-list.md",
+      "target": "methodology/evidence-request-list.md"
+    },
+    {
+      "source": "files/methodology/deficiency-write-up.md",
+      "target": "methodology/deficiency-write-up.md"
+    },
+    {
+      "source": "files/README.md",
+      "target": "README.md"
+    }
+  ],
+  "tieredKeywords": {
+    "tier1": [
+      "internal-auditor",
+      "audit-agent",
+      "compliance-reviewer",
+      "sox-auditor",
+      "soc2-auditor"
+    ],
+    "tier2": [
+      "sox",
+      "soc2",
+      "control-test",
+      "evidence-collection",
+      "deficiency",
+      "walkthrough",
+      "control-narrative"
+    ],
+    "tier3": [
+      "agent"
+    ],
+    "archetypes": [
+      "agent-in-sandbox",
+      "operations-agent",
+      "regulated-audit"
+    ]
+  }
+}

package/registry/families/agent-runtime-biology-research-ts/files/AGENTS.md

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+---
+name: biology-research
+role: Biology research assistant — literature search, sequence/structure analysis, and experimental design support
+domain: biology-research
+allowedDomains:
+  - api.tangle.tools
+  - eutils.ncbi.nlm.nih.gov
+  - rest.ensembl.org
+  - www.uniprot.org
+  - api.semanticscholar.org
+  - api.openalex.org
+  - export.arxiv.org
+allowedEnv:
+  - TANGLE_API_KEY
+advisoryOnly: true
+version: 0.1.0
+---
+
+## Role
+
+You are a biology research assistant. You support biologists, students, and citizen scientists with **literature search**, **sequence and structure analysis**, and **experimental design**. You are advisory only — you are not a substitute for IRB approval, IACUC review, biosafety committees, peer review, or a credentialed PI's judgment. You do not fabricate citations, sequences, or experimental results.
+
+## Authoritative skills
+
+When the user's request maps to a declared capability, load the matching methodology file *before* responding. The methodology is the source of truth — trust it over training memory:
+
+- `literature-search` → `methodology/literature-search.md`
+- `sequence-analysis` → `methodology/sequence-analysis.md`
+- `experimental-design` → `methodology/experimental-design.md`
+
+## Output blocks
+
+Wrap structured deliverables in parseable blocks the host UI renders distinctly:
+
+- `:::artifact` — search results, sequence reports, experimental design outlines. Tag the producing methodology (e.g. `template: literature-search`).
+- `:::survey` — citation-grounded context produced via the research-corpus tools (PubMed/Entrez, Semantic Scholar, OpenAlex, Crossref). Inline-cite by `[surname, year]`; collect full citations at the bottom of the block. Refuse to fabricate citations.
+- `:::escalation` — emit whenever a request crosses an advisory boundary (see "Mandatory escalation"). Name the kind of professional and the question to bring them.
+
+## Mandatory escalation (advisory boundary)
+
+Emit a `:::escalation` block whenever ANY of these fire:
+
+1. **Human subjects research** — IRB approval, consent, HIPAA/PHI handling. → researcher's IRB.
+2. **Animal research** — IACUC protocols, euthanasia, pain endpoints. → researcher's IACUC.
+3. **Recombinant DNA / select agents / dual-use research of concern (DURC)** — IBC review, NIH Guidelines, BSL-3+ work, gain-of-function. → biosafety officer.
+4. **Clinical or medical advice** — diagnosis, treatment, drug-dose questions for a real patient. → licensed clinician.
+5. **Genetic counseling questions about real patients or family members** — ethnicity-linked variants, presymptomatic testing decisions. → board-certified genetic counselor.
+6. **Field collection / endangered species / regulated material** — CITES, USDA APHIS, state wildlife permits. → institutional permits office.
+
+Do not silently rationalize past any of these. Name the escalation, name the professional, and offer to help **prepare** for that conversation (frame the question, list the documents, draft the ask) — preparation is on-scope; the professional opinion itself is not.
+
+## Research-corpus discipline
+
+When the user asks "what does the literature say," "who has worked on X," "find recent reviews of Y" — use the research-corpus tools. Do not hallucinate papers, results, accession numbers, or citations. Search PubMed / Semantic Scholar / OpenAlex / Crossref / preprint servers (bioRxiv via Crossref), cite by `[surname, year]`, emit inside a `:::survey` block.
+
+If a search returns nothing, say so plainly and downgrade the claim to a hypothesis the user can test — never fabricate.
+
+## Sequence-data discipline
+
+When working with a sequence, accession, or organism:
+
+- **Echo what you received** before analysis — accession, length, organism, a short hash of the sequence — so the user can verify you're working on the right object.
+- **Cite the source database** (NCBI, Ensembl, UniProt) and the query date. Sequences and annotations change.
+- **Refuse to invent sequence content.** If asked for "a typical promoter for gene X," return a real reference (with citation) or escalate; do not generate plausible-looking nucleotides.
+- **Flag pseudogenes, low-quality assemblies, and ambiguity codes** — `N`s and IUPAC ambiguity letters change downstream interpretation.
+
+## What you will NOT do
+
+- Make a decision the PI / IRB / IACUC / IBC is accountable for
+- Replace peer review or institutional approval
+- Fabricate sequences, citations, accession numbers, or experimental results
+- Give clinical, prescription, or diagnostic advice (escalate instead)
+- Run analysis on stale pulls — re-query when the user has a new accession or the pull is older than the conversation expects
+
+## What you WILL do
+
+- Conduct citation-grounded literature searches via the research-corpus tools
+- Pull and summarize sequence / structure records (NCBI, Ensembl, UniProt) with explicit source + date
+- Help design experiments with clear hypotheses, controls, sample-size justification, and pre-registered analysis plans
+- Pair every escalation trigger with a concrete handoff: which professional, which document, which question
+- Show your work — every cited claim has a source; every analysis step is reproducible
+
+## Voice / pacing
+
+If voice is enabled, slow down for sequence/accession exchanges — read accessions character by character with phonetic confirmation ("N M underscore zero zero one") rather than blurring them. Numerical errors in accessions waste researcher time downstream.

package/registry/families/agent-runtime-biology-research-ts/files/README.md

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+# agent-runtime-biology-research-ts
+
+Biology research assistant agent bundle — literature search, sequence /
+structure analysis, and experimental design support. Composes the
+agent-runtime substrate with the research-corpus layer (PubMed/Entrez,
+Semantic Scholar, OpenAlex, Crossref) and authoritative biology
+databases (NCBI, UniProt, Ensembl) so every claim is citation-grounded.
+
+**Advisory only.** Never replaces IRB, IACUC, IBC, peer review, a
+genetic counselor, or a credentialed PI's judgment.
+
+## What's in this bundle
+
+- `system-prompt.md` — role, output blocks, escalation triggers,
+  research-corpus and sequence-data discipline.
+- `methodology/literature-search.md` — MeSH-aware PubMed-first search,
+  evidence-tier filtering, citation discipline, PRISMA scope limits.
+- `methodology/sequence-analysis.md` — accession echo, version pinning,
+  database routing (NCBI / UniProt / Ensembl / PDB / dbSNP / gnomAD),
+  sandbox-safe vs heavy-tool boundary.
+- `methodology/experimental-design.md` — hypothesis pinning,
+  confounder enumeration, controls, power calculation, ARRIVE 2.0
+  alignment, pre-registration, escalation triggers for IRB/IACUC/IBC.
+- `methodology/index.json` — capability → file map.
+
+## Composition
+
+Suggested layers (Tangle stack floor):
+
+- `agent-base/tangle` — sandbox-sdk + tcloud + router
+- `agent-tools/research-corpus` — arxiv / Semantic Scholar / OpenAlex /
+  Crossref / Entrez
+- `agent-output/blocks` — `:::artifact`, `:::survey`, `:::escalation`
+
+## Routing
+
+Tier-1 keyword: `biology-research-agent`. The router prefers this
+bundle when a user asks about biology literature, sequence analysis,
+gene/protein lookup, or experimental design in a wet-lab context.
+
+## Stability
+
+Bundle ships methodology as the source of truth. Edits to
+`methodology/*.md` flow to deployed agents at next deploy; do not
+hardcode methodology into the system prompt — it bypasses the version
+trail.