med-autoscience

name

med-autoscience

description

Use when Codex needs MedAutoScience (MAS) to plan, conduct, review, or publish medical research, including research questions, study design, cohorts and endpoints, evidence synthesis, bounded analysis, scientific figures/tables, manuscript writing, quality review, and publication handoff. Do not use for patient-specific diagnosis, treatment, triage, or emergency advice; medical grant applications; or generic Office formatting without a research objective.

MedAutoScience

Canonical OPL Agent id is mas; med-autoscience is the package/plugin Skill locator. Operate MAS through OPL-generated interfaces while MAS retains medical, evidence, artifact, quality, and publication authority.

Admission

• Admit MAS only when the requested outcome is medical research or a research artifact tied to an identifiable study, evidence question, dataset/cohort, manuscript, or publication package.
• Do not route patient-specific clinical-care requests to MAS. Keep diagnosis, treatment choice, dosing, triage, and emergency guidance outside this research Agent and direct the user to appropriate clinical care when needed.
• Route funding-call strategy and grant application authoring to MAG. Route generic slides to RCA and generic document formatting to the relevant document capability unless the work is subordinate to a MAS research artifact.
• Bind the current research objective, source/data cohort, study/workspace identity, accepted upstream refs, and intended claim before selecting an action. Do not infer scientific readiness from file presence or package/runtime status.

Action Routing

Choose the earliest unresolved owning Stage action from the installed OPL-generated interface:

• direction_and_route_selection: define or repair the research question, route, feasibility, and governing assumptions.
• baseline_and_evidence_setup: establish the protocol/method baseline, evidence/source map, cohort/phenotype, endpoints, governance, and analysis readiness.
• bounded_analysis_campaign: execute a bounded, reproducible analysis against an accepted design and frozen inputs.
• manuscript_authoring: write or materially revise the scientific manuscript and its display artifacts from current evidence refs.
• review_and_quality_gate: run independent scientific, statistical, evidence-integrity, reference, figure/table, or manuscript review.
• finalize_and_publication_handoff: assemble the final publication handoff after current review evidence and explicit human submission authority.

qualification_work_item_provisioning_authority_evaluate, study_lifecycle_reactivation_authority_evaluate, candidate_admission_authority_evaluate, build_dependency_currentness_authority_evaluate, and paper_mission_authority_evaluate are internal registry-bound authority actions. They have no public CLI, MCP, Skill, product-entry, OpenAI, or AI SDK route and must not be invoked as user actions.

Default Workflow

1. Select one public action from the research intent and current accepted refs; do not begin with package lifecycle or environment commands when the user asked for research work.
2. For an inactive study receiving an explicit manuscript-revision instruction, first persist durable user-instruction evidence and a reviewer_revision intake that binds the full checklist, independent review packet, first owning Stage, and allowed revision scope. Use the hosted lifecycle admission flow; runtime activity alone never reactivates MAS business truth.
3. Preserve one OPL StageRun lineage and exact source/data/artifact refs while Codex routes among declared MAS stages.
4. Use the installed mas-scholar-skills capability package for focused medical methods. Acquire another external Skill only for a named or demonstrated coverage gap after provenance, permissions, data/credential scope, and compatibility review.
5. For every initial draft, apply the MAS-owned initial_draft_evidence_integrity_requirements in contracts/manuscript_first_draft_quality_policy.json at their declared earliest Stage owners. Missing or unresolved requirements are quality debt and cannot be hidden by prose, Skill output, render success, or runtime completion.
   • Write as the manuscript authors. Route scientific evidence gaps back, but preserve the ideal manuscript structure for author-supplied objective facts and insert the minimum local [AUTHOR INPUT: ...] annotation. Bind every annotation and its derived To-Do projection through one author_stance_integrity_ref; pending author facts never justify defensive workflow prose.
6. Prepare the declarative runtime environment only when the selected analysis/display work requires it. An environment receipt proves execution readiness only, never medical or publication quality.
7. Separate producing and independent reviewer/auditor invocations, task records, and receipts before closing a formal quality gate.
8. Freeze one candidate after bounded previews, then run complete export, exact-byte inventory, and affected independent review once for that candidate.

Quality And Hard Stops

• Treat raw/partial artifacts, negative or null results, failed attempts, review findings, and no-output diagnostics as route context. A consumable delta may advance as completed_with_quality_debt.
• Do not edit submission/ or launch a Stage from a paused, delivered-paused, or stopped business projection. Reactivation requires a current MAS receipt plus matching OPL all-or-rollback materialization receipt; neither a Temporal-running signal nor provider completion is sufficient.
• A qualification-only work item may prove Full VM identity and lifecycle transport only. It never authorizes a Stage body, business action, publication, or submission, even after its MAS provisioning receipt and matching OPL materialization receipt are current.
• Retry, review, and repair limits are quality budgets. Exhaustion preserves the best evidence-bearing artifact and closes quality, publication, export, and submission-ready claims; it does not create an infinite stage loop.
• Negative findings remain evidence. Preserve lineage and route back to the owning hypothesis, cohort/data, endpoint, analysis design, writing, or review stage instead of optimizing for a positive result.
• For new or materially repaired paper-facing figures, use medical-figure-design; use medical-figure-style for final visual QA and medical-figure-composer only for separately assembled panels.
• Only executor unavailability, wrong-target identity/currentness, real authority/safety/credential boundaries, irreversible action, protected data/material, or an explicit human decision may hard-stop progress.

Output Expectations

• Return the selected public action and Stage, exact research/source/data/artifact refs, methods or analysis outputs, review/authority refs, typed blockers, remaining quality debt, and the next owning Stage.
• Match every scientific claim to its evidence class and locator. Do not promote external Skill output, preview/cache evidence, runtime receipts, generated descriptors, or provider completion into MAS authority.
• Name artifact maturity precisely: plan, frozen baseline, bounded analysis result, manuscript draft, review finding, publication handoff candidate, or owner-authorized final handoff.
• Preserve MAS-owned owner receipts and publication/submission authority; OPL may transport and persist refs but cannot author medical truth or sign those decisions.

References

• contracts/action_catalog.json
• agent/stages/manifest.json
• contracts/artifact_iteration_efficiency_policy.json
• contracts/stage_quality_cycle_policy.json
• contracts/runtime_environment_requirements.json
• contracts/owner_receipt_contract.json
• contracts/domain_handler_registry.json