tool-registry.json

{
  "schema_version": 1,
  "registry_kind": "biosymphony_ferm_doe_tool_registry",
  "generated_on": "2026-08-30",
  "maintainer_note": "Curated public reference for optional tools, sidecars, and watchlist repositories. The 2026-08-30 alignment added the shipped SciPy and Plotly integrations. Refresh upstream facts before changing dependencies or making version, activity, deprecation, or archival claims.",
  "refresh_policy": {
    "default_refresh_days": 90,
    "refresh_before": [
      "adding or changing optional dependencies",
      "running a live optional-tool smoke",
      "claiming a package is current, active, deprecated, or archived",
      "turning a watchlist or sidecar tool into an adapter"
    ]
  },
  "source_notes": [
    "docs/open-source-bioprocess-tool-survey-2026-05-15.md",
    "docs/BOFIRE_POSITIONING.md",
    "pyproject.toml",
    "docs/ENTMOOT_SWAP_DESIGN.md",
    "docs/BOFIRE_CONSTRAINT_PATTERNS.md",
    "src/biosymphony_ferm_doe/adapters/pubmed_mcp.py",
    "docs/research/bo-tools-survey-2026-05-16.md",
    "docs/research/tool-registry-refresh-2026-06-21.md"
  ],
  "decision_rules": [
    {
      "rule_id": "stdlib_core_first",
      "description": "Core engine remains stdlib-first; heavy scientific tools are optional adapters or sidecars."
    },
    {
      "rule_id": "bofire_route",
      "description": "Use BoFire only for non-box constraints, multi-objective optimization, multi-fidelity scale structure, or explicit operator request."
    },
    {
      "rule_id": "license_boundary",
      "description": "GPL and AGPL tools are boundary-only or avoid unless repository distribution posture is explicitly changed."
    },
    {
      "rule_id": "no_platform_pileup",
      "description": "Do not add workflow platforms that duplicate the campaign manifest and task-request contracts unless repeated computational DAGs justify another workflow language."
    }
  ],
  "tools": [
    {
      "tool_id": "bofire",
      "name": "BoFire",
      "category": "adaptive_design",
      "priority": "P0",
      "status": "adopted_optional",
      "posture": "primary optional adaptive adapter",
      "package": "bofire>=0.3.1,<0.4",
      "pyproject_extra": "bofire",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/experimental-design/bofire",
        "docs": "https://experimental-design.github.io/bofire/"
      },
      "docs_in_repo": [
        "docs/BOFIRE_POSITIONING.md",
        "docs/BOFIRE_CONSTRAINT_PATTERNS.md"
      ],
      "last_checked": "2026-08-30",
      "upstream_version": "0.5.0",
      "upstream_released_on": "2026-08-11",
      "current_signal": "PyPI 0.5.0 is current upstream. The primary adapter remains on bofire>=0.3.1,<0.4 because later releases require Python 3.11 or newer and carry breaking API and dependency changes. BoFire 0.4 tagged generalized NChooseK DoE support; the separate adaptive-nchoosek-doe extra pins 0.4.1 as an unverified candidate.",
      "fit": "Constrained media optimization, mixed spaces, multi-objective BO, and future scale-fidelity planning.",
      "risks": "Heavy Torch/BoTorch stack; pre-1.0 API; fermentation phase and feed semantics remain BioSymphony-owned. The 0.3.1 audit found failures for SoboStrategy with NChooseK and multi-fidelity strategies with non-box constraints. The related upstream issues are closed, but later tags have not been retested here; retain OMLT, ENTMOOT, and parallel-arm fallbacks.",
      "route": [
        "non_box_constraints",
        "multi_objective_responses",
        "scale_fidelity_structure",
        "operator_requested_bofire"
      ],
      "route_reasons": [
        "non_box_constraints",
        "multi_objective_responses",
        "scale_fidelity_structure",
        "operator_requested_bofire"
      ],
      "claim_level": "bofire_adapter_planning",
      "fail_closed_behavior": "Write bofire_strategy_report.json and fall back to stdlib planning when missing or untranslated.",
      "local_lane": "nox -s adaptive_smoke",
      "live_lane": "nox -s adaptive_live"
    },
    {
      "tool_id": "pydoe",
      "name": "pydoe",
      "category": "classical_doe",
      "priority": "P1",
      "status": "watch",
      "posture": "current lightweight DOE-family backend to evaluate against the shipped pyDOE3 adapter",
      "package": "pydoe>=1.0.1",
      "pyproject_extra": "",
      "license": "BSD-3-Clause",
      "links": {
        "pypi": "https://pypi.org/project/pyDOE/",
        "docs": "https://pydoe.github.io/pydoe/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "1.5.0",
      "upstream_released_on": "2026-08-20",
      "current_signal": "PyPI 1.5.0 is current upstream. This repository still ships its classical-design compatibility adapter through the pydoe3 extra.",
      "fit": "Plackett-Burman, factorial, RSM, and Latin-hypercube style fast paths.",
      "risks": "No bioprocess constraints, adaptive posterior, or scale-bridge semantics.",
      "route": [
        "screening",
        "rsm_fit",
        "space_filling_scout"
      ],
      "claim_level": "adapter_backed_classical_doe",
      "fail_closed_behavior": "Report dependency missing and use stdlib design family where available."
    },
    {
      "tool_id": "pydoe3",
      "name": "pyDOE3",
      "category": "classical_doe",
      "priority": "P1",
      "status": "compatibility_only",
      "posture": "compatibility adapter for extended Box-Behnken and maximin LHS paths",
      "package": "pyDOE3>=1.0",
      "pyproject_extra": "pydoe3",
      "license": "BSD-3-Clause",
      "links": {
        "pypi": "https://pypi.org/project/pyDOE3/",
        "docs": "https://pydoe3.readthedocs.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "1.6.2",
      "upstream_released_on": "2026-01-12",
      "current_signal": "PyPI 1.6.2 is current upstream. The compatibility-only status describes this repository's existing adapter route, not the upstream project's maintenance status.",
      "fit": "Existing pyDOE3-specific adapter for larger Box-Behnken coverage and maximin Latin-hypercube generation.",
      "risks": "The adapter covers a narrow subset of pyDOE3. Evaluate current pydoe before adding new classical-design dependency surface.",
      "route": [
        "extended_box_behnken",
        "latin_hypercube_maximin",
        "legacy_pydoe3_adapter"
      ],
      "claim_level": "compatibility_adapter",
      "fail_closed_behavior": "Report pyDOE3 missing and use pydoe or stdlib design family where available."
    },
    {
      "tool_id": "scipy",
      "name": "SciPy",
      "category": "statistical_analysis",
      "priority": "P0",
      "status": "adopted_optional",
      "posture": "optional statistical and quasi-random design adapter",
      "package": "scipy>=1.11",
      "pyproject_extra": "scipy",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/scipy/scipy",
        "docs": "https://docs.scipy.org/doc/scipy/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "1.18.1",
      "upstream_released_on": "2026-08-21",
      "current_signal": "PyPI 1.18.1 is current upstream and requires Python 3.12 or newer. The repository retains scipy>=1.11 for its wider Python support and uses scipy.stats and scipy.stats.qmc through optional paths.",
      "fit": "Small-sample p-values, power quantiles, and quasi-random space-filling designs.",
      "risks": "SciPy improves statistical calculations and design generation but does not validate assay quality or campaign conclusions.",
      "route": [
        "analysis_pvalues",
        "doe_power_quantiles",
        "qmc_space_filling"
      ],
      "claim_level": "adapter_backed_statistical_analysis",
      "fail_closed_behavior": "Use stdlib distribution approximations and space-filling generators when SciPy is absent."
    },
    {
      "tool_id": "salib",
      "name": "SALib",
      "category": "sensitivity",
      "priority": "P0",
      "status": "adopted_optional",
      "posture": "optional diagnostics adapter",
      "package": "SALib>=1.5.2",
      "pyproject_extra": "sensitivity",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/SALib/SALib",
        "docs": "https://salib.readthedocs.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "1.5.2",
      "upstream_released_on": "2025-10-12",
      "current_signal": "PyPI 1.5.2 remains current upstream.",
      "fit": "PAWN, delta, and Sobol sensitivity analysis for factor prioritization and assumption checks.",
      "risks": "Not an optimizer; precision depends on declared ranges and response models.",
      "route": [
        "sensitivity_screening",
        "assumption_attack",
        "scale_recipe_uncertainty"
      ],
      "claim_level": "sensitivity_screening",
      "fail_closed_behavior": "Skip optional sensitivity outputs and preserve the base dossier."
    },
    {
      "tool_id": "frictionless",
      "name": "Frictionless Framework",
      "category": "data_contracts",
      "priority": "P0",
      "status": "adopted_optional",
      "posture": "CSV/table schema reference; stdlib validator remains default",
      "package": "frictionless>=5,<6",
      "pyproject_extra": "contracts",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/frictionlessdata/frictionless-py",
        "docs": "https://framework.frictionlessdata.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "5.19.0",
      "upstream_released_on": "2026-04-13",
      "current_signal": "PyPI 5.19.0 is current upstream. The stdlib validator remains the default runtime path.",
      "fit": "CSV/table contracts for ledgers, evidence tables, result templates, inventories, and run sheets.",
      "risks": "Table-shape validation is not scientific semantics.",
      "route": [
        "table_contracts"
      ],
      "claim_level": "contract_validation",
      "fail_closed_behavior": "Stdlib table_contracts validator remains authoritative when the package is absent."
    },
    {
      "tool_id": "plotly",
      "name": "Plotly.py",
      "category": "reporting",
      "priority": "P1",
      "status": "adopted_optional",
      "posture": "optional interactive charts for the BoFire HTML report",
      "package": "plotly>=6.0",
      "pyproject_extra": "report",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/plotly/plotly.py",
        "docs": "https://plotly.com/python/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "7.0.0",
      "upstream_released_on": "2026-08-25",
      "current_signal": "PyPI 7.0.0 is current upstream. The public reporter uses Plotly for feasibility slices, candidate cost stacks, and factor-coverage heatmaps.",
      "fit": "Interactive charts in standalone BoFire HTML reports.",
      "risks": "Embedded JavaScript increases report size; the tabular report remains authoritative.",
      "route": [
        "bofire_html_constraint_slice",
        "bofire_html_cost_stack",
        "bofire_html_factor_heatmap"
      ],
      "claim_level": "optional_report_visualization",
      "fail_closed_behavior": "Omit Plotly sections and preserve the stdlib tabular report when Plotly is absent."
    },
    {
      "tool_id": "ro_crate",
      "name": "RO-Crate",
      "category": "provenance",
      "priority": "P0",
      "status": "adopted_optional",
      "posture": "minimal dossier provenance envelope",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0 docs/spec materials; verify implementation package if added",
      "links": {
        "docs": "https://www.researchobject.org/ro-crate/",
        "spec_repo": "https://github.com/ResearchObject/ro-crate",
        "workflow_run_profile": "https://www.researchobject.org/workflow-run-crate/",
        "rocrate_py": "https://github.com/ResearchObject/ro-crate-py",
        "validator": "https://github.com/crs4/rocrate-validator"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "1.3.0 spec; 0.15.1 rocrate",
      "upstream_released_on": "2026-07-10",
      "current_signal": "RO-Crate 1.3.0 and rocrate 0.15.1 are current upstream references. Keep the repository's stdlib metadata writer authoritative unless a profile-aware validator is adopted and tested.",
      "fit": "Dossier metadata, file inventory, hashes, source refs, license, claim boundaries, and future workflow-run provenance.",
      "risks": "JSON-LD can become overbuilt; validator and package APIs add churn. Keep a minimal crate profile and treat profile-aware validation as optional.",
      "route": [
        "compile_dossier",
        "workflow_run_provenance",
        "profile_validation_candidate"
      ],
      "claim_level": "provenance_metadata",
      "fail_closed_behavior": "Dossier check fails if required ro-crate-metadata.json is missing."
    },
    {
      "tool_id": "eln_file_format",
      "name": "ELN file format (.eln)",
      "category": "experiment_packet_interchange",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "ELN/LIMS-neutral run-packet interchange candidate built on RO-Crate conventions",
      "package": "",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/TheELNConsortium/TheELNFileFormat",
        "iana": "https://www.iana.org/assignments/media-types/application/vnd.eln+zip",
        "ro_crate_use_case": "https://www.researchobject.org/ro-crate/eln"
      },
      "last_checked": "2026-06-21",
      "current_signal": "The public survey recorded active consortium work in April-June 2026. The format is a zip-based interchange convention for ELN exports and imports.",
      "fit": "Public-safe synthetic run packets, sample tables, and dossier exports that should move across ELN/LIMS tools without encoding private tracker details.",
      "risks": "Import behavior varies across ELNs and the format still carries implementation quirks; do not claim validated ELN compatibility without round-trip fixture tests.",
      "route": [
        "eln_export_candidate",
        "run_packet_interchange",
        "ro_crate_profile_reference"
      ],
      "claim_level": "interchange_candidate",
      "fail_closed_behavior": "Keep the existing run packet and table contracts authoritative when .eln export is absent or not round-trip tested."
    },
    {
      "tool_id": "grobid_fulltext",
      "name": "GROBID",
      "category": "evidence_enrichment",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "public scholarly PDF structuring sidecar for open-access evidence",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0",
      "links": {
        "repo": "https://github.com/grobidOrg/grobid",
        "docs": "https://grobid.readthedocs.io/",
        "releases": "https://github.com/grobidOrg/grobid/releases"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.9.1",
      "upstream_released_on": "2026-08-04",
      "current_signal": "GROBID 0.9.1 is the current tagged release.",
      "fit": "Convert public or open-license PDFs into structured TEI/BibTeX/citation-context inputs for dossier evidence tables.",
      "risks": "Java/Docker service surface; copyright boundaries are source-specific. Do not ingest paywalled or non-permitted full text into public fixtures.",
      "route": [
        "public_pdf_structuring",
        "dossier_evidence_harvest",
        "citation_context_extraction"
      ],
      "claim_level": "evidence_extraction_sidecar",
      "fail_closed_behavior": "Use PubMed fixture mode or manually curated evidence rows when GROBID is unavailable or source license is unclear."
    },
    {
      "tool_id": "openalex_official",
      "name": "OpenAlex official CLI/API",
      "category": "literature_harvesting",
      "priority": "P2",
      "status": "watch",
      "posture": "broad public literature and citation-graph context source",
      "package": "",
      "pyproject_extra": "",
      "license": "MIT for client tooling; OpenAlex data is CC0",
      "links": {
        "docs": "https://developers.openalex.org/",
        "pypi": "https://pypi.org/project/openalex-official/",
        "paper": "https://arxiv.org/abs/2205.01833"
      },
      "last_checked": "2026-06-21",
      "current_signal": "PyPI openalex-official 0.3.3 was released 2026-03-18; API access and free-tier limits changed in 2026.",
      "fit": "Citation graph, topic, institution, and source metadata context beyond PubMed when building public literature dossiers.",
      "risks": "API keys and billing/rate limits must stay outside repos and fixtures; metadata breadth does not imply source quality or full-text rights.",
      "route": [
        "public_literature_context",
        "citation_graph_harvest"
      ],
      "claim_level": "metadata_harvest_watch",
      "fail_closed_behavior": "Skip OpenAlex enrichment and preserve fixture-backed PubMed/manual evidence rows when the API is unavailable."
    },
    {
      "tool_id": "europe_pmc_api",
      "name": "Europe PMC APIs",
      "category": "evidence_enrichment",
      "priority": "P2",
      "status": "watch",
      "posture": "public life-science literature and annotations source",
      "package": "",
      "pyproject_extra": "",
      "license": "API/source records vary by article and endpoint",
      "links": {
        "developers": "https://europepmc.org/developers",
        "rest": "https://europepmc.org/RestfulWebService",
        "annotations": "https://europepmc.org/AnnotationsApi"
      },
      "last_checked": "2026-06-21",
      "current_signal": "Official REST and annotations APIs remain public and cover life-science articles, preprints, patents, open full text, and text-mined annotations.",
      "fit": "Complement PubMed MCP for public literature harvesting, preprint coverage, open full-text lookup, and concept evidence tables.",
      "risks": "Full-text reuse depends on article license; API responses must be fixture-backed in tests and source licenses must be recorded in dossiers.",
      "route": [
        "public_life_science_search",
        "open_fulltext_lookup",
        "annotation_harvest"
      ],
      "claim_level": "metadata_harvest_watch",
      "fail_closed_behavior": "Skip Europe PMC enrichment and keep existing citation fixtures when the endpoint is unavailable or source rights are unclear."
    },
    {
      "tool_id": "nox",
      "name": "Nox",
      "category": "execution_lanes",
      "priority": "P0",
      "status": "adopted_optional",
      "posture": "repo task lane runner",
      "package": "nox>=2024.4",
      "pyproject_extra": "dev",
      "license": "Apache-2.0",
      "links": {
        "repo": "https://github.com/wntrblm/nox",
        "docs": "https://nox.thea.codes/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "2026.8.17",
      "upstream_released_on": "2026-08-18",
      "current_signal": "PyPI 2026.8.17 is current upstream. The repository retains nox>=2024.4 as its supported development-tool floor.",
      "fit": "Stable command surface for unit, table_contracts, dossier_smoke, adaptive_smoke, adaptive_live, and release checks.",
      "risks": "Not an environment lock by itself.",
      "route": [
        "local_validation",
        "optional_lanes"
      ],
      "claim_level": "execution_lane",
      "fail_closed_behavior": "Direct Python scripts remain callable without Nox."
    },
    {
      "tool_id": "botorch",
      "name": "BoTorch",
      "category": "adaptive_design",
      "priority": "P1",
      "status": "adopted_optional",
      "posture": "low-level expert backend",
      "package": "botorch>=0.9",
      "pyproject_extra": "botorch",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/meta-pytorch/botorch",
        "docs": "https://botorch.org/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.18.1",
      "upstream_released_on": "2026-06-08",
      "current_signal": "PyPI 0.18.1 is current upstream and requires Python 3.11 or newer. The repository keeps a broad lower bound for its narrow optional adapter and does not claim untested latest-version compatibility.",
      "fit": "Custom acquisition experiments when BoFire abstractions block a needed route.",
      "risks": "Too low-level for campaign-facing contracts and easy to overfit into research code.",
      "route": [
        "experimental_adaptive_adapter"
      ],
      "claim_level": "experimental_adapter",
      "runtime_claim_level": "bayesian_optimization_planned",
      "fail_closed_behavior": "Prefer BoFire; if direct BoTorch route fails, write route report and fall back."
    },
    {
      "tool_id": "xopt",
      "name": "Xopt",
      "category": "adaptive_design",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "arbitrary scientific optimization and experiment-control comparison backend",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0",
      "links": {
        "repo": "https://github.com/xopt-org/Xopt",
        "docs": "https://xopt.xopt.org/",
        "pypi": "https://pypi.org/project/xopt/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "3.2.1",
      "upstream_released_on": "2026-07-31",
      "current_signal": "PyPI 3.2.1 is current upstream. Official docs describe constrained, serial, parallel, and multi-objective Bayesian optimization plus evolutionary methods for arbitrary simulations and control systems.",
      "fit": "Candidate comparison backend for constrained media fixtures, scale-bridge simulations, and arbitrary expensive objective loops when manifest boundaries are preserved.",
      "risks": "Accelerator/control-systems origin; BioSymphony must own assay readiness, constraint translation, cost/scale semantics, and candidate-table validation.",
      "route": [
        "adaptive_backend_comparison",
        "constrained_bo",
        "multi_objective_bo",
        "parallel_evaluation"
      ],
      "claim_level": "not_yet_evaluated",
      "fail_closed_behavior": "Do not emit Xopt candidates as authoritative designs until a fixture route report exists; fall back to BoFire, ENTMOOT, OMLT, BoTorch, or stdlib planning."
    },
    {
      "tool_id": "trieste",
      "name": "Trieste",
      "category": "adaptive_design",
      "priority": "P2",
      "status": "watch",
      "posture": "TensorFlow-based BO research toolbox and complex-acquisition comparison target",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0",
      "links": {
        "repo": "https://github.com/secondmind-labs/trieste",
        "docs": "https://secondmind-labs.github.io/trieste/",
        "pypi": "https://pypi.org/project/trieste/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "4.6.0",
      "upstream_released_on": "2026-06-17",
      "current_signal": "PyPI 4.6.0 remains current upstream. Public docs describe ask-tell, batch, asynchronous, constrained, multi-fidelity, and multi-objective BO.",
      "fit": "Useful landscape comparison for complex follow-up planning and acquisition-function research, especially when TensorFlow/GPflow is already present in an external evaluation lane.",
      "risks": "Heavy TensorFlow/GPflow stack and no fermentation-specific semantics; not a near-term public adapter unless a fixture demonstrates a route that BoFire/BayBE/Ax do not cover.",
      "route": [
        "complex_acquisition_reference",
        "ask_tell_bo_watch",
        "multi_fidelity_bo_watch"
      ],
      "claim_level": "watch_only",
      "fail_closed_behavior": "Do not add as dependency or campaign route without an explicit evaluation report."
    },
    {
      "tool_id": "pymoo",
      "name": "pymoo",
      "category": "pareto_tournament",
      "priority": "P2",
      "status": "evaluate_next",
      "posture": "candidate-table Pareto and tournament sidecar",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0",
      "links": {
        "docs": "https://pymoo.org/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.6.2",
      "upstream_released_on": "2026-06-28",
      "current_signal": "PyPI 0.6.2 is current upstream and provides constrained and mixed-variable multi-objective algorithms.",
      "fit": "Posthoc Pareto sorting, hypervolume diagnostics, and design-tournament scoring.",
      "risks": "Evolutionary optimizer rather than Bayesian sample-efficient planning; use for diagnostics, not as the primary refinement loop.",
      "route": [
        "pareto_report",
        "design_tournament"
      ],
      "claim_level": "candidate_table_diagnostic",
      "fail_closed_behavior": "Keep existing stdlib tournament and emit no pymoo report when unavailable."
    },
    {
      "tool_id": "smt",
      "name": "SMT",
      "category": "surrogate_modeling",
      "priority": "P2",
      "status": "evaluate_next",
      "posture": "scale-bridge surrogate diagnostic candidate",
      "package": "",
      "pyproject_extra": "",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/SMTorg/smt",
        "docs": "https://smt.readthedocs.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "2.14.1",
      "upstream_released_on": "2026-06-22",
      "current_signal": "PyPI 2.14.1 is current upstream.",
      "fit": "Co-kriging and multi-fidelity surrogate diagnostics for plate/flask/reactor bridges.",
      "risks": "Surrogate toolbox, not campaign optimizer; requires careful adapter design.",
      "route": [
        "scale_bridge_diagnostic"
      ],
      "claim_level": "surrogate_diagnostic",
      "fail_closed_behavior": "Keep scale_recipe and BoFire route reports; do not block dossier compilation."
    },
    {
      "tool_id": "pyomo_dae",
      "name": "Pyomo.DAE",
      "category": "dynamic_feasibility",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "advanced feed/profile feasibility sidecar",
      "package": "",
      "pyproject_extra": "",
      "license": "BSD-style",
      "links": {
        "docs": "https://pyomo.readthedocs.io/en/stable/explanation/modeling/dae.html"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "Pyomo 6.10.1",
      "current_signal": "Pyomo 6.10.1 is current upstream. Pyomo.DAE remains a candidate sidecar for dynamic fed-batch and feed-control feasibility models.",
      "fit": "Continuous feed profile optimization, volume/substrate/oxygen constraints, and dynamic feasibility.",
      "risks": "Solver stack and initialization can become site-specific and heavy.",
      "route": [
        "fed_batch_feasibility",
        "dynamic_constraints"
      ],
      "claim_level": "deterministic_feasibility_sidecar",
      "fail_closed_behavior": "Do not run dynamic optimization; preserve static feasibility warnings."
    },
    {
      "tool_id": "pyplate",
      "name": "PyPlate",
      "category": "plate_execution",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "plate/deep-well recipe sidecar candidate",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0",
      "links": {
        "docs": "https://pyplate-hte.readthedocs.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.4.7",
      "current_signal": "PyPI 0.4.7 remains the latest release; the upstream repository has newer activity. Keep as an evaluation candidate for high-throughput experiment representation.",
      "fit": "Plate recipe exports, well-volume checks, reagent transforms, and liquid-handling artifacts.",
      "risks": "Plate-centric; not a fermentation scale-bridge model.",
      "route": [
        "plate_arm_manifest",
        "plate_recipe_export"
      ],
      "claim_level": "execution_recipe_sidecar",
      "fail_closed_behavior": "Emit BioSymphony plate manifest only; do not claim liquid-handler readiness."
    },
    {
      "tool_id": "fedbatchdesigner",
      "name": "FedBatchDesigner",
      "category": "fed_batch_modeling",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "reference model/example candidate",
      "package": "",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/julibeg/FedBatchDesigner",
        "paper": "https://pubs.acs.org/doi/abs/10.1021/acssynbio.5c00357"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "snapshot-20250711",
      "current_signal": "The 2025-07-11 publication snapshot remains the latest tagged release. It provides constant and exponential feeding models, case-study notebooks, and CSV or image export.",
      "fit": "Feed-volume/time stage math and growth-arrested fed-batch planning references.",
      "risks": "Low adoption signal; may not cover ordinary microbial or mammalian fed-batch oxygen limits.",
      "route": [
        "fed_batch_reference_example"
      ],
      "claim_level": "reference_sidecar",
      "fail_closed_behavior": "Keep BioSymphony feed policy fields and skip reference comparison."
    },
    {
      "tool_id": "biosteam",
      "name": "BioSTEAM",
      "category": "process_economics",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "cost/downstream sidecar",
      "package": "",
      "pyproject_extra": "",
      "license": "University of Illinois/NCSA Open Source License",
      "links": {
        "repo": "https://github.com/BioSTEAMDevelopmentGroup/biosteam",
        "docs": "https://biosteam.readthedocs.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "2.53.11",
      "current_signal": "PyPI 2.53.11 is current and the upstream repository remains active. BioSTEAM stays an evaluation candidate for process-economic and life-cycle sidecars, not a core DoE planner.",
      "fit": "Cost/L, downstream context, feedstock/media cost projections, TEA/LCA examples.",
      "risks": "Biorefinery scope can distract from upstream executability.",
      "route": [
        "cost_rollup_sidecar",
        "downstream_context"
      ],
      "claim_level": "economic_context_sidecar",
      "fail_closed_behavior": "Use existing cost_rollup with declared assumptions."
    },
    {
      "tool_id": "sbml_runtime_stack",
      "name": "SBML runtime stack (libRoadRunner/Tellurium/AMICI)",
      "category": "mechanistic_model_sidecar",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "model import/export sidecar",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0/BSD-3-Clause mix; verify per runtime",
      "links": {
        "roadrunner": "https://github.com/sys-bio/roadrunner",
        "tellurium": "https://github.com/sys-bio/tellurium",
        "amici": "https://pypi.org/project/amici/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "libRoadRunner 2.10.0; Tellurium 2.2.11.2; AMICI 1.0.1",
      "current_signal": "Current tagged components are libRoadRunner 2.10.0, Tellurium 2.2.11.2, and AMICI 1.0.1. Keep this stack as a mechanistic-model and parameter-estimation sidecar candidate.",
      "fit": "Growth/substrate/product kinetics, parameter tables, event/feed schedules, and model provenance.",
      "risks": "Public SBML models rarely encode full vessel/feed/oxygen-transfer semantics.",
      "route": [
        "mechanistic_model_sidecar"
      ],
      "claim_level": "simulation_sidecar",
      "fail_closed_behavior": "Record model as external evidence and skip runtime execution."
    },
    {
      "tool_id": "petab_libpetab",
      "name": "PEtab / libpetab-python",
      "category": "model_calibration_contracts",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "parameter-estimation table contract candidate for mechanistic sidecars",
      "package": "",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/PEtab-dev/libpetab-python",
        "docs": "https://petab.readthedocs.io/",
        "pypi": "https://pypi.org/project/petab/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.8.2",
      "upstream_released_on": "2026-03-12",
      "current_signal": "PyPI 0.8.2 remains current upstream. The package reads, writes, and validates PEtab files and installs the petablint validator.",
      "fit": "Portable public calibration fixtures around SBML/ODE models before pyPESTO, AMICI, or RoadRunner-side evaluation.",
      "risks": "Systems-biology parameter-estimation semantics are not fermentation manifest semantics; keep response, factor, assay, cost, and scale contracts BioSymphony-owned.",
      "route": [
        "mechanistic_model_contract",
        "parameter_estimation_fixture",
        "petab_validation"
      ],
      "claim_level": "calibration_contract_candidate",
      "fail_closed_behavior": "Skip PEtab export/import and keep the campaign manifest plus table contracts authoritative when no validated PEtab fixture exists."
    },
    {
      "tool_id": "pypesto",
      "name": "pyPESTO",
      "category": "mechanistic_model_sidecar",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "parameter-estimation and uncertainty sidecar for public mechanistic models",
      "package": "",
      "pyproject_extra": "",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/ICB-DCM/pyPESTO",
        "docs": "https://pypesto.readthedocs.io/",
        "pypi": "https://pypi.org/project/pypesto/",
        "paper": "https://doi.org/10.1093/bioinformatics/btad711"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.6.0",
      "upstream_released_on": "2026-03-19",
      "current_signal": "PyPI 0.6.0 remains current upstream. Official docs describe multi-start and global optimization, simulator interfaces, PEtab/SBML pipelines, and uncertainty quantification.",
      "fit": "Candidate calibration sidecar for public or synthetic kinetic and cell-culture models, with uncertainty reports that can feed evidence and assumption checks.",
      "risks": "Heavy optional stack and calibration outputs can look more authoritative than the available data supports; never bypass readiness, assay-power, scale, or claim-boundary checks.",
      "route": [
        "mechanistic_parameter_estimation",
        "uncertainty_quantification_sidecar",
        "petab_sbml_pipeline"
      ],
      "claim_level": "calibration_sidecar_candidate",
      "fail_closed_behavior": "Treat pyPESTO results as external evidence rows unless an in-repo fixture validates the full route; skip calibration when dependencies or model contracts are absent."
    },
    {
      "tool_id": "pseudobatch",
      "name": "Pseudobatch",
      "category": "fed_batch_data_transform",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "fed-batch sample-withdrawal correction reference and preprocessing candidate",
      "package": "",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/biosustain/pseudobatch",
        "docs": "https://biosustain.github.io/pseudobatch/",
        "pypi": "https://pypi.org/project/pseudobatch/",
        "preprint": "https://doi.org/10.1101/2024.05.27.596043"
      },
      "last_checked": "2026-06-21",
      "current_signal": "PyPI pseudobatch 1.0.1 released 2025-01-10; README and package page describe transformations for fed-batch data where samples are withdrawn during cultivation.",
      "fit": "Preprocessing note for public fed-batch ledgers before growth-rate, biomass, or response modeling when sample withdrawal creates mass-balance artifacts.",
      "risks": "Specific correction method, not a general fermentation simulator or scale-transfer model; error-propagation extra brings CmdStan complexity.",
      "route": [
        "fed_batch_sample_withdrawal",
        "ledger_preprocessing",
        "growth_rate_transform_reference"
      ],
      "claim_level": "preprocessing_candidate",
      "fail_closed_behavior": "Leave raw and corrected values explicit in evidence tables; skip transformation when volume/sample metadata are missing."
    },
    {
      "tool_id": "pixi",
      "name": "Pixi",
      "category": "dependency_lanes",
      "priority": "P1",
      "status": "watch",
      "posture": "future multi-environment lock/task candidate",
      "package": "",
      "pyproject_extra": "",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/prefix-dev/pixi"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.78.0",
      "current_signal": "Pixi 0.78.0 is current upstream. It remains a watch item for reproducible optional dependency lanes if the current venv and Nox approach becomes insufficient.",
      "fit": "Named environments for stdlib, contracts, adaptive, release, and optional-tool smoke profiles.",
      "risks": "Adds another environment manager.",
      "route": [
        "dependency_locking"
      ],
      "claim_level": "developer_tooling",
      "fail_closed_behavior": "Continue using direct Python scripts and Nox."
    },
    {
      "tool_id": "cwl",
      "name": "Common Workflow Language / cwltool provenance",
      "category": "portable_handoff",
      "priority": "P1",
      "status": "watch",
      "posture": "portable workflow handoff candidate",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0",
      "links": {
        "docs": "https://www.commonwl.org/",
        "provenance": "https://cwltool.readthedocs.io/en/latest/CWLProv.html"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "cwltool 3.2.20260720092025",
      "current_signal": "CWL and CWLProv remain active; cwltool 3.2.20260720092025 is current. Keep as a watch item for portable declared inputs, outputs, and workflow provenance.",
      "fit": "Narrow remote execution bundles with explicit command provenance.",
      "risks": "Verbose for simple scripts and unnecessary while the manifest and task-request contracts remain sufficient.",
      "route": [
        "portable_handoff_bundle"
      ],
      "claim_level": "workflow_provenance_sidecar",
      "fail_closed_behavior": "Use Nox plus the explicit JSON handoff contracts."
    },
    {
      "tool_id": "dwsim",
      "name": "DWSIM",
      "category": "external_flowsheet",
      "priority": "P2",
      "status": "boundary_only",
      "posture": "external export/import only",
      "package": "",
      "pyproject_extra": "",
      "license": "GPL-3.0",
      "links": {
        "site": "https://dwsim.org/",
        "repo": "https://github.com/DanWBR/dwsim"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "9.0.5",
      "current_signal": "DWSIM 9.0.5 is the latest tagged release. The linked GitHub repository is archived; GPL licensing and the heavy runtime keep it boundary-only.",
      "fit": "Downstream, biorefinery, and process-economics reference simulations.",
      "risks": "GPL embedding risk and GUI/heavy runtime.",
      "route": [
        "external_flowsheet_export"
      ],
      "claim_level": "external_reference",
      "fail_closed_behavior": "Do not import as dependency; export assumptions only."
    },
    {
      "tool_id": "cadet",
      "name": "CADET",
      "category": "downstream_modeling",
      "priority": "P2",
      "status": "boundary_only",
      "posture": "external downstream sidecar only",
      "package": "",
      "pyproject_extra": "",
      "license": "GPL-3.0",
      "links": {
        "repo": "https://github.com/cadet"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "CADET-Core 5.1.1",
      "current_signal": "CADET-Core 5.1.1 is current upstream. CADET remains relevant to downstream unit-operation modeling and outside the core upstream DoE planner.",
      "fit": "Chromatography/filtration sidecars when dossiers grow downstream.",
      "risks": "GPL embedding risk and uncertain upstream fermentation fit.",
      "route": [
        "downstream_external_sidecar"
      ],
      "claim_level": "external_reference",
      "fail_closed_behavior": "Keep downstream assumptions as evidence rows."
    },
    {
      "tool_id": "cobrapy",
      "name": "COBRApy",
      "category": "metabolic_evidence",
      "priority": "P2",
      "status": "boundary_only",
      "posture": "evidence sidecar only",
      "package": "",
      "pyproject_extra": "",
      "license": "GPL-2.0",
      "links": {
        "repo": "https://github.com/opencobra/cobrapy",
        "docs": "https://cobrapy.readthedocs.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.32.1",
      "current_signal": "COBRApy 0.32.1 is current upstream. Keep it boundary-only unless public metabolic-model priors enter the evidence layer.",
      "fit": "Substrate/product feasibility priors and yield-bound sanity checks.",
      "risks": "GEM predictions are not process readiness; GPL and model-license variance.",
      "route": [
        "metabolic_evidence_sidecar"
      ],
      "claim_level": "evidence_sidecar",
      "fail_closed_behavior": "Represent model conclusions as reviewed evidence rows only."
    },
    {
      "tool_id": "snakemake",
      "name": "Snakemake",
      "category": "workflow_platform",
      "priority": "P2",
      "status": "watch",
      "posture": "defer unless repeated computational DAGs dominate",
      "package": "",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "docs": "https://snakemake.github.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "9.26.1",
      "current_signal": "Snakemake 9.26.1 is current upstream. It remains a capable workflow engine that is not needed for the repository's current contract and dossier flow.",
      "fit": "Benchmark sweeps or repeated simulation campaigns.",
      "risks": "Another DSL and execution model competing with existing orchestration.",
      "route": [
        "batch_benchmark_dag"
      ],
      "claim_level": "workflow_sidecar",
      "fail_closed_behavior": "Keep the manifest, task-request, and Nox lanes."
    },
    {
      "tool_id": "nextflow",
      "name": "Nextflow",
      "category": "workflow_platform",
      "priority": "P2",
      "status": "watch",
      "posture": "defer unless large cloud/HPC workflows appear",
      "package": "",
      "pyproject_extra": "",
      "license": "Apache-2.0",
      "links": {
        "docs": "https://www.nextflow.io/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "26.04.6",
      "current_signal": "Nextflow 26.04.6 is the latest tagged release. Keep it as a watch item for larger containerized pipelines rather than adding a second workflow language now.",
      "fit": "Large computational analysis pipelines.",
      "risks": "Groovy DSL and cloud-pipeline posture do not align with current Python/stdlib repo shape.",
      "route": [
        "large_compute_pipeline"
      ],
      "claim_level": "workflow_sidecar",
      "fail_closed_behavior": "Keep the manifest, task-request, and Nox lanes."
    },
    {
      "tool_id": "scikit_optimize",
      "name": "scikit-optimize",
      "category": "avoid",
      "priority": "Avoid",
      "status": "avoid",
      "posture": "do not add",
      "package": "",
      "pyproject_extra": "",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/scikit-optimize/scikit-optimize"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.10.2",
      "current_signal": "PyPI 0.10.2 remains the latest release and the original repository remains archived. Use the separately tracked ProcessOptimizer continuation for any new evaluation.",
      "fit": "None for new integration.",
      "risks": "Stale dependency and limited fit for constrained multi-objective scale-bridge work.",
      "route": [],
      "claim_level": "not_applicable",
      "fail_closed_behavior": "Do not integrate; keep any legacy references as historical only."
    },
    {
      "tool_id": "pysamoo",
      "name": "pysamoo",
      "category": "avoid",
      "priority": "Avoid",
      "status": "avoid",
      "posture": "do not add without explicit license decision",
      "package": "",
      "pyproject_extra": "",
      "license": "AGPL",
      "links": {
        "repo": "https://github.com/anyoptimization/pysamoo"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.1.2",
      "current_signal": "PyPI 0.1.2 remains current while the repository has newer activity. The AGPL license keeps this surrogate-assisted multi-objective tool outside the adopted adapter set.",
      "fit": "None for current repo.",
      "risks": "AGPL distribution obligations.",
      "route": [],
      "claim_level": "not_applicable",
      "fail_closed_behavior": "Do not integrate."
    },
    {
      "tool_id": "entmoot",
      "name": "ENTMOOT v2",
      "category": "adaptive_design",
      "priority": "P1",
      "status": "adopted_optional",
      "posture": "in-repo adapter wraps ENTMOOT v2; min_count, min-active coupling, tie-cycle handling, and HiGHS fallback are adapter-enforced",
      "package": "entmoot==2.1.1",
      "pyproject_extra": "entmoot",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/cog-imperial/entmoot",
        "design_doc": "https://github.com/cog-imperial/entmoot"
      },
      "docs_in_repo": [
        "docs/ENTMOOT_SWAP_DESIGN.md",
        "src/biosymphony_ferm_doe/adapters/entmoot_strategy.py",
        "tests/test_entmoot_adapter.py"
      ],
      "last_checked": "2026-08-30",
      "upstream_version": "2.1.1",
      "upstream_released_on": "2026-02-19",
      "current_signal": "PyPI 2.1.1 remains current upstream. The public adapter adds min_count emission, min-active lower coupling, HiGHS solver support, and tie-cycle handling at the repository boundary.",
      "fit": "MIP-encoded NChooseK cardinality first-class; addresses BoFire NChooseK+SoboStrategy stall (issue #450). In-repo adapter exposes adapter_backed_nchoosek BO route with HiGHS default solver.",
      "risks": "Raw upstream ENTMOOT APIs can still mislead if used directly; use the in-repo adapter so min_count, min-active coupling, solver fallback, and fail-closed route reports are preserved.",
      "route": [
        "nchoosek_cardinality_bo",
        "tree_based_surrogate",
        "in_repo_adapter"
      ],
      "claim_level": "adapter_backed_nchoosek_bo",
      "runtime_claim_level": "entmoot_adapter_planning",
      "route_reasons": [
        "nchoosek_constraint_with_bo",
        "tree_surrogate_requested",
        "bofire_sobo_known_stall"
      ],
      "fail_closed_behavior": "Adapter raises RuntimeError at instantiation if entmoot or chosen solver not available; degrades to \"not_available\" in plan reports without raising."
    },
    {
      "tool_id": "pubmed_mcp_adapter",
      "name": "PubMed MCP Adapter",
      "category": "evidence_enrichment",
      "priority": "P0",
      "status": "adopted_optional",
      "posture": "in-repo adapter normalises PubMed records into the CITATIONS.json schema. Fixture mode is the primary integration path; the direct MCP hook (_try_mcp_fetch) is a stub awaiting an in-process bridge. Live enrichment is harness-mediated and fed in via fixtures.",
      "package": "",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "source": "https://github.com/BioSymphony/ferm-doe",
        "mcp_server": "https://pubmed.ncbi.nlm.nih.gov/"
      },
      "docs_in_repo": [
        "src/biosymphony_ferm_doe/adapters/pubmed_mcp.py",
        "tests/test_pubmed_adapter.py"
      ],
      "last_checked": "2026-08-30",
      "current_signal": "The in-repo adapter supports fixture normalization and fallback behavior. Direct in-process MCP calls remain unwired; live retrieval must be performed by the calling harness and handed to the fixture interface.",
      "fit": "Fixture-driven PubMed citation enrichment, dossier BibTeX export, --use-pubmed-fixture CLI flag for deterministic test mode. A direct in-process MCP hook is reserved (_try_mcp_fetch).",
      "risks": "Direct MCP mode is currently a stub; the practical path for live enrichment is harness-mediated harvest plus fixture handoff. Fixture mode required for offline/CI runs.",
      "route": [
        "dossier_citation_enrichment",
        "bibtex_export"
      ],
      "claim_level": "fixture_normalization_and_harness_mediated_enrichment",
      "fail_closed_behavior": "When MCP unreachable, adapter falls back to fixture mode or empty enrichment with explicit warning."
    },
    {
      "tool_id": "ax",
      "name": "Ax",
      "category": "adaptive_design",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "adaptive experimentation infrastructure and custom-generation-strategy candidate; not default static DoE route",
      "package": "ax-platform==1.2.4",
      "pyproject_extra": "backend-eval",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/facebook/Ax",
        "docs": "https://ax.dev/"
      },
      "docs_in_repo": [
        "docs/BIOMANUFACTURING_ADAPTIVE_BACKENDS.md",
        "docs/adaptive-backend-evaluation.json"
      ],
      "last_checked": "2026-08-30",
      "upstream_version": "1.3.1",
      "upstream_released_on": "2026-06-09",
      "current_signal": "PyPI 1.3.1 is current upstream and requires Python 3.11 or newer. The backend-eval extra remains pinned to 1.2.4, so this entry does not claim latest-version compatibility.",
      "fit": "Production adaptive-experiment orchestration, custom GenerationStrategy/BoTorch routing, trial lifecycle and resume semantics when a campaign outgrows a simple ask/tell adapter.",
      "risks": "Heavier translation surface than BoFire or BayBE; not chemistry-first or bioprocess-first; can duplicate campaign orchestration if adopted too early.",
      "route": [
        "adaptive_orchestration_pilot",
        "custom_generation_strategy",
        "botorch_infrastructure"
      ],
      "claim_level": "not_yet_evaluated",
      "fail_closed_behavior": "Do not block dossier compilation; if Ax is unavailable or cannot preserve the manifest boundary, write an evaluation report and fall back to BoFire, direct BoTorch, or stdlib planning.",
      "local_lane": "nox -s adaptive_backend_surface"
    },
    {
      "tool_id": "botorch_direct",
      "name": "BoTorch (direct usage, EIpu)",
      "category": "adaptive_design",
      "priority": "P2",
      "status": "watch",
      "posture": "alternative cost-aware BO path bypassing BoFire abstraction",
      "package": "botorch>=0.10",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/meta-pytorch/botorch",
        "docs": "https://botorch.org/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.18.1",
      "upstream_released_on": "2026-06-08",
      "current_signal": "PyPI 0.18.1 is current upstream. A dated repository review selected direct BoTorch as the watch path for cost-aware acquisition experiments that need lower-level surrogate control.",
      "fit": "Expected Improvement per unit cost (EIpu) for cost-aware Pareto front; direct surrogate control without BoFire constraint-translation overhead.",
      "risks": "Reimplements problem encoding from scratch; loses BoFire's data-model + factor-space scaffolding.",
      "route": [
        "cost_aware_acquisition",
        "direct_surrogate_control"
      ],
      "claim_level": "not_yet_evaluated",
      "fail_closed_behavior": "N/A \u2014 not wired."
    },
    {
      "tool_id": "atlas",
      "name": "Atlas (gryffin/golem successor)",
      "category": "adaptive_design",
      "priority": "P2",
      "status": "watch",
      "posture": "tree-based BO with categorical-aware kernels",
      "package": "matter-atlas",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/the-matter-lab/atlas"
      },
      "last_checked": "2026-08-30",
      "current_signal": "The canonical repository is now under the-matter-lab. The last reviewed release was v0.0.1; this remains a watch item for categorical and unknown-feasibility workflows.",
      "fit": "Unknown-feasibility BO via Anubis variational GP classifier. Multi-fidelity also supported. NOT a NChooseK fix \u2014 use ENTMOOT (via BoFire EntingStrategy) for cardinality.",
      "risks": "Smaller community than BoFire/BoTorch; chemistry-first not bioprocess-first.",
      "route": [
        "categorical_aware_bo"
      ],
      "claim_level": "not_yet_evaluated",
      "fail_closed_behavior": "N/A \u2014 not wired."
    },
    {
      "tool_id": "baybe",
      "name": "BayBe (Bayesian Back End)",
      "category": "adaptive_design",
      "priority": "P1",
      "status": "evaluate_next",
      "posture": "low-data/hybrid/transfer-learning BO comparison target next to BoFire; Apache-2.0",
      "package": "baybe==0.14.3; python_version < '3.14'",
      "pyproject_extra": "backend-eval",
      "license": "Apache-2.0",
      "links": {
        "repo": "https://github.com/emdgroup/baybe",
        "docs": "https://emdgroup.github.io/baybe/",
        "paper": "https://pubs.rsc.org/en/content/articlehtml/2025/dd/d5dd00050e"
      },
      "docs_in_repo": [
        "docs/BIOMANUFACTURING_ADAPTIVE_BACKENDS.md",
        "docs/adaptive-backend-evaluation.json",
        "examples/adaptive-backend-eval/README.md"
      ],
      "last_checked": "2026-08-30",
      "upstream_version": "0.15.0",
      "upstream_released_on": "2026-06-11",
      "current_signal": "PyPI 0.15.0 is current upstream and supports Python >=3.10,<3.15. The backend-eval extra remains pinned to 0.14.3 because 0.15.0 includes breaking API changes; no latest-version compatibility is claimed.",
      "fit": "Compare next to BoFire for low-data-regime design, discrete/hybrid campaign surfaces, transfer-learning across related campaigns, asynchronous result arrival, and substance/categorical encodings. Good match to cumulative-dossier learning if kept behind a manifest boundary.",
      "risks": "Smaller classical constrained-DoE/IPOPT surface than BoFire and a pre-1.0 API. Any adapter must preserve the manifest, scale-bridge, assay, cost-stack, and handoff boundaries.",
      "route": [
        "bofire_alternative_adapter",
        "categorical_substance_encoding",
        "transfer_learning_across_campaigns",
        "low_data_regime_design"
      ],
      "claim_level": "not_yet_evaluated",
      "fail_closed_behavior": "Do not materialize BayBE candidates as authoritative designs until a fixture route report exists. If BayBE is missing or cannot preserve the manifest boundary, write an evaluation report and fall back to BoFire or stdlib planning.",
      "local_lane": "nox -s adaptive_backend_surface"
    },
    {
      "tool_id": "obsidian_apo",
      "name": "obsidian (Algorithmic Process Optimization)",
      "category": "adaptive_design",
      "priority": "P2",
      "status": "boundary_only",
      "posture": "GPL-3.0 boundary-only; documented as Dash UI + SHAP pattern exemplar",
      "package": "",
      "pyproject_extra": "",
      "license": "GPL-3.0",
      "links": {
        "repo": "https://github.com/MSDLLCpapers/obsidian",
        "docs": "https://msdllcpapers.github.io/obsidian/",
        "pypi": "https://pypi.org/project/obsidian-apo/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.8.6",
      "current_signal": "PyPI 0.8.6 remains the latest release and the repository remains active. The project provides GP-based Bayesian optimization, batch recommendations, and an optional application UI.",
      "fit": "Reference for Dash UI patterns and SHAP-based explainability for process development scientists. Not embeddable due to GPL-3.0.",
      "risks": "GPL-3.0 embedding risk per registry license_boundary decision rule. Closed-source corporate-affiliated maintainer (Merck & Co.).",
      "route": [
        "dash_ui_reference",
        "shap_explanation_reference"
      ],
      "claim_level": "external_reference",
      "fail_closed_behavior": "Do not import as dependency; document patterns only."
    },
    {
      "tool_id": "estim8",
      "name": "estim8 (JuBiotech parameter estimation)",
      "category": "mechanistic_model_sidecar",
      "priority": "P2",
      "status": "boundary_only",
      "posture": "AGPL-3.0 boundary-only; FMI bridge for Modelica parameter estimation",
      "package": "",
      "pyproject_extra": "",
      "license": "AGPL-3.0",
      "links": {
        "repo": "https://github.com/JuBiotech/estim8",
        "org": "https://github.com/JuBiotech"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "0.1.6",
      "upstream_released_on": "2026-07-13",
      "current_signal": "PyPI 0.1.6 is current upstream. The package supports FMI-based parameter estimation for dynamic bioprocess models.",
      "fit": "First-class FMI bridge \u2014 can ingest Modelica models from external upstream model authors and run estimation in Python. Useful when a campaign sponsor brings Modelica vessel/control models.",
      "risks": "AGPL-3.0 prohibits embedding under the registry license boundary. Maintenance horizon remains uncertain.",
      "route": [
        "fmi_modelica_parameter_estimation",
        "external_bioprocess_model_ingest"
      ],
      "claim_level": "external_reference",
      "fail_closed_behavior": "Do not import; treat operator-run results as external evidence rows."
    },
    {
      "tool_id": "bletl",
      "name": "bletl (JuBiotech BioLector parser)",
      "category": "data_contracts",
      "priority": "P2",
      "status": "boundary_only",
      "posture": "AGPL-3.0 boundary-only; BioLector raw-file parser with PyMC inference",
      "package": "",
      "pyproject_extra": "",
      "license": "AGPL-3.0",
      "links": {
        "repo": "https://github.com/JuBiotech/bletl",
        "org": "https://github.com/JuBiotech"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "1.7.1",
      "current_signal": "PyPI 1.7.1 remains current and the repository remains active. The package parses BioLector data and provides uncertainty-aware growth-rate analysis.",
      "fit": "Canonical Python ingest path for BioLector microbioreactor data. Operator runs externally; biosymphony ingests CSV output.",
      "risks": "AGPL-3.0 prohibits embedding per registry license_boundary decision rule. Previous survey did not flag the AGPL license; this entry exists to make the boundary explicit.",
      "route": [
        "external_biolector_ingest"
      ],
      "claim_level": "external_reference",
      "fail_closed_behavior": "Do not import; ingest CSV exports as evidence rows."
    },
    {
      "tool_id": "processoptimizer",
      "name": "ProcessOptimizer (Novo Nordisk scikit-optimize fork)",
      "category": "adaptive_design",
      "priority": "P2",
      "status": "watch",
      "posture": "scikit-optimize maintained continuation; pharma-affiliated maintainer",
      "package": "",
      "pyproject_extra": "",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/novonordisk-research/ProcessOptimizer",
        "paper": "https://pubs.acs.org/doi/10.1021/acs.jcim.4c02240"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "1.1.2",
      "upstream_released_on": "2026-02-13",
      "current_signal": "PyPI 1.1.2 is current upstream. The maintained scikit-optimize lineage provides Gaussian-process, multi-objective, batch, and plotting features.",
      "fit": "Migration target when campaign sponsor brings scikit-optimize code. Lighter than BoFire/BayBe; keeps the scikit-optimize lineage alive.",
      "risks": "Smaller ecosystem signal than BoFire/BayBe. Inherits scikit-optimize's pre-existing limitations (no NChooseK first-class, no cost-aware).",
      "route": [
        "scikit_optimize_migration_target"
      ],
      "claim_level": "not_yet_evaluated",
      "fail_closed_behavior": "N/A \u2014 not wired."
    },
    {
      "tool_id": "tabpfn_v2",
      "name": "TabPFN (foundation-model surrogate)",
      "category": "surrogate_modeling",
      "priority": "P2",
      "status": "adopted_optional",
      "posture": "optional low-data surrogate adapter; this repository requires a runtime token for noninteractive use",
      "package": "tabpfn>=8,<9",
      "pyproject_extra": "tabpfn",
      "license": "Prior Labs License for code and v2 weights; non-commercial license for default TabPFN-3 weights",
      "links": {
        "repo": "https://github.com/PriorLabs/TabPFN",
        "paper": "https://www.nature.com/articles/s41586-024-08328-6",
        "pypi": "https://pypi.org/project/tabpfn/"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "8.5.0",
      "upstream_released_on": "2026-08-27",
      "current_signal": "PyPI 8.5.0 is current upstream and uses TabPFN-3 by default. This repository's noninteractive adapter requires TABPFN_TOKEN at runtime; upstream also supports interactive browser-based license acceptance.",
      "fit": "Low-data tabular regression surrogate for sequential planning when n<20 or the operator explicitly requests a TabPFN-backed planning experiment.",
      "risks": "Default TabPFN-3 weights are non-commercial, while the code and v2 weights carry the Prior Labs License with an attribution provision. Review terms before use. No native NChooseK ownership; the repository wrapper and post-hoc validation handle constraints. Predictions are model suggestions, not lab validation.",
      "route": [
        "foundation_model_surrogate_pilot",
        "small_data_tabular_regression",
        "optional_in_repo_adapter"
      ],
      "claim_level": "tabpfn_adapter_planning",
      "route_reasons": [
        "low_data_regime",
        "small_factor_count",
        "operator_requested_tabpfn"
      ],
      "fail_closed_behavior": "Adapter remains importable without token or package; plan reports degrade to not_available and stdlib fallback remains authoritative.",
      "docs_in_repo": [
        "src/biosymphony_ferm_doe/adapters/tabpfn_strategy.py",
        "tests/test_tabpfn_strategy.py",
        "docs/TOOL_REGISTRY.md"
      ]
    },
    {
      "tool_id": "tabicl_v2",
      "name": "TabICLv2",
      "category": "surrogate_modeling",
      "priority": "P2",
      "status": "watch",
      "posture": "open tabular foundation-model watch item next to TabPFN",
      "package": "",
      "pyproject_extra": "",
      "license": "BSD-3-Clause with Apache-2.0-derived forecast subdirectory",
      "links": {
        "repo": "https://github.com/soda-inria/tabicl",
        "docs": "https://tabicl.readthedocs.io/",
        "pypi": "https://pypi.org/project/tabicl/",
        "paper_v2": "https://arxiv.org/abs/2602.11139",
        "paper_v1": "https://arxiv.org/abs/2502.05564"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "2.1.1",
      "upstream_released_on": "2026-04-29",
      "current_signal": "PyPI tabicl 2.1.1 released 2026-04-29; official repo describes TabICLv2 as the ICML 2026 successor to TabICL with open inference code and weights, scikit-learn compatibility, regression/classification support, and larger-table scaling.",
      "fit": "Watch as a possible TabPFN comparison surrogate for larger public result tables, especially when zero-tuning tabular regression is useful but TabPFN's small-data posture is limiting.",
      "risks": "No native DoE constraint ownership, assay semantics, or scale context; checkpoint download and GPU memory behavior need a fixture before any adapter work.",
      "route": [
        "foundation_model_surrogate_watch",
        "tabpfn_comparison",
        "larger_table_regression_watch"
      ],
      "claim_level": "watch_only",
      "fail_closed_behavior": "Do not add as dependency or route until a fixture shows constraint-preserving regression behavior under BioSymphony validation."
    },
    {
      "tool_id": "llambo",
      "name": "LLAMBO (LLM-warmstart sampler)",
      "category": "adaptive_design",
      "priority": "P2",
      "status": "watch",
      "posture": "LLM warmstart pilot candidate via OptunaHub; warmstart-only scope",
      "package": "",
      "pyproject_extra": "",
      "license": "MIT",
      "links": {
        "repo": "https://github.com/tennisonliu/LLAMBO",
        "paper": "https://arxiv.org/abs/2402.03921",
        "optunahub": "https://hub.optuna.org/samplers/llambo/"
      },
      "last_checked": "2026-08-30",
      "current_signal": "The ICLR 2024 reference repository has no tagged release and its latest public activity remains from 2024. Keep LLAMBO as a literature reference rather than a load-bearing adapter.",
      "fit": "Warmstart-only \u2014 beats random init at trial 1-10 because the LLM has read the literature. After that ~GP-equivalent. Strong scoping due to Gupta 2024 negative result on LLM-in-the-inner-loop.",
      "risks": "The cited label-permutation study found that the evaluated LLM-only BO agents were insensitive to experimental feedback. Do not use this route for the inner BO loop. External model-service cost and credential requirements apply, and the OptunaHub sampler delegates categorical factors to random search.",
      "route": [
        "llm_warmstart_first_batch",
        "optuna_sampler_pilot"
      ],
      "claim_level": "not_yet_evaluated",
      "fail_closed_behavior": "N/A \u2014 not wired."
    },
    {
      "tool_id": "omlt",
      "name": "OMLT (Optimization & Machine Learning Toolkit)",
      "category": "surrogate_modeling",
      "priority": "P1",
      "status": "adopted_optional",
      "posture": "optional in-repo adapter for MIP-optimized surrogate planning with explicit linear and NChooseK constraints",
      "package": "omlt>=1.2.2,<2",
      "pyproject_extra": "omlt",
      "license": "BSD-3-Clause",
      "links": {
        "repo": "https://github.com/cog-imperial/OMLT",
        "paper": "https://jmlr.org/papers/v23/22-0277.html"
      },
      "last_checked": "2026-08-30",
      "upstream_version": "1.2.2",
      "upstream_released_on": "2025-03-21",
      "current_signal": "PyPI 1.2.2 remains current upstream. The public optional adapter is import-safe without heavy dependencies and emits not_available or solver_unavailable reports unless its solver and surrogate stack is installed.",
      "fit": "MIP-backed surrogate optimization for linear, categorical, and NChooseK-heavy candidate generation when a fitted surrogate plus hard constraints is the right planning surface.",
      "risks": "Surrogate quality bounds candidate quality; solver stack is heavier than stdlib/BoFire. It must not bypass BioSymphony readiness, assay, evidence, cost, or scale-transfer gates.",
      "route": [
        "mip_surrogate_optimization",
        "nchoosek_cardinality_bo",
        "optional_in_repo_adapter"
      ],
      "claim_level": "omlt_adapter_planning",
      "route_reasons": [
        "non_box_constraints",
        "operator_requested_omlt",
        "categorical_factor_present",
        "trained_surrogate_artifact_present"
      ],
      "fail_closed_behavior": "Adapter remains importable without optional dependencies; plan reports degrade to not_available or solver_unavailable without raising.",
      "docs_in_repo": [
        "src/biosymphony_ferm_doe/adapters/omlt_strategy.py",
        "tests/test_omlt_strategy.py",
        "docs/TOOL_REGISTRY.md"
      ]
    }
  ]
}