{ "gate_run_id": "gate_20260917T182405Z", "created_utc": "2026-09-17T18:24:06.106184+00:00", "reps": 5, "mode": "live_fred", "basis_path": "/home/singh/sim/corpus/seed/precedents/comparability_basis.json", "backend_identity": { "schema": "sim.gate_backend_identity.v4", "captured": true, "captured_at_utc": "2026-09-17T18:24:05.706426+00:00", "label": "CONFIGURATION OBSERVED AT RUN TIME, NOT VERIFIED MODEL IDENTITY", "container": { "name": "fred-v030", "resolved_by": "port binding 127.0.0.1:8105, not by name (R30)", "image": "fred:v0.3.0", "image_id": "sha256:9033380caffaafa1e4e0e4dc6be968cbf70981c3a166e355af9b6c593d1bfe20", "repo_digests": "[fred@sha256:9033380caffaafa1e4e0e4dc6be968cbf70981c3a166e355af9b6c593d1bfe20]", "repo_digest_is_registry_verifiable": false, "repo_digest_note": "RepoDigest equals local ImageID: locally built, digest is not verifiable against any registry", "created": "2026-09-08T16:37:32.240892054Z" }, "image_digest_pins": "the fred HARNESS container, NOT the reasoning model. The model is served from outside this image; the digest attests neither which model answered nor that the tag was stable across the gate.", "fred_model_configured_tag": "kimi-k2.6:cloud", "fred_model_tag_note": "the tag CONFIGURED on the container, not a record of what answered. A remote tag can move under a fixed name.", "ollama_base_url": "http://host.docker.internal:11434/v1", "other_env_names_only": [], "env_filter": { "applied": "^(FRED_MODEL|OLLAMA_BASE_URL|[A-Za-z0-9_]*_HOST)=", "superseded": "(FRED_MODEL|OLLAMA_BASE_URL|.*_HOST)=", "deviation_reason": "the superseded pattern is unanchored on the right; '.*_HOST=' can match on the VALUE side and record a secret in full (R32)", "values_recorded_for": [ "FRED_MODEL", "OLLAMA_BASE_URL" ] }, "health": { "wire_version": "1.2", "status": "ok", "fred_version": "0.3.0", "current_run_id": null }, "health_note": "/v1/health carries no model field, so it corroborates that fred is up and which fred_version is running --- not which model answered.", "code_state": { "captured": true, "repo": "/home/singh/sim", "head": "8ddbf9aa6472e458fc8e448e1d858694273268c4", "dirty": false, "dirty_paths_count": 0, "note": "the commit checked out when the gate started. If dirty is true this sha does NOT describe the code that ran." }, "model_probe": { "endpoint_base": "http://127.0.0.1:11434", "queried_tag": "kimi-k2.6:cloud", "tags": { "reachable": true, "name": "kimi-k2.6:cloud", "model": "kimi-k2.6:cloud", "remote_model": "kimi-k2.6", "remote_host": "https://ollama.com:443", "digest": "a90cd0d1590c53b9f9f4e0f66218e4c514d190652b8bed2842528e2530e34dc6", "modified_at": "2026-04-24T20:00:03.980908081+01:00", "details": { "parent_model": "", "format": "", "family": "kimi-k2", "families": [ "kimi-k2" ], "parameter_size": "1T", "quantization_level": "int4" }, "size_bytes": 384 }, "show": { "reachable": true, "capabilities": [ "vision", "thinking", "completion", "tools" ], "details": { "parent_model": "kimi-k2.6", "format": "", "family": "kimi-k2", "families": null, "parameter_size": "1042000000000", "quantization_level": "INT4" }, "model_info": { "general.architecture": "kimi-k2", "general.parameter_count": 1042000000000, "kimi-k2.context_length": 262144, "kimi-k2.embedding_length": 2048 }, "modified_at": "2026-04-20T00:00:00Z" }, "modified_at_agree": false, "parameter_size_agree": false, "note": "the LOCAL POINTER and the remote's DECLARED metadata, captured at gate start. A size of a few hundred bytes shows the local entry is a pointer, not weights. NEITHER modified_at attests which weights answered and neither is a model file's mtime. A remote tag can move mid-gate; a start-time probe does not cover the gate's duration. parameter_size_agree can read false for a difference of representation alone." }, "tool_inventory": { "schema": "sim.fred_tool_inventory.v1", "url": "http://127.0.0.1:8105/v1/tools", "reachable": true, "wire_version": "1.2", "tool_count": 10, "tool_names": [ "brave_search", "check_lipinski", "get_compound_properties", "get_protein_info", "get_target_info", "read_file", "search_compounds", "search_pathways", "search_publications", "write_file" ], "tool_args": { "read_file": [ "path" ], "write_file": [ "content", "path" ], "brave_search": [ "max_results", "query" ], "search_compounds": [ "max_results", "query" ], "get_compound_properties": [ "cid", "name" ], "check_lipinski": [ "properties" ], "get_protein_info": [ "identifier", "max_results", "organism_id" ], "search_pathways": [ "max_results", "query", "species" ], "get_target_info": [ "identifier" ], "search_publications": [ "max_results", "query" ] }, "body_bytes": 7810, "body_sha256": "be89b8bcf15acaee52b354a9ef65f1560da1e004cc943df729a8fa0917506183", "reason": null, "note": "ENUMERATED AT GATE START FROM THE RUNNING SERVICE, NEVER FROM A CONSTANT. It records what fred OFFERED, not what any run called. A tool absent from tool_names that appears in a call is an UNKNOWN TOOL and must be reported as one rather than defaulted. fred is frozen: SIM enumerates and buckets, and never edits or removes a tool. NO JUDGEMENT IS RECORDED HERE -- not which tools return literature, not which matter, and no order." }, "tool_egress": { "schema": "sim.fred_tool_egress.v1", "answerable": true, "reason": null, "basis": "SIM'S OWN READING OF THE VENDOR'S TOOL DESCRIPTIONS. NOT A MEASUREMENT OF NETWORK TRAFFIC: no packets were observed. A tool naming an upstream is evidence of intent; a tool naming none could still egress. THE SIBLING tool_inventory RECORDS NO JUDGEMENT BY DESIGN -- this block is where judgement lives, and the judgement is SIM's, not the vendor's.", "derived_by": "SIM", "source": { "path": "/home/singh/sim/sim_composition/fred_tool_egress.json", "sha256": "5dc0d640c406484db1652b7f63bc2411fb18a53fa3e8227a3ec6ff8fa6863c85", "classified_wire_version": "1.2", "classified_tool_count": 10 }, "live_wire_version": "1.2", "wire_version_matches": true, "external": [ "brave_search", "get_compound_properties", "get_protein_info", "get_target_info", "search_compounds", "search_pathways", "search_publications" ], "local": [ "check_lipinski", "read_file", "write_file" ], "by_tool": { "brave_search": { "egress": "external", "upstream": "Brave Search", "what_leaves_the_machine": "free-text query" }, "check_lipinski": { "egress": "local", "upstream": null, "what_leaves_the_machine": null }, "get_compound_properties": { "egress": "external", "upstream": "PubChem", "what_leaves_the_machine": "PubChem CID, or a compound name when no CID is given" }, "get_protein_info": { "egress": "external", "upstream": "UniProt", "what_leaves_the_machine": "UniProt accession or gene name, plus organism id" }, "get_target_info": { "egress": "external", "upstream": "OpenTargets", "what_leaves_the_machine": "Ensembl gene id or gene name" }, "read_file": { "egress": "local", "upstream": null, "what_leaves_the_machine": null }, "search_compounds": { "egress": "external", "upstream": "PubChem", "what_leaves_the_machine": "compound name string" }, "search_pathways": { "egress": "external", "upstream": "Reactome", "what_leaves_the_machine": "gene name, pathway concept or biological term, plus species" }, "search_publications": { "egress": "external", "upstream": "NCBI PubMed", "what_leaves_the_machine": "free-text PubMed query" }, "write_file": { "egress": "local", "upstream": null, "what_leaves_the_machine": null } }, "unclassified": [], "unclassified_count": 0, "classified_not_offered": [], "limits": [ "THIS IS NOT A MEASUREMENT OF NETWORK TRAFFIC. No packets were observed. A tool that names an upstream is evidence of intent; a tool that names none could still egress.", "The basis is the vendor service's declaration about itself. fred is a frozen vendor boundary and its source was not read.", "THIS IS SIM'S JUDGEMENT, NOT THE VENDOR'S. The sibling tool_inventory record deliberately holds no taxonomy; this file is the taxonomy and is authored here.", "local does not mean no network is involved in the workflow: check_lipinski performs no call but its input is normally the output of get_compound_properties, which does.", "read_file and write_file do not egress, but write_file is an autonomous local side effect inside the fred workspace bind, and fred calls tools autonomously even when SIM dispatches tools=[].", "Classification covers the ten tools present at this wire version. A TOOL ADDED LATER IS OUTSIDE IT and must surface in the unclassified list rather than defaulting to no egress." ], "note": "EGRESS AS DECLARED, JOINED TO THE TOOLS THIS RUN'S SERVICE ACTUALLY OFFERED. answerable=false means NO per-tool answer was possible and the lists below are EMPTY -- it never means nothing egressed. unclassified is the safety-relevant field: a tool offered by the service and not covered by the classification." } }, "claims_requested": [ "chronic_safety_margin", "target_rationale", "target_engagement", "central_target_engagement", "in_vivo_pharmacology", "selectivity", "cns_penetrance", "admet_pk_hepatic", "developability", "human_dose_projection" ], "claims_excluded": [], "exclusion_rule": "A readout with no authored liability (payload.known_flaw absent, null, or blank) produces NO CLAIM, not a repaired sentence. cns_penetrance is exempt: its claim_text is the Part 5 constant and does not derive from known_flaw.", "claims": [ { "readout": "chronic_safety_margin", "status": "resolved", "claim_label": "chronic_safety_margin_sufficiency", "claim_text": "The candidate's chronic-dosing safety margin (~3.4-fold, established over 14 days in one species against dosing intended to run for years) is sufficient to nominate it as a Development Candidate and commit it to IND-enabling GLP toxicology, on the strength of the NLRP3 class safety record.", "claim_text_source": "part5_centerpiece_constant", "basis_alignment": "shared_basis_not_claim_specific", "readout_fields_dropped": [ "flaw_must_be_flagged", "known_flaw" ], "readout_inputs": { "supplied": { "id": "readout.chronic_safety_margin", "synthetic": true, "dataset": "Chronic-dosing safety margin (projected efficacious exposure vs repeat-dose toxicology finding)", "value": { "projected_efficacious_Cav_ss_unbound_nM": 312.0, "lowest_effect_exposure_Cav_ss_unbound_nM": 1060.0, "chronic_safety_margin_fold": 3.4, "projected_efficacious_brain_unbound_nM": 69, "tox_finding": "dose-dependent transaminase elevation in the high-dose group, reversible on washout", "tox_study": "14-day repeat-dose rat with day-14 toxicokinetics; no non-rodent repeat-dose study has been run and no non-rodent species has been selected", "intended_clinical_dosing": "chronic daily oral dosing in an elderly Alzheimer's population, 12 months or longer", "note": "the margin is a 14-day, single-species, plasma-compartment figure read against dosing intended to run for years" }, "assay_basis": { "assay_type": "14-day repeat-dose rodent toxicology with day-14 toxicokinetics, read against the projected efficacious exposure carried from the in-vivo efficacy exposure-response", "units": "nM (unbound plasma Cav,ss); fold (margin); days (study duration)", "reference_conditions": "unbound plasma average steady-state concentration on both sides of the ratio, same species and same bioanalytical method; the brain unbound figure is INFERRED from Kp,uu 0.22 and was not measured in the toxicology arm" }, "numeric_provenance": { "raw_source": "raw/candidate/chronic_safety_margin_raw.json#readout.chronic_safety_margin", "measurement_type": "chronic_safety_margin_composite", "quantities": { "projected_efficacious_Cav_ss_unbound_nM": { "raw_source": "raw/candidate/chronic_safety_margin_raw.json#readout.chronic_safety_margin", "measurement_type": "concentration_linear", "canonical_unit": "nM", "replicates_total": 3, "dropped": [], "excluded_run_ids": [], "outliers": [], "aggregation": "arithmetic_mean", "n_used": 3, "estimate": 312.0, "display_value": 312.0, "spread": { "sd": 14.0, "ddof": 1 }, "censored": false, "derivation": null, "stat_test": null, "divergence_from_target": { "asserted": 312, "derived": 312.0, "rel_diff": 0.0, "material": false, "threshold_rel": 0.15, "boundary_rule": "material iff rel_diff strictly greater than threshold" } }, "lowest_effect_exposure_Cav_ss_unbound_nM": { "raw_source": "raw/candidate/chronic_safety_margin_raw.json#readout.chronic_safety_margin", "measurement_type": "concentration_linear", "canonical_unit": "nM", "replicates_total": 3, "dropped": [], "excluded_run_ids": [], "outliers": [], "aggregation": "arithmetic_mean", "n_used": 3, "estimate": 1060.0, "display_value": 1060.0, "spread": { "sd": 50.0, "ddof": 1 }, "censored": false, "derivation": null, "stat_test": null, "divergence_from_target": { "asserted": 1060, "derived": 1060.0, "rel_diff": 0.0, "material": false, "threshold_rel": 0.15, "boundary_rule": "material iff rel_diff strictly greater than threshold" } }, "chronic_safety_margin_fold": { "raw_source": "raw/candidate/chronic_safety_margin_raw.json#readout.chronic_safety_margin", "measurement_type": "margin_ratio_derived", "canonical_unit": "fold", "derivation": { "formula": "margin = C_LOEL / C_eff", "method": "first_order_delta_propagation", "assumptions": "independent numerator and denominator; small relative errors; first-order", "C_eff": { "mean": 312.0, "sd": 14.0, "n": 3 }, "C_LOEL": { "mean": 1060.0, "sd": 50.0, "n": 3 }, "margin_fold": 3.3974358974358974, "sigma_first_order": 0.22118505569286448, "sigma_note": null, "mc_crosscheck": { "mc_ratio_mean": 3.4030908376120323, "mc_ratio_sd": 0.22236005469913137, "draws": 20000, "discarded_nonpositive_ab": 0, "seed": 20260720 }, "mc_note": "MC is a parametric normal model at n=3 per arm, an indicative cross-check under a normality assumption, NOT a bootstrap; first-order is the reported error", "first_order_vs_mc": { "first_order_sigma": 0.22118505569286448, "mc_sigma": 0.22236005469913137, "rel_diff": 0.005312289307187546, "material": false } }, "estimate": 3.3974358974358974, "display_value": 3.4, "divergence_from_target": { "asserted": 3.4, "derived": 3.3974358974358974, "rel_diff": 0.0007541478129713397, "material": false, "threshold_rel": 0.15, "boundary_rule": "material iff rel_diff strictly greater than threshold" } } }, "stat_test": null } }, "withheld_by_decision": { "flaw_must_be_flagged": "an instruction to flag a liability, not evidence of one; crossing it supplies the conclusion the adversarial loop exists to reach", "known_flaw": "authored characterization of the candidate's flaw. THE EARLIER REASON HERE SAID IT WAS ALREADY CARRIED VERBATIM IN THE CLAIM TEXT AND THAT WAS MEASURED FALSE: the string occurs verbatim nowhere in the corpus outside its own readout file. It is not a duplicate, so crossing it would be ADDITIVE authored prose in front of the arms, which is a stronger reason to withhold than the one it replaces" }, "unallowed_unexplained": [], "allowed_fields": [ "assay_basis", "dataset", "numeric_provenance", "value" ] }, "retrieval": { "source": "/home/singh/sim/corpus/index/retrievable.json", "seed_dir": "/home/singh/sim/corpus/seed/precedents", "offered": 15, "joined": 15, "joined_refs": [ "NCT05981040; NCT05924243; NCT06556173; NCT06822517; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29; NCT04015076", "NCT05981040; NCT07023835; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "ClinicalTrials:NCT06556173", "PMID:34219728", "DOI:10.1016/j.isci.2024.109733", "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "DOI:10.1038/s44400-025-00011-5", "PMID:31207457", "PMID:31748742; PMID:23254930; PMID:30381407", "ClinicalTrials:NCT05932069", "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "PMC:13132802", "PMID:37577847; ClinicalTrials:NCT05981040", "PMID:40792655; PMID:37874905" ], "join_misses": [], "public_ref_namespaces": { "total": 15, "well_formed_by_namespace": { "ClinicalTrials": 2, "PMID": 2, "DOI": 2, "PMC": 1 }, "malformed_count": 8, "malformed": [ { "citation": "NCT05981040; NCT05924243; NCT06556173; NCT06822517; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "reason": "no namespace prefix and not a bare PMID" }, { "citation": "ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29; NCT04015076", "reason": "no namespace prefix and not a bare PMID" }, { "citation": "NCT05981040; NCT07023835; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "reason": "no namespace prefix and not a bare PMID" }, { "citation": "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:31748742; PMID:23254930; PMID:30381407", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:37577847; ClinicalTrials:NCT05981040", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:40792655; PMID:37874905", "reason": "string carries more than one accession; not split here" } ], "syntax_only": true, "note": "well_formed is a SYNTAX claim over the five seed namespaces; it is never a claim that an accession resolves or exists" }, "deduped": [ "precedent_pc7b071" ], "supplied": 14, "supplied_ids": [ "negative_longest_exposure_twelve_weeks", "negative_no_ad_dosing", "negative_no_positive_neuro_efficacy", "precedent_p12682b", "precedent_p17d8f1", "precedent_p26a1fb", "precedent_p340e7b", "precedent_p57a9d7", "precedent_p5bb765", "precedent_p7bbc38", "precedent_p8a117d", "precedent_pcf4b44", "precedent_pdeb9af", "precedent_peb7226" ], "supplied_refs": [ { "id": "negative_longest_exposure_twelve_weeks", "public_ref": "NCT05981040; NCT05924243; NCT06556173; NCT06822517; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29" }, { "id": "negative_no_ad_dosing", "public_ref": "ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29; NCT04015076" }, { "id": "negative_no_positive_neuro_efficacy", "public_ref": "NCT05981040; NCT07023835; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29" }, { "id": "precedent_p12682b", "public_ref": "ClinicalTrials:NCT06556173" }, { "id": "precedent_p17d8f1", "public_ref": "PMID:34219728" }, { "id": "precedent_p26a1fb", "public_ref": "DOI:10.1016/j.isci.2024.109733" }, { "id": "precedent_p340e7b", "public_ref": "ISRCTN:85338453; DOI:10.15252/embj.2018101064" }, { "id": "precedent_p57a9d7", "public_ref": "DOI:10.1038/s44400-025-00011-5" }, { "id": "precedent_p5bb765", "public_ref": "PMID:31207457" }, { "id": "precedent_p7bbc38", "public_ref": "PMID:31748742; PMID:23254930; PMID:30381407" }, { "id": "precedent_p8a117d", "public_ref": "ClinicalTrials:NCT05932069" }, { "id": "precedent_pcf4b44", "public_ref": "PMC:13132802" }, { "id": "precedent_pdeb9af", "public_ref": "PMID:37577847; ClinicalTrials:NCT05981040" }, { "id": "precedent_peb7226", "public_ref": "PMID:40792655; PMID:37874905" } ], "fields_dropped_vs_precedent_view": [ "penetrance_status", "verification_tier", "precedent_numerics" ], "note": "surfaced precedent crosses as flat text (molecule + mechanistic_record) PLUS the public_ref joined from its seed record; the paired precedent still crosses as a structured firewalled record" }, "run_id": "sim_chronic_safety_margin_sufficiency_20260917T182406Z", "run_dir": "/home/singh/sim/corpus/runtime/outputs/sim_chronic_safety_margin_sufficiency_20260917T182406Z", "validation_dir": "/home/singh/sim/corpus/runtime/validation/sim_chronic_safety_margin_sufficiency_20260917T182406Z/fred", "any_low_confidence": false, "verdict_sequence": [ "B", "B", "B", "B", "A" ], "counts": { "A": 1, "B": 4, "both": 0, "neither": 0, "unresolved": 0 }, "counts_no_verdict": 0 }, { "readout": "target_rationale", "status": "resolved_low_conf", "claim_label": "target_rationale_sufficiency", "claim_text": "On the Target and disease rationale for NLRP3 inhibition in Alzheimer's disease (documentary readout) readout, the noted liability -- the human genetic argument does not reach the target: no genome-wide significant Alzheimer's association exists at NLRP3 itself, and the package's human-genetic support runs entirely through microglial modifiers -- an Alzheimer's-associated gene whose loss of function activates the inflammasome, and a protective variant reported to suppress it -- which establishes that the pathway is disease-relevant and does not establish that inhibiting this node is beneficial; the human tissue evidence the package leans on is contradictory, with post-mortem reports of elevated NLRP3 around plaques set against a matched temporal-cortex study that found no significant difference in any inflammasome component and stated it found no evidence of specific NLRP3 involvement, and the package does not reconcile the two or say which it relies on; the requirement for CENTRAL inhibition is assumed rather than argued anywhere in the package, so a brain-penetrant molecule is being nominated without a stated position on whether peripheral inhibition would suffice, and a large controlled trial in biomarker-confirmed early Alzheimer's has since reported that reducing a peripheral inflammatory marker did not alter the clinical course, its authors reasoning that the disease's inflammatory effects are more central than peripheral; and the disease stage at which the target is expected to be engageable is unstated, so the rationale cannot be read against the population the program intends to treat -- is sufficient to nominate the candidate as a Development Candidate and commit it to IND-enabling GLP toxicology studies.", "claim_text_source": "templated_from_readout", "basis_alignment": "shared_basis_not_claim_specific", "readout_fields_dropped": [ "flaw_must_be_flagged", "known_flaw" ], "readout_inputs": { "supplied": { "id": "readout.target_rationale", "synthetic": true, "dataset": "Target and disease rationale for NLRP3 inhibition in Alzheimer's disease (documentary readout)", "value": { "direct_human_genetic_support_at_the_target": "absent as a genome-wide association: NLRP3 itself is not an established genome-wide significant Alzheimer's risk locus. Candidate-gene association reports exist in specific populations and are not equivalent", "human_genetic_route_relied_on": "microglial modifiers rather than the target: reduced activity of the Alzheimer's-associated myeloid gene INPP5D, encoding SHIP1, induces NLRP3 inflammasome formation, caspase-1 cleavage and IL-1beta and IL-18 secretion in human iPSC-derived microglia; the protective PLCG2-P522R variant is reported to suppress the inflammasome in microglia", "strength_of_the_modifier_route": "one step removed from the target in both directions: a modifier that regulates the pathway is evidence that the pathway is disease-relevant, not evidence that inhibiting this node is beneficial", "human_tissue_evidence": "contradictory and not reconciled in this package: post-mortem work reports increased NLRP3 in frontal cortex and hippocampus and in activated microglia around plaques, while a temporal-cortex study of Alzheimer's cases against age- and sex-matched controls found no significant difference in NLRP3, ASC, caspase-1, IL-1beta or IL-18 and reported no evidence of specific NLRP3 involvement", "target_expression_in_the_relevant_cell_type_and_stage": "asserted at the level of cell type, microglia, and unstated at the level of disease stage; the package does not say at which stage of Alzheimer's the target is expected to be engageable or beneficial", "requirement_for_central_inhibition": "assumed rather than argued: the package treats brain penetrance as a design goal and nowhere establishes that central inhibition is required, or that peripheral inhibition would be insufficient", "carried_target_risk": "not stated as carried: the package argues the target is valid rather than stating how far the human evidence reaches into sporadic Alzheimer's and what risk is being carried forward", "note": "this readout is documentary. It records what the package contains about the target rationale and asserts no new experimental result about the molecule." }, "assay_basis": { "assay_type": "documentary review of the target and disease rationale as assembled for this gate; NOT AN ASSAY and no experiment is claimed", "units": "none; qualitative status fields only", "reference_conditions": "the Development Candidate package as assembled for this gate; the rationale is judged against sporadic Alzheimer's disease in an elderly population, which is the indication the program intends, rather than against inflammasome biology in general" }, "numeric_provenance": { "cleaned": true, "reason": "qualitative readout; no numerics" } }, "withheld_by_decision": { "flaw_must_be_flagged": "an instruction to flag a liability, not evidence of one; crossing it supplies the conclusion the adversarial loop exists to reach", "known_flaw": "authored characterization of the candidate's flaw. THE EARLIER REASON HERE SAID IT WAS ALREADY CARRIED VERBATIM IN THE CLAIM TEXT AND THAT WAS MEASURED FALSE: the string occurs verbatim nowhere in the corpus outside its own readout file. 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crossing it supplies the conclusion the adversarial loop exists to reach", "known_flaw": "authored characterization of the candidate's flaw. THE EARLIER REASON HERE SAID IT WAS ALREADY CARRIED VERBATIM IN THE CLAIM TEXT AND THAT WAS MEASURED FALSE: the string occurs verbatim nowhere in the corpus outside its own readout file. It is not a duplicate, so crossing it would be ADDITIVE authored prose in front of the arms, which is a stronger reason to withhold than the one it replaces" }, "unallowed_unexplained": [], "allowed_fields": [ "assay_basis", "dataset", "numeric_provenance", "value" ] }, "retrieval": { "source": "/home/singh/sim/corpus/index/retrievable.json", "seed_dir": "/home/singh/sim/corpus/seed/precedents", "offered": 15, "joined": 15, "joined_refs": [ "NCT05981040; NCT05924243; NCT06556173; NCT06822517; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29; NCT04015076", "NCT05981040; NCT07023835; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "ClinicalTrials:NCT06556173", "PMID:34219728", "DOI:10.1016/j.isci.2024.109733", "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "DOI:10.1038/s44400-025-00011-5", "PMID:31207457", "PMID:31748742; PMID:23254930; PMID:30381407", "ClinicalTrials:NCT05932069", "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "PMC:13132802", "PMID:37577847; ClinicalTrials:NCT05981040", "PMID:40792655; PMID:37874905" ], "join_misses": [], "public_ref_namespaces": { "total": 15, "well_formed_by_namespace": { "ClinicalTrials": 2, "PMID": 2, "DOI": 2, "PMC": 1 }, "malformed_count": 8, "malformed": [ { "citation": "NCT05981040; NCT05924243; NCT06556173; NCT06822517; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "reason": "no namespace prefix and not a bare PMID" }, { "citation": "ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29; NCT04015076", "reason": "no namespace prefix and not a bare PMID" }, { "citation": "NCT05981040; NCT07023835; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "reason": "no namespace prefix and not a bare PMID" }, { "citation": "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:31748742; PMID:23254930; PMID:30381407", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:37577847; ClinicalTrials:NCT05981040", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:40792655; PMID:37874905", "reason": "string carries more than one accession; not split here" } ], "syntax_only": true, "note": "well_formed is a SYNTAX claim over the five seed namespaces; it is never a claim that an accession resolves or exists" }, "deduped": [ "precedent_pc7b071" ], "supplied": 14, "supplied_ids": [ "negative_longest_exposure_twelve_weeks", "negative_no_ad_dosing", "negative_no_positive_neuro_efficacy", "precedent_p12682b", "precedent_p17d8f1", "precedent_p26a1fb", "precedent_p340e7b", "precedent_p57a9d7", "precedent_p5bb765", "precedent_p7bbc38", "precedent_p8a117d", "precedent_pcf4b44", "precedent_pdeb9af", "precedent_peb7226" ], "supplied_refs": [ { "id": "negative_longest_exposure_twelve_weeks", "public_ref": "NCT05981040; NCT05924243; NCT06556173; NCT06822517; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29" }, { "id": "negative_no_ad_dosing", "public_ref": "ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29; NCT04015076" }, { "id": "negative_no_positive_neuro_efficacy", "public_ref": "NCT05981040; NCT07023835; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29" }, { "id": "precedent_p12682b", "public_ref": "ClinicalTrials:NCT06556173" }, { "id": "precedent_p17d8f1", "public_ref": "PMID:34219728" }, { "id": "precedent_p26a1fb", "public_ref": "DOI:10.1016/j.isci.2024.109733" }, { "id": "precedent_p340e7b", "public_ref": "ISRCTN:85338453; DOI:10.15252/embj.2018101064" }, { "id": "precedent_p57a9d7", "public_ref": "DOI:10.1038/s44400-025-00011-5" }, { "id": "precedent_p5bb765", "public_ref": "PMID:31207457" }, { "id": "precedent_p7bbc38", "public_ref": "PMID:31748742; PMID:23254930; PMID:30381407" }, { "id": "precedent_p8a117d", "public_ref": "ClinicalTrials:NCT05932069" }, { "id": "precedent_pcf4b44", "public_ref": "PMC:13132802" }, { "id": "precedent_pdeb9af", "public_ref": "PMID:37577847; ClinicalTrials:NCT05981040" }, { "id": "precedent_peb7226", "public_ref": "PMID:40792655; PMID:37874905" } ], "fields_dropped_vs_precedent_view": [ "penetrance_status", "verification_tier", "precedent_numerics" ], "note": "surfaced precedent crosses as flat text (molecule + mechanistic_record) PLUS the public_ref joined from its seed record; the paired precedent still crosses as a structured firewalled record" }, "run_id": "sim_developability_sufficiency_20260918T040520Z", "run_dir": "/home/singh/sim/corpus/runtime/outputs/sim_developability_sufficiency_20260918T040520Z", "validation_dir": "/home/singh/sim/corpus/runtime/validation/sim_developability_sufficiency_20260918T040520Z/fred", "any_low_confidence": true, "verdict_sequence": [ "A", "unresolved", "B", "A", "B" ], "counts": { "A": 2, "B": 2, "both": 0, "neither": 0, "unresolved": 1 }, "counts_no_verdict": 0 }, { "readout": "human_dose_projection", "status": "resolved_low_conf", "claim_label": "human_dose_projection_sufficiency", "claim_text": "On the Human dose projection and the written three-pillar argument (governance readout) readout, the noted liability -- the package contains no human dose projection and no written three-pillar argument, and neither absence depends on how the carried efficacious exposure is read: no predicted human clearance, no allometric or PBPK basis, no projected clinical dose or regimen, and no statement of what fraction of target this candidate would cover over a dosing interval in either compartment are recorded anywhere, so the dose that would achieve adequate central target coverage in an elderly Alzheimer's patient has never been estimated; the carried exposure's own species basis is unstated, which is a defect rather than a detail, because the same figure is the denominator of the chronic-dosing safety margin and a margin whose numerator and denominator may not share a species is not a margin; the three-pillar argument therefore cannot be written down in the compartment the program depends on, since pillar one rests on a brain concentration inferred from plasma and a Kp,uu rather than measured, pillar two is not established in that compartment and readout.central_target_engagement owns that record rather than this one, and pillar three rests on one AD model whose translational fluid biomarker only trends; the projection is load-bearing twice over, so if it is wrong the safety margin is wrong in the same direction and the two claims fail together rather than independently, which is the property a reviewer would attack first -- is sufficient to nominate the candidate as a Development Candidate and commit it to IND-enabling GLP toxicology studies.", "claim_text_source": "templated_from_readout", "basis_alignment": "shared_basis_not_claim_specific", "readout_fields_dropped": [ "flaw_must_be_flagged", "known_flaw" ], "readout_inputs": { "supplied": { "id": "readout.human_dose_projection", "synthetic": true, "dataset": "Human dose projection and the written three-pillar argument (governance readout)", "value": { "human_dose_projection_status": "not derived", "carried_efficacious_exposure_origin": "an in-vivo AD-model exposure-response; see readout.chronic_safety_margin for the figure and readout.cns_penetrance for the Kp,uu through which its brain value is inferred. NOT RESTATED HERE.", "carried_exposure_species_basis": "not stated: the package does not record whether the carried efficacious exposure is a mouse exposure, a rat-scaled exposure or a projected human exposure", "predicted_human_clearance": "not recorded", "allometric_or_pbpk_basis": "none recorded", "projected_clinical_dose_and_regimen": "not recorded", "projected_fractional_target_coverage_over_the_dosing_interval": "not stated for either compartment", "three_pillar_argument": { "written_down": false, "pillar_1_free_drug_at_the_site_of_action": "inferred, not measured: the brain unbound concentration is derived from a plasma exposure and a Kp,uu, and no direct measurement of unbound drug in brain or CSF is recorded", "pillar_2_target_engagement_at_the_site_of_action": "not established in the compartment this projection depends on; see readout.central_target_engagement, which OWNS the central engagement record and states the basis on which it is unestablished, including why occupancy imaging is not an available substitute for this target. NOT RESTATED HERE", "pillar_3_pharmacology_expressed_from_the_site_of_action": "single-model and partly indirect: reduced brain IL-1beta and IL-18 with partial cognitive rescue in one AD model, with the translational fluid biomarker only trending" }, "note": "this readout is documentary. It records what the package contains about the dose projection and the three-pillar argument, and asserts nothing new about the molecule." }, "assay_basis": { "assay_type": "documentary review of the human dose projection and the three-pillar argument; NOT AN ASSAY and no experiment is claimed", "units": "none; qualitative status fields only", "reference_conditions": "the Development Candidate package as assembled for this gate; each pillar is judged in the compartment the claim depends on, which for an AD-indicated brain-penetrant candidate is the brain and not plasma" }, "numeric_provenance": { "cleaned": false, "reason": "qualitative_readout_no_numerics" } }, "withheld_by_decision": { "flaw_must_be_flagged": "an instruction to flag a liability, not evidence of one; crossing it supplies the conclusion the adversarial loop exists to reach", "known_flaw": "authored characterization of the candidate's flaw. THE EARLIER REASON HERE SAID IT WAS ALREADY CARRIED VERBATIM IN THE CLAIM TEXT AND THAT WAS MEASURED FALSE: the string occurs verbatim nowhere in the corpus outside its own readout file. It is not a duplicate, so crossing it would be ADDITIVE authored prose in front of the arms, which is a stronger reason to withhold than the one it replaces" }, "unallowed_unexplained": [], "allowed_fields": [ "assay_basis", "dataset", "numeric_provenance", "value" ] }, "retrieval": { "source": "/home/singh/sim/corpus/index/retrievable.json", "seed_dir": "/home/singh/sim/corpus/seed/precedents", "offered": 15, "joined": 15, "joined_refs": [ "NCT05981040; NCT05924243; NCT06556173; NCT06822517; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29; NCT04015076", "NCT05981040; NCT07023835; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29", "ClinicalTrials:NCT06556173", "PMID:34219728", "DOI:10.1016/j.isci.2024.109733", "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "DOI:10.1038/s44400-025-00011-5", "PMID:31207457", "PMID:31748742; PMID:23254930; PMID:30381407", "ClinicalTrials:NCT05932069", "PMID:33257576; 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PMID:30381407", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:37577847; ClinicalTrials:NCT05981040", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:40792655; PMID:37874905", "reason": "string carries more than one accession; not split here" } ], "syntax_only": true, "note": "well_formed is a SYNTAX claim over the five seed namespaces; it is never a claim that an accession resolves or exists" }, "deduped": [ "precedent_pc7b071" ], "supplied": 14, "supplied_ids": [ "negative_longest_exposure_twelve_weeks", "negative_no_ad_dosing", "negative_no_positive_neuro_efficacy", "precedent_p12682b", "precedent_p17d8f1", "precedent_p26a1fb", "precedent_p340e7b", "precedent_p57a9d7", "precedent_p5bb765", "precedent_p7bbc38", "precedent_p8a117d", "precedent_pcf4b44", "precedent_pdeb9af", "precedent_peb7226" ], "supplied_refs": [ { "id": "negative_longest_exposure_twelve_weeks", "public_ref": "NCT05981040; NCT05924243; NCT06556173; NCT06822517; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29" }, { "id": "negative_no_ad_dosing", "public_ref": "ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29; NCT04015076" }, { "id": "negative_no_positive_neuro_efficacy", "public_ref": "NCT05981040; NCT07023835; ADDF Cognitive Vitality report, NLRP3 Inhibitors, updated 2025-12-29" }, { "id": "precedent_p12682b", "public_ref": "ClinicalTrials:NCT06556173" }, { "id": "precedent_p17d8f1", "public_ref": "PMID:34219728" }, { "id": "precedent_p26a1fb", "public_ref": "DOI:10.1016/j.isci.2024.109733" }, { "id": "precedent_p340e7b", "public_ref": "ISRCTN:85338453; DOI:10.15252/embj.2018101064" }, { "id": "precedent_p57a9d7", "public_ref": "DOI:10.1038/s44400-025-00011-5" }, { "id": "precedent_p5bb765", "public_ref": "PMID:31207457" }, { "id": "precedent_p7bbc38", "public_ref": "PMID:31748742; PMID:23254930; PMID:30381407" }, { "id": "precedent_p8a117d", "public_ref": "ClinicalTrials:NCT05932069" }, { "id": "precedent_pcf4b44", "public_ref": "PMC:13132802" }, { "id": "precedent_pdeb9af", "public_ref": "PMID:37577847; ClinicalTrials:NCT05981040" }, { "id": "precedent_peb7226", "public_ref": "PMID:40792655; PMID:37874905" } ], "fields_dropped_vs_precedent_view": [ "penetrance_status", "verification_tier", "precedent_numerics" ], "note": "surfaced precedent crosses as flat text (molecule + mechanistic_record) PLUS the public_ref joined from its seed record; the paired precedent still crosses as a structured firewalled record" }, "run_id": "sim_human_dose_projection_sufficiency_20260918T052043Z", "run_dir": "/home/singh/sim/corpus/runtime/outputs/sim_human_dose_projection_sufficiency_20260918T052043Z", "validation_dir": "/home/singh/sim/corpus/runtime/validation/sim_human_dose_projection_sufficiency_20260918T052043Z/fred", "any_low_confidence": true, "verdict_sequence": [ "B", "B", "B", "B", "B" ], "counts": { "A": 0, "B": 5, "both": 0, "neither": 0, "unresolved": 0 }, "counts_no_verdict": 0 } ], "sc3_pre_inventory": { "state": "VERIFIED", "path": "/home/singh/sim_patches/sc3_inventory/inventory_pre_20260917T192317.json", "sha256": "0e19ff7c9316e550d6baf36f1f0521ab4dcd04a02c419e9ab15bbb65a733de27", "entries_sha256": "cb82a839196439ba625312ec9eaad8da5c96fd0bd081ddc4df736a73df36053f", "entry_count": 382, "root": "/home/singh/fred-vendor-v030/workspace", "inventory_mtime_utc": "2026-09-17T18:23:17.233571+00:00", "launch_utc": "2026-09-17T18:24:05.706300+00:00", "age_seconds": 48, "note": "R284, procedural. The workspace state at launch is KNOWN because it was inventoried and the artifact's digest is recorded here. THIS DOES NOT ESTABLISH THAT THE STATE WAS ACCEPTABLE, CLEAN OR FRESH. Freshness is not enforced; age_seconds is recorded so staleness is auditable rather than assumed. The inventory sees names and metadata only and cannot see an id inside a file." }, "loop_complete": true, "invocations": [ { "started_utc": "2026-09-17T18:24:06.106231+00:00", "claims_requested": [ "chronic_safety_margin", "target_rationale", "target_engagement", "central_target_engagement", "in_vivo_pharmacology", "selectivity", "cns_penetrance", "admet_pk_hepatic", "developability", "human_dose_projection" ], "claims_retained": [ "chronic_safety_margin", "target_rationale", "target_engagement", "central_target_engagement", "in_vivo_pharmacology", "selectivity", "cns_penetrance", "admet_pk_hepatic", "developability", "human_dose_projection" ], "reps": 5, "backend_identity": { "schema": "sim.gate_backend_identity.v4", "captured": true, "captured_at_utc": "2026-09-17T18:24:05.706426+00:00", "label": "CONFIGURATION OBSERVED AT RUN TIME, NOT VERIFIED MODEL IDENTITY", "container": { "name": "fred-v030", "resolved_by": "port binding 127.0.0.1:8105, not by name (R30)", "image": "fred:v0.3.0", "image_id": "sha256:9033380caffaafa1e4e0e4dc6be968cbf70981c3a166e355af9b6c593d1bfe20", "repo_digests": "[fred@sha256:9033380caffaafa1e4e0e4dc6be968cbf70981c3a166e355af9b6c593d1bfe20]", "repo_digest_is_registry_verifiable": false, "repo_digest_note": "RepoDigest equals local ImageID: locally built, digest is not verifiable against any registry", "created": "2026-09-08T16:37:32.240892054Z" }, "image_digest_pins": "the fred HARNESS container, NOT the reasoning model. The model is served from outside this image; the digest attests neither which model answered nor that the tag was stable across the gate.", "fred_model_configured_tag": "kimi-k2.6:cloud", "fred_model_tag_note": "the tag CONFIGURED on the container, not a record of what answered. A remote tag can move under a fixed name.", "ollama_base_url": "http://host.docker.internal:11434/v1", "other_env_names_only": [], "env_filter": { "applied": "^(FRED_MODEL|OLLAMA_BASE_URL|[A-Za-z0-9_]*_HOST)=", "superseded": "(FRED_MODEL|OLLAMA_BASE_URL|.*_HOST)=", "deviation_reason": "the superseded pattern is unanchored on the right; '.*_HOST=' can match on the VALUE side and record a secret in full (R32)", "values_recorded_for": [ "FRED_MODEL", "OLLAMA_BASE_URL" ] }, "health": { "wire_version": "1.2", "status": "ok", "fred_version": "0.3.0", "current_run_id": null }, "health_note": "/v1/health carries no model field, so it corroborates that fred is up and which fred_version is running --- not which model answered.", "code_state": { "captured": true, "repo": "/home/singh/sim", "head": "8ddbf9aa6472e458fc8e448e1d858694273268c4", "dirty": false, "dirty_paths_count": 0, "note": "the commit checked out when the gate started. If dirty is true this sha does NOT describe the code that ran." }, "model_probe": { "endpoint_base": "http://127.0.0.1:11434", "queried_tag": "kimi-k2.6:cloud", "tags": { "reachable": true, "name": "kimi-k2.6:cloud", "model": "kimi-k2.6:cloud", "remote_model": "kimi-k2.6", "remote_host": "https://ollama.com:443", "digest": "a90cd0d1590c53b9f9f4e0f66218e4c514d190652b8bed2842528e2530e34dc6", "modified_at": "2026-04-24T20:00:03.980908081+01:00", "details": { "parent_model": "", "format": "", "family": "kimi-k2", "families": [ "kimi-k2" ], "parameter_size": "1T", "quantization_level": "int4" }, "size_bytes": 384 }, "show": { "reachable": true, "capabilities": [ "vision", "thinking", "completion", "tools" ], "details": { "parent_model": "kimi-k2.6", "format": "", "family": "kimi-k2", "families": null, "parameter_size": "1042000000000", "quantization_level": "INT4" }, "model_info": { "general.architecture": "kimi-k2", "general.parameter_count": 1042000000000, "kimi-k2.context_length": 262144, "kimi-k2.embedding_length": 2048 }, "modified_at": "2026-04-20T00:00:00Z" }, "modified_at_agree": false, "parameter_size_agree": false, "note": "the LOCAL POINTER and the remote's DECLARED metadata, captured at gate start. A size of a few hundred bytes shows the local entry is a pointer, not weights. NEITHER modified_at attests which weights answered and neither is a model file's mtime. A remote tag can move mid-gate; a start-time probe does not cover the gate's duration. parameter_size_agree can read false for a difference of representation alone." }, "tool_inventory": { "schema": "sim.fred_tool_inventory.v1", "url": "http://127.0.0.1:8105/v1/tools", "reachable": true, "wire_version": "1.2", "tool_count": 10, "tool_names": [ "brave_search", "check_lipinski", "get_compound_properties", "get_protein_info", "get_target_info", "read_file", "search_compounds", "search_pathways", "search_publications", "write_file" ], "tool_args": { "read_file": [ "path" ], "write_file": [ "content", "path" ], "brave_search": [ "max_results", "query" ], "search_compounds": [ "max_results", "query" ], "get_compound_properties": [ "cid", "name" ], "check_lipinski": [ "properties" ], "get_protein_info": [ "identifier", "max_results", "organism_id" ], "search_pathways": [ "max_results", "query", "species" ], "get_target_info": [ "identifier" ], "search_publications": [ "max_results", "query" ] }, "body_bytes": 7810, "body_sha256": "be89b8bcf15acaee52b354a9ef65f1560da1e004cc943df729a8fa0917506183", "reason": null, "note": "ENUMERATED AT GATE START FROM THE RUNNING SERVICE, NEVER FROM A CONSTANT. It records what fred OFFERED, not what any run called. A tool absent from tool_names that appears in a call is an UNKNOWN TOOL and must be reported as one rather than defaulted. fred is frozen: SIM enumerates and buckets, and never edits or removes a tool. NO JUDGEMENT IS RECORDED HERE -- not which tools return literature, not which matter, and no order." }, "tool_egress": { "schema": "sim.fred_tool_egress.v1", "answerable": true, "reason": null, "basis": "SIM'S OWN READING OF THE VENDOR'S TOOL DESCRIPTIONS. NOT A MEASUREMENT OF NETWORK TRAFFIC: no packets were observed. A tool naming an upstream is evidence of intent; a tool naming none could still egress. THE SIBLING tool_inventory RECORDS NO JUDGEMENT BY DESIGN -- this block is where judgement lives, and the judgement is SIM's, not the vendor's.", "derived_by": "SIM", "source": { "path": "/home/singh/sim/sim_composition/fred_tool_egress.json", "sha256": "5dc0d640c406484db1652b7f63bc2411fb18a53fa3e8227a3ec6ff8fa6863c85", "classified_wire_version": "1.2", "classified_tool_count": 10 }, "live_wire_version": "1.2", "wire_version_matches": true, "external": [ "brave_search", "get_compound_properties", "get_protein_info", "get_target_info", "search_compounds", "search_pathways", "search_publications" ], "local": [ "check_lipinski", "read_file", "write_file" ], "by_tool": { "brave_search": { "egress": "external", "upstream": "Brave Search", "what_leaves_the_machine": "free-text query" }, "check_lipinski": { "egress": "local", "upstream": null, "what_leaves_the_machine": null }, "get_compound_properties": { "egress": "external", "upstream": "PubChem", "what_leaves_the_machine": "PubChem CID, or a compound name when no CID is given" }, "get_protein_info": { "egress": "external", "upstream": "UniProt", "what_leaves_the_machine": "UniProt accession or gene name, plus organism id" }, "get_target_info": { "egress": "external", "upstream": "OpenTargets", "what_leaves_the_machine": "Ensembl gene id or gene name" }, "read_file": { "egress": "local", "upstream": null, "what_leaves_the_machine": null }, "search_compounds": { "egress": "external", "upstream": "PubChem", "what_leaves_the_machine": "compound name string" }, "search_pathways": { "egress": "external", "upstream": "Reactome", "what_leaves_the_machine": "gene name, pathway concept or biological term, plus species" }, "search_publications": { "egress": "external", "upstream": "NCBI PubMed", "what_leaves_the_machine": "free-text PubMed query" }, "write_file": { "egress": "local", "upstream": null, "what_leaves_the_machine": null } }, "unclassified": [], "unclassified_count": 0, "classified_not_offered": [], "limits": [ "THIS IS NOT A MEASUREMENT OF NETWORK TRAFFIC. No packets were observed. A tool that names an upstream is evidence of intent; a tool that names none could still egress.", "The basis is the vendor service's declaration about itself. fred is a frozen vendor boundary and its source was not read.", "THIS IS SIM'S JUDGEMENT, NOT THE VENDOR'S. The sibling tool_inventory record deliberately holds no taxonomy; this file is the taxonomy and is authored here.", "local does not mean no network is involved in the workflow: check_lipinski performs no call but its input is normally the output of get_compound_properties, which does.", "read_file and write_file do not egress, but write_file is an autonomous local side effect inside the fred workspace bind, and fred calls tools autonomously even when SIM dispatches tools=[].", "Classification covers the ten tools present at this wire version. A TOOL ADDED LATER IS OUTSIDE IT and must surface in the unclassified list rather than defaulting to no egress." ], "note": "EGRESS AS DECLARED, JOINED TO THE TOOLS THIS RUN'S SERVICE ACTUALLY OFFERED. answerable=false means NO per-tool answer was possible and the lists below are EMPTY -- it never means nothing egressed. unclassified is the safety-relevant field: a tool offered by the service and not covered by the classification." } } } ], "orchestrator_log": "orchestrator.log", "orchestrator_log_segment": "orchestrator.log", "orchestrator_logs": [ "orchestrator.log" ] }