SDK bibliography verification notes¶
Date: 2026-09-09. Existing user files paper.bib, paper.md and CITATION.cff were not overwritten. This audit changes neither the equations nor the packaged evidence registry.
Repository sources reviewed¶
src/iints/presets/evidence_sources.yaml: packaged scientific references.docs/FORMULA_REGISTRY.mdanddocs/PHYSIOLOGY_REFERENCE.md: equation and physiology references.docs/REGENERATIVE_ISLET_RESEARCH.md: transplantation, islet and proteomics context.src/iints/data/datasets.json: acquisition catalogue, not a record of completed experiments.src/iints_desktop/evidence_connectors.py: connector names, links and integration status.src/iints/research/glucofm.py: explicitly referenced GlucoFM preprint version.docs/SOURCE_LIBRARY.md,docs/EVIDENCE_BASE.mdandpaper.bib: existing source lists.pyproject.toml: declared direct Python dependencies, including optional groups.
This is a repository-source audit, not an exhaustive historical or experimental-use audit. No official CGM-JEPA paper or checkpoint citation was inferred solely from a module name.
Important corrections¶
- OhioT1DM: use CEUR Vol. 2675, paper11.pdf, pages 71–74, 5th workshop. The registry pointed to paper2; another dataset record called it the 6th workshop.
- OpenCOR: correct DOI 10.3389/fphys.2015.00026. The old DOI names a different CellML/OpenCMISS paper.
- Cobry: correct DOI 10.1089/dia.2009.0112, Diabetes Technology & Therapeutics 12(3):173–177. The old DOI names a diabetic-foot wound-monitor article.
- Renal glucose handling: the DOI metadata names Ghezzi, Loo and Wright, not the Hummel author list in the registry.
- ADAPT: the DOI metadata names Choudhary as first author, rather than Benhamou in the registry.
- Visentin: use the actual title The UVA/Padova Type 1 Diabetes Simulator Goes From Single Meal to Single Day and DOI metadata, not the mixed title/pages in the registry.
- The faster-aspart and ultra-rapid-lispro title/DOI combinations were not accepted. A separately labelled verified Heise paper is provided as replacement reading, not represented as historical use.
Entries not accepted as verified citations¶
| Existing key | Identifier | Reason |
|---|---|---|
heise_2017_fiasp_pkpd |
10.1007/s40262-017-0510-8 |
Existing title/DOI combination is not reliable; excluded from the submission bibliography. |
klaff_2020_urli_pkpd |
10.1111/dom.14049 |
Existing title/DOI combination is not reliable; excluded from the submission bibliography. |
wentholt_2004_cgm_lag |
10.1089/dia.2004.6.615 |
Existing title/DOI combination is not reliable; excluded from the submission bibliography. |
Verification ledger¶
“Crossref metadata” verifies bibliographic identity, not the full paper or its implementation. API rate limits were retried. Resource and dataset catalogue entries retain a lower verification level explicitly. No patient-level data were read or exported.
| Number | Citation key | Evidence for record |
|---|---|---|
| 1 | ada_2026_glycemic_goals |
Crossref metadata, 2026-09-09 |
| 2 | ada_2026_diabetes_technology |
Crossref metadata, 2026-09-09 |
| 3 | attd_2019_time_in_range |
Crossref metadata, 2026-09-09 |
| 4 | nejm_2019_control_iq |
Crossref metadata, 2026-09-09 |
| 5 | adapt_2022_ahcl |
Crossref metadata, 2026-09-09 |
| 6 | cobry_2010_meal_bolus_timing |
Crossref metadata, 2026-09-09 |
| 7 | dalla_man_2007_meal_model |
Crossref metadata, 2026-09-09 |
| 8 | visentin_2018_uvapadova |
Crossref metadata, 2026-09-09 |
| 9 | mujahid_2024_generative_t1d_simulator |
Crossref metadata, 2026-09-09 |
| 10 | riddell_2017_exercise_consensus |
Crossref metadata, 2026-09-09 |
| 11 | idc_2025_agp_report_overview |
Repository record; web-page metadata not independently re-audited |
| 12 | bergman_1979_minimal_model |
Crossref metadata, 2026-09-09 |
| 13 | hovorka_2004_nmpc_t1d |
Crossref metadata, 2026-09-09 |
| 14 | gerich_1979_counterregulation |
Crossref metadata, 2026-09-09 |
| 15 | cryer_2013_haaf_mechanisms |
Crossref metadata, 2026-09-09 |
| 16 | cryer_2013_haaf_diabetes |
Crossref metadata, 2026-09-09 |
| 17 | lv_2013_exogenous_glucagon_pk |
Crossref metadata, 2026-09-09 |
| 18 | haidar_2013_dual_hormone_ap |
Crossref metadata, 2026-09-09 |
| 19 | haidar_2013_insulin_glucagon_pk |
Crossref metadata, 2026-09-09 |
| 20 | hummel_2018_renal_glucose_handling |
Crossref metadata, 2026-09-09 |
| 21 | defronzo_2013_renal_reabsorption_splay |
Crossref metadata, 2026-09-09 |
| 22 | mandelbrot_1968_fractional_brownian |
Crossref metadata, 2026-09-09 |
| 23 | campbell_1985_dawn_phenomenon |
Crossref metadata, 2026-09-09 |
| 24 | richter_2013_glut4_exercise |
Crossref metadata, 2026-09-09 |
| 25 | naslund_1999_glp1_gastric_emptying |
Crossref metadata, 2026-09-09 |
| 26 | formula_source_4 |
Crossref metadata, 2026-09-09 |
| 27 | formula_source_5 |
Crossref metadata, 2026-09-09 |
| 28 | formula_source_6 |
Crossref metadata, 2026-09-09 |
| 29 | formula_source_7 |
Crossref metadata, 2026-09-09 |
| 30 | formula_source_8 |
Crossref metadata, 2026-09-09 |
| 31 | formula_source_10 |
Crossref metadata, 2026-09-09 |
| 32 | formula_source_11 |
Crossref metadata, 2026-09-09 |
| 33 | formula_source_12 |
Crossref metadata, 2026-09-09 |
| 34 | formula_source_13 |
Crossref metadata, 2026-09-09 |
| 35 | formula_source_14 |
Crossref metadata, 2026-09-09 |
| 36 | dallaman2014 |
Crossref metadata, 2026-09-09 |
| 37 | kovatchev1997 |
Crossref metadata, 2026-09-09 |
| 38 | kovatchev1998 |
Crossref metadata, 2026-09-09 |
| 39 | heise2017_corrected_context |
Crossref metadata, 2026-09-09 |
| 40 | johansen1984 |
Crossref metadata, 2026-09-09 |
| 41 | peng2022 |
Crossref metadata, 2026-09-09 |
| 42 | numpy2020 |
Crossref metadata, 2026-09-09 |
| 43 | scipy2020 |
Crossref metadata, 2026-09-09 |
| 44 | matplotlib2007 |
Crossref metadata, 2026-09-09 |
| 45 | pinn2019 |
Crossref metadata, 2026-09-09 |
| 46 | neldermead1965 |
Crossref metadata, 2026-09-09 |
| 47 | glucofm2026v2 |
arXiv version page, 2026-09-09 |
| 48 | bindingdb_2016 |
Crossref metadata, 2026-09-09 |
| 49 | ncbi_clinvar_classification_representation |
Repository record; web-page metadata not independently re-audited |
| 50 | jumper2021 |
Crossref metadata, 2026-09-09 |
| 51 | varadi2024 |
Crossref metadata, 2026-09-09 |
| 52 | reichman2025 |
Crossref metadata, 2026-09-09 |
| 53 | carlsson2025 |
Crossref metadata, 2026-09-09 |
| 54 | balboa2022 |
Crossref metadata, 2026-09-09 |
| 55 | augsornworawat2023 |
Crossref metadata, 2026-09-09 |
| 56 | maxquant2008 |
Crossref metadata, 2026-09-09 |
| 57 | diann2020 |
Crossref metadata, 2026-09-09 |
| 58 | sintov2022 |
Crossref metadata, 2026-09-09 |
| 59 | resource_alphafold-db |
Link and status from SDK connector registry; not independent use verification |
| 60 | resource_ensembl-vep-alphamissense |
Link and status from SDK connector registry; not independent use verification |
| 61 | resource_open-targets |
Link and status from SDK connector registry; not independent use verification |
| 62 | resource_reactome |
Link and status from SDK connector registry; not independent use verification |
| 63 | resource_rcsb-pdb |
Link and status from SDK connector registry; not independent use verification |
| 64 | resource_uniprot |
Link and status from SDK connector registry; not independent use verification |
| 65 | resource_human-protein-atlas |
Link and status from SDK connector registry; not independent use verification |
| 66 | resource_gtex |
Link and status from SDK connector registry; not independent use verification |
| 67 | resource_chembl |
Link and status from SDK connector registry; not independent use verification |
| 68 | resource_clinpgx-pharmgkb |
Link and status from SDK connector registry; not independent use verification |
| 69 | resource_opencor-physiome |
Link and status from SDK connector registry; not independent use verification |
| 70 | resource_bindingdb |
Link and status from SDK connector registry; not independent use verification |
| 71 | resource_string-db |
Link and status from SDK connector registry; not independent use verification |
| 72 | resource_clinvar |
Link and status from SDK connector registry; not independent use verification |
| 73 | resource_fair4rs |
Link and status from SDK connector registry; not independent use verification |
| 74 | resource_pubmed |
Link and status from SDK connector registry; not independent use verification |
| 75 | resource_clinicaltrials-gov |
Link and status from SDK connector registry; not independent use verification |
| 76 | resource_zenodo |
Link and status from SDK connector registry; not independent use verification |
| 77 | pride |
Repository-linked resource; project-level metadata not fully revalidated |
| 78 | proteomexchange |
Repository-linked resource; project-level metadata not fully revalidated |
| 79 | pxd001539 |
Repository-linked resource; project-level metadata not fully revalidated |
| 80 | pxd064528 |
Repository-linked resource; project-level metadata not fully revalidated |
| 81 | spectronaut |
Repository-linked resource; project-level metadata not fully revalidated |
| 82 | trial_zimislecel |
Repository-linked resource; project-level metadata not fully revalidated |
| 83 | sbml_2019_l3v2_core |
Crossref metadata, 2026-09-09 |
| 84 | libroadrunner_2015 |
Crossref metadata, 2026-09-09 |
| 85 | copasi_2006 |
Crossref metadata, 2026-09-09 |
| 86 | opencor_2015 |
Crossref metadata, 2026-09-09 |
| 87 | fmi_3_0_2_standard |
Repository record; web-page metadata not independently re-audited |
| 88 | fmpy_0_3 |
Repository record; web-page metadata not independently re-audited |
| 89 | myvariant_query_api |
Repository record; web-page metadata not independently re-audited |
| 90 | fair2016 |
Crossref metadata, 2026-09-09 |
| 91 | resource_ro-crate |
Link and status from SDK connector registry; not independent use verification |
| 92 | resource_biomodels |
Link and status from SDK connector registry; not independent use verification |
| 93 | resource_libroadrunner |
Link and status from SDK connector registry; not independent use verification |
| 94 | resource_copasi |
Link and status from SDK connector registry; not independent use verification |
| 95 | resource_sed-ml |
Link and status from SDK connector registry; not independent use verification |
| 96 | resource_sbml |
Link and status from SDK connector registry; not independent use verification |
| 97 | marling_2020_ohiot1dm |
CEUR proceedings and paper, 2026-09-09 |
| 98 | dataset_sample |
Dataset registry entry; publication metadata not independently revalidated |
| 99 | dataset_diatrend |
Dataset registry entry; publication metadata not independently revalidated |
| 100 | dataset_t1d_uom |
Dataset registry entry; publication metadata not independently revalidated |
| 101 | dataset_t1d_granada |
Dataset registry entry; publication metadata not independently revalidated |
| 102 | dataset_aide_t1d |
Dataset registry entry; publication metadata not independently revalidated |
| 103 | dataset_azt1d |
Dataset registry entry; publication metadata not independently revalidated |
| 104 | dataset_hupa_ucm |
Dataset registry entry; publication metadata not independently revalidated |
| 105 | dataset_openaps_data_commons |
Dataset registry entry; publication metadata not independently revalidated |
| 106 | dataset_tidepool_bigdata |
Dataset registry entry; publication metadata not independently revalidated |
| 107 | dataset_niddk_central |
Dataset registry entry; publication metadata not independently revalidated |
| 108 | dataset_t1d_exchange |
Dataset registry entry; publication metadata not independently revalidated |
| 109 | dataset_d1namo |
Dataset registry entry; publication metadata not independently revalidated |
| 110 | dataset_t1dexi |
Dataset registry entry; publication metadata not independently revalidated |
| 111 | dataset_dclp3_idcl |
Dataset registry entry; publication metadata not independently revalidated |
| 112 | dataset_metabonet |
Dataset registry entry; publication metadata not independently revalidated |
| 113 | dataset_glucose_ml |
Dataset registry entry; publication metadata not independently revalidated |
| 114 | python |
Implementation/project documentation reference; no new access-date claim |
| 115 | rust |
Implementation/project documentation reference; no new access-date claim |
| 116 | tauri |
Implementation/project documentation reference; no new access-date claim |
| 117 | pyside |
Implementation/project documentation reference; no new access-date claim |
| 118 | ollama |
Implementation/project documentation reference; no new access-date claim |
| 119 | mistral |
Implementation/project documentation reference; no new access-date claim |
| 120 | huggingface |
Implementation/project documentation reference; no new access-date claim |
| 121 | pytorch |
Implementation/project documentation reference; no new access-date claim |
| 122 | pandas |
Implementation/project documentation reference; no new access-date claim |
| 123 | plotly |
Implementation/project documentation reference; no new access-date claim |
| 124 | scienceplots |
Implementation/project documentation reference; no new access-date claim |
| 125 | seaborn |
Implementation/project documentation reference; no new access-date claim |
| 126 | fpdf2 |
Implementation/project documentation reference; no new access-date claim |
| 127 | pymol |
Implementation/project documentation reference; no new access-date claim |
| 128 | openaps |
Implementation/project documentation reference; no new access-date claim |
| 129 | simglucose |
Implementation/project documentation reference; no new access-date claim |
| 130 | raspberry |
Implementation/project documentation reference; no new access-date claim |
| 131 | arduino |
Implementation/project documentation reference; no new access-date claim |
| 132 | jetson |
Implementation/project documentation reference; no new access-date claim |
| 133 | mkdocs |
Implementation/project documentation reference; no new access-date claim |
| 134 | material |
Implementation/project documentation reference; no new access-date claim |
| 135 | mermaid |
Implementation/project documentation reference; no new access-date claim |
| 136 | pytest |
Implementation/project documentation reference; no new access-date claim |
| 137 | hypothesis |
Implementation/project documentation reference; no new access-date claim |
| 138 | git |
Implementation/project documentation reference; no new access-date claim |
| 139 | github |
Implementation/project documentation reference; no new access-date claim |
Before submission¶
- Remove sources not used in the submitted work, or retain them only in a clearly labelled supplementary catalogue.
- Match each scientific claim to a supporting passage, not merely to a relevant title.
- Record dataset accession, sample selection, release, licence and held-out split from actual experiment manifests.
- Record model/checkpoint versions and software environment.
- Resolve the remaining historical manufacturer/regulatory and literature references before claiming a complete historical audit.