% IINTS-AF SDK bibliography. Generated from reviewed source records, 2026-09-09.

@article{ada_2026_glycemic_goals,
  author = {{American Diabetes Association Professional Practice Committee for Diabetes} and Bajaj, Mandeep and McCoy, Rozalina G. and Balapattabi, Kirthikaa and Bannuru, Raveendhara R. and Bellini, Natalie J. and Bennett, Allison K. and Beverly, Elizabeth A. and Briggs Early, Kathaleen and ChallaSivaKanaka, Sathyavathi and Echouffo-Tcheugui, Justin B. and . Everett, Brendan M and Garg, Rajesh and Laffel, Lori M. and Lal, Rayhan and Matfin, Glenn and Pandya, Naushira and . Pekas, Elizabeth J and . Peters, Anne L and Pilla, Scott J. and Romeo, Giulio R. and Rosas, Sylvia E. and Segal, Alissa R. and Szmuilowicz, Emily D. and ElSayed, Nuha A.},
  title = {{6. Glycemic Goals, Hypoglycemia, and Hyperglycemic Crises: Standards of Care in Diabetes—2026}},
  year = {2026},
  journal = {Diabetes Care},
  volume = {49},
  pages = {S132-S149},
  doi = {10.2337/dc26-S006},
  url = {https://doi.org/10.2337/dc26-S006},
  number = {Supplement\_1},
  note = {validation\_targets; source recorded in the packaged evidence registry.}
}

@article{ada_2026_diabetes_technology,
  author = {{American Diabetes Association Professional Practice Committee for Diabetes} and Bajaj, Mandeep and McCoy, Rozalina G. and Balapattabi, Kirthikaa and Bannuru, Raveendhara R. and Bellini, Natalie J. and Bennett, Allison K. and Beverly, Elizabeth A. and Briggs Early, Kathaleen and ChallaSivaKanaka, Sathyavathi and Echouffo-Tcheugui, Justin B. and Everett, Brendan M. and Garg, Rajesh and Laffel, Lori M. and Lal, Rayhan and Matfin, Glenn and Pandya, Naushira and Pekas, Elizabeth J. and Peters, Anne L. and Pilla, Scott J. and Romeo, Giulio R. and Rosas, Sylvia E. and Segal, Alissa R. and Szmuilowicz, Emily D. and ElSayed, Nuha A.},
  title = {{7. Diabetes Technology: Standards of Care in Diabetes—2026}},
  year = {2026},
  journal = {Diabetes Care},
  volume = {49},
  pages = {S150-S165},
  doi = {10.2337/dc26-S007},
  url = {https://doi.org/10.2337/dc26-S007},
  number = {Supplement\_1},
  note = {cgm\_and\_aid\_context; source recorded in the packaged evidence registry.}
}

@article{attd_2019_time_in_range,
  author = {Battelino, Tadej and Danne, Thomas and Bergenstal, Richard M. and Amiel, Stephanie A. and Beck, Roy and Biester, Torben and Bosi, Emanuele and Buckingham, Bruce A. and Cefalu, William T. and Close, Kelly L. and Cobelli, Claudio and Dassau, Eyal and DeVries, J. Hans and Donaghue, Kim C. and Dovc, Klemen and Doyle, Francis J. and Garg, Satish and Grunberger, George and Heller, Simon and Heinemann, Lutz and Hirsch, Irl B. and Hovorka, Roman and Jia, Weiping and Kordonouri, Olga and Kovatchev, Boris and Kowalski, Aaron and Laffel, Lori and Levine, Brian and Mayorov, Alexander and Mathieu, Chantal and Murphy, Helen R. and Nimri, Revital and Nørgaard, Kirsten and Parkin, Christopher G. and Renard, Eric and Rodbard, David and Saboo, Banshi and Schatz, Desmond and Stoner, Keaton and Urakami, Tatsuiko and Weinzimer, Stuart A. and Phillip, Moshe},
  title = {{Clinical Targets for Continuous Glucose Monitoring Data Interpretation: Recommendations From the International Consensus on Time in Range}},
  year = {2019},
  journal = {Diabetes Care},
  volume = {42},
  pages = {1593-1603},
  doi = {10.2337/dci19-0028},
  url = {https://doi.org/10.2337/dci19-0028},
  number = {8},
  note = {metrics\_targets; source recorded in the packaged evidence registry.}
}

@article{nejm_2019_control_iq,
  author = {Brown, Sue A. and Kovatchev, Boris P. and Raghinaru, Dan and Lum, John W. and Buckingham, Bruce A. and Kudva, Yogish C. and Laffel, Lori M. and Levy, Carol J. and Pinsker, Jordan E. and Wadwa, R. Paul and Dassau, Eyal and Doyle, Francis J. and Anderson, Stacey M. and Church, Mei Mei and Dadlani, Vikash and Ekhlaspour, Laya and Forlenza, Gregory P. and Isganaitis, Elvira and Lam, David W. and Kollman, Craig and Beck, Roy W.},
  title = {{Six-Month Randomized, Multicenter Trial of Closed-Loop Control in Type 1 Diabetes}},
  year = {2019},
  journal = {New England Journal of Medicine},
  volume = {381},
  pages = {1707-1717},
  doi = {10.1056/NEJMoa1907863},
  url = {https://doi.org/10.1056/NEJMoa1907863},
  number = {18},
  note = {aid\_benchmarking; source recorded in the packaged evidence registry.}
}

@article{adapt_2022_ahcl,
  author = {Choudhary, Pratik and Kolassa, Ralf and Keuthage, Winfried and Kroeger, Jens and Thivolet, Charles and Evans, Mark and Ré, Roseline and de Portu, Simona and Vorrink, Linda and Shin, John and Habteab, Aklilu and Castañeda, Javier and da Silva, Julien and Cohen, Ohad},
  title = {{Advanced hybrid closed loop therapy versus conventional treatment in adults with type 1 diabetes (ADAPT): a randomised controlled study}},
  year = {2022},
  journal = {The Lancet Diabetes \& Endocrinology},
  volume = {10},
  pages = {720-731},
  doi = {10.1016/S2213-8587(22)00212-1},
  url = {https://doi.org/10.1016/S2213-8587(22)00212-1},
  number = {10},
  note = {aid\_benchmarking; source recorded in the packaged evidence registry.}
}

@article{cobry_2010_meal_bolus_timing,
  author = {Cobry, Erin and McFann, Kim and Messer, Laurel and Gage, Victoria and VanderWel, Brandon and Horton, Lauren and Chase, H. Peter},
  title = {{Timing of Meal Insulin Boluses to Achieve Optimal Postprandial Glycemic Control in Patients with Type 1 Diabetes}},
  year = {2010},
  journal = {Diabetes Technology \& Therapeutics},
  volume = {12},
  pages = {173-177},
  doi = {10.1089/dia.2009.0112},
  url = {https://doi.org/10.1089/dia.2009.0112},
  number = {3},
  note = {prebolus\_timing; source recorded in the packaged evidence registry.}
}

@article{dalla_man_2007_meal_model,
  author = {Dalla Man, Chiara and Rizza, Robert A. and Cobelli, Claudio},
  title = {{Meal Simulation Model of the Glucose-Insulin System}},
  year = {2007},
  journal = {IEEE Transactions on Biomedical Engineering},
  volume = {54},
  pages = {1740-1749},
  doi = {10.1109/TBME.2007.893506},
  url = {https://doi.org/10.1109/TBME.2007.893506},
  number = {10},
  note = {virtual\_patient\_dynamics; source recorded in the packaged evidence registry.}
}

@article{visentin_2018_uvapadova,
  author = {Visentin, Roberto and Campos-Náñez, Enrique and Schiavon, Michele and Lv, Dayu and Vettoretti, Martina and Breton, Marc and Kovatchev, Boris P. and Dalla Man, Chiara and Cobelli, Claudio},
  title = {{The UVA/Padova Type 1 Diabetes Simulator Goes From Single Meal to Single Day}},
  year = {2018},
  journal = {Journal of Diabetes Science and Technology},
  volume = {12},
  pages = {273-281},
  doi = {10.1177/1932296818757747},
  url = {https://doi.org/10.1177/1932296818757747},
  number = {2},
  note = {simulation\_validation; source recorded in the packaged evidence registry.}
}

@article{mujahid_2024_generative_t1d_simulator,
  author = {Mujahid, Omer and Contreras, Ivan and Beneyto, Aleix and Vehi, Josep},
  title = {{Generative deep learning for the development of a type 1 diabetes simulator}},
  year = {2024},
  journal = {Communications Medicine},
  volume = {4},
  pages = {51},
  doi = {10.1038/s43856-024-00476-0},
  url = {https://doi.org/10.1038/s43856-024-00476-0},
  number = {1},
  note = {simulation\_realism; source recorded in the packaged evidence registry.}
}

@article{riddell_2017_exercise_consensus,
  author = {Riddell, Michael C and Gallen, Ian W and Smart, Carmel E and Taplin, Craig E and Adolfsson, Peter and Lumb, Alistair N and Kowalski, Aaron and Rabasa-Lhoret, Remi and McCrimmon, Rory J and Hume, Carin and Annan, Francesca and Fournier, Paul A and Graham, Claudia and Bode, Bruce and Galassetti, Pietro and Jones, Timothy W and Millán, Iñigo San and Heise, Tim and Peters, Anne L and Petz, Andreas and Laffel, Lori M},
  title = {{Exercise management in type 1 diabetes: a consensus statement}},
  year = {2017},
  journal = {The Lancet Diabetes \& Endocrinology},
  volume = {5},
  pages = {377-390},
  doi = {10.1016/S2213-8587(17)30014-1},
  url = {https://doi.org/10.1016/S2213-8587(17)30014-1},
  number = {5},
  note = {exercise\_stress\_scenarios; source recorded in the packaged evidence registry.}
}

@misc{idc_2025_agp_report_overview,
  author = {{HealthPartners Institute / International Diabetes Center}},
  title = {{Guide to Understanding the Ambulatory Glucose Profile (AGP) Report}},
  url = {https://www.healthpartners.com/institute/wp-content/uploads/2025/05/Ambulatory-Glucose-Profile-Report-Overview.pdf},
  note = {agp\_style\_reporting; official resource recorded in source registry.}
}

@article{bergman_1979_minimal_model,
  author = {Bergman, R N and Ider, Y Z and Bowden, C R and Cobelli, C},
  title = {{Quantitative estimation of insulin sensitivity.}},
  year = {1979},
  journal = {American Journal of Physiology-Endocrinology and Metabolism},
  volume = {236},
  pages = {E667},
  doi = {10.1152/ajpendo.1979.236.6.E667},
  url = {https://doi.org/10.1152/ajpendo.1979.236.6.E667},
  number = {6},
  note = {virtual\_patient\_dynamics; source recorded in the packaged evidence registry.}
}

@article{hovorka_2004_nmpc_t1d,
  author = {Hovorka, Roman and Canonico, Valentina and Chassin, Ludovic J and Haueter, Ulrich and Massi-Benedetti, Massimo and Federici, Marco Orsini and Pieber, Thomas R and Schaller, Helga C and Schaupp, Lukas and Vering, Thomas and Wilinska, Malgorzata E},
  title = {{Nonlinear model predictive control of glucose concentration in subjects with type 1 diabetes}},
  year = {2004},
  journal = {Physiological Measurement},
  volume = {25},
  pages = {905-920},
  doi = {10.1088/0967-3334/25/4/010},
  url = {https://doi.org/10.1088/0967-3334/25/4/010},
  number = {4},
  note = {hovorka\_patient\_model; source recorded in the packaged evidence registry.}
}

@article{gerich_1979_counterregulation,
  author = {Gerich, J and Davis, J and Lorenzi, M and Rizza, R and Bohannon, N and Karam, J and Lewis, S and Kaplan, R and Schultz, T and Cryer, P},
  title = {{Hormonal mechanisms of recovery from insulin-induced hypoglycemia in man.}},
  year = {1979},
  journal = {American Journal of Physiology-Endocrinology and Metabolism},
  volume = {236},
  pages = {E380},
  doi = {10.1152/ajpendo.1979.236.4.E380},
  url = {https://doi.org/10.1152/ajpendo.1979.236.4.E380},
  number = {4},
  note = {endogenous\_counterregulation; source recorded in the packaged evidence registry.}
}

@article{cryer_2013_haaf_mechanisms,
  author = {Cryer, Philip E.},
  title = {{Mechanisms of Hypoglycemia-Associated Autonomic Failure in Diabetes}},
  year = {2013},
  journal = {New England Journal of Medicine},
  volume = {369},
  pages = {362-372},
  doi = {10.1056/NEJMra1215228},
  url = {https://doi.org/10.1056/NEJMra1215228},
  number = {4},
  note = {haaf\_memory\_model; source recorded in the packaged evidence registry.}
}

@incollection{cryer_2013_haaf_diabetes,
  author = {Cryer, Philip E.},
  title = {{Hypoglycemia-associated autonomic failure in diabetes}},
  year = {2013},
  volume = {117},
  pages = {295-307},
  doi = {10.1016/B978-0-444-53491-0.00023-7},
  url = {https://doi.org/10.1016/B978-0-444-53491-0.00023-7},
  note = {haaf\_memory\_model; source recorded in the packaged evidence registry.},
  booktitle = {Handbook of Clinical Neurology}
}

@article{lv_2013_exogenous_glucagon_pk,
  author = {Lv, Dayu and Breton, Marc D. and Farhy, Leon S.},
  title = {{Pharmacokinetics Modeling of Exogenous Glucagon in Type 1 Diabetes Mellitus Patients}},
  year = {2013},
  journal = {Diabetes Technology \& Therapeutics},
  volume = {15},
  pages = {935-941},
  doi = {10.1089/dia.2013.0150},
  url = {https://doi.org/10.1089/dia.2013.0150},
  number = {11},
  note = {exogenous\_glucagon\_pkpd; source recorded in the packaged evidence registry.}
}

@article{haidar_2013_dual_hormone_ap,
  author = {Haidar, Ahmad and Legault, Laurent and Dallaire, Maryse and Alkhateeb, Ammar and Coriati, Adèle and Messier, Virginie and Cheng, Peiyao and Millette, Maude and Boulet, Benoit and Rabasa-Lhoret, Rémi},
  title = {{Glucose-responsive insulin and glucagon delivery (dual-hormone artificial pancreas) in adults with type 1 diabetes: a randomized crossover controlled trial}},
  year = {2013},
  journal = {Canadian Medical Association Journal},
  volume = {185},
  pages = {297-305},
  doi = {10.1503/cmaj.121265},
  url = {https://doi.org/10.1503/cmaj.121265},
  number = {4},
  note = {dual\_hormone\_context; source recorded in the packaged evidence registry.}
}

@article{haidar_2013_insulin_glucagon_pk,
  author = {Haidar, Ahmad and Duval, Claire and Legault, Laurent and Rabasa-Lhoret, Rémi},
  title = {{Pharmacokinetics of Insulin Aspart and Glucagon in Type 1 Diabetes during Closed-Loop Operation}},
  year = {2013},
  journal = {Journal of Diabetes Science and Technology},
  volume = {7},
  pages = {1507-1512},
  doi = {10.1177/193229681300700610},
  url = {https://doi.org/10.1177/193229681300700610},
  number = {6},
  note = {exogenous\_glucagon\_pkpd; source recorded in the packaged evidence registry.}
}

@article{hummel_2018_renal_glucose_handling,
  author = {Ghezzi, Chiara and Loo, Donald D. F. and Wright, Ernest M.},
  title = {{Physiology of renal glucose handling via SGLT1, SGLT2 and GLUT2}},
  year = {2018},
  journal = {Diabetologia},
  volume = {61},
  pages = {2087-2097},
  doi = {10.1007/s00125-018-4656-5},
  url = {https://doi.org/10.1007/s00125-018-4656-5},
  number = {10},
  note = {renal\_glucose\_clearance; source recorded in the packaged evidence registry.}
}

@article{defronzo_2013_renal_reabsorption_splay,
  author = {DeFronzo, Ralph A. and Hompesch, Marcus and Kasichayanula, Sreeneeranj and Liu, Xiaoni and Hong, Ying and Pfister, Marc and Morrow, Linda A. and Leslie, Bruce R. and Boulton, David W. and Ching, Agatha and LaCreta, Frank P. and Griffen, Steven C.},
  title = {{Characterization of Renal Glucose Reabsorption in Response to Dapagliflozin in Healthy Subjects and Subjects With Type 2 Diabetes}},
  year = {2013},
  journal = {Diabetes Care},
  volume = {36},
  pages = {3169-3176},
  doi = {10.2337/dc13-0387},
  url = {https://doi.org/10.2337/dc13-0387},
  number = {10},
  note = {renal\_glucose\_clearance; source recorded in the packaged evidence registry.}
}

@article{mandelbrot_1968_fractional_brownian,
  author = {Mandelbrot, Benoit B. and Van Ness, John W.},
  title = {{Fractional Brownian Motions, Fractional Noises and Applications}},
  year = {1968},
  journal = {SIAM Review},
  volume = {10},
  pages = {422-437},
  doi = {10.1137/1010093},
  url = {https://doi.org/10.1137/1010093},
  number = {4},
  note = {cgm\_noise\_model; source recorded in the packaged evidence registry.}
}

@article{campbell_1985_dawn_phenomenon,
  author = {Campbell, Peter J. and Bolli, Geremia B. and Cryer, Philip E. and Gerich, John E.},
  title = {{Pathogenesis of the Dawn Phenomenon in Patients with Insulin-Dependent Diabetes Mellitus}},
  year = {1985},
  journal = {New England Journal of Medicine},
  volume = {312},
  pages = {1473-1479},
  doi = {10.1056/NEJM198506063122302},
  url = {https://doi.org/10.1056/NEJM198506063122302},
  number = {23},
  note = {circadian\_egp\_model; source recorded in the packaged evidence registry.}
}

@article{richter_2013_glut4_exercise,
  author = {Richter, Erik A. and Hargreaves, Mark},
  title = {{Exercise, GLUT4, and Skeletal Muscle Glucose Uptake}},
  year = {2013},
  journal = {Physiological Reviews},
  volume = {93},
  pages = {993-1017},
  doi = {10.1152/physrev.00038.2012},
  url = {https://doi.org/10.1152/physrev.00038.2012},
  number = {3},
  note = {exercise\_glut4\_model; source recorded in the packaged evidence registry.}
}

@article{naslund_1999_glp1_gastric_emptying,
  author = {Näslund, Erik and Bogefors, Jesper and Skogar, Staffan and Grybäck, Per and Jacobsson, Hans and Holst, Jens Juul and Hellström, Per M.},
  title = {{GLP-1 slows solid gastric emptying and inhibits  insulin, glucagon, and PYY release in humans}},
  year = {1999},
  journal = {American Journal of Physiology-Regulatory, Integrative and Comparative Physiology},
  volume = {277},
  pages = {R910-R916},
  doi = {10.1152/ajpregu.1999.277.3.R910},
  url = {https://doi.org/10.1152/ajpregu.1999.277.3.R910},
  number = {3},
  note = {glp1\_gastric\_emptying\_model; source recorded in the packaged evidence registry.}
}

@article{formula_source_4,
  author = {Alkhateeb, Haneen and El Fathi, Anas and Ghanbari, Milad and Haidar, Ahmad},
  title = {{Modelling glucose dynamics during moderate exercise in individuals with type 1 diabetes}},
  year = {2021},
  journal = {PLOS ONE},
  volume = {16},
  pages = {e0248280},
  doi = {10.1371/journal.pone.0248280},
  url = {https://doi.org/10.1371/journal.pone.0248280},
  number = {3},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_5,
  author = {Romeres, Davide and Schiavon, Michele and Basu, Ananda and Cobelli, Claudio and Basu, Rita and Dalla Man, Chiara},
  title = {{Exercise effect on insulin-dependent and insulin-independent glucose utilization in healthy individuals and individuals with type 1 diabetes: a modeling study}},
  year = {2021},
  journal = {American Journal of Physiology-Endocrinology and Metabolism},
  volume = {321},
  pages = {E122-E129},
  doi = {10.1152/ajpendo.00084.2021},
  url = {https://doi.org/10.1152/ajpendo.00084.2021},
  number = {1},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_6,
  author = {Mallad, Ashwini and Hinshaw, Ling and Dalla Man, Chiara and Cobelli, Claudio and Basu, Rita and Lingineni, Ravi and Carter, Rickey E. and Kudva, Yogish C. and Basu, Ananda},
  title = {{Nocturnal Glucose Metabolism in Type 1 Diabetes: A Study Comparing Single Versus Dual Tracer Approaches}},
  year = {2015},
  journal = {Diabetes Technology \& Therapeutics},
  volume = {17},
  pages = {587-595},
  doi = {10.1089/dia.2015.0011},
  url = {https://doi.org/10.1089/dia.2015.0011},
  number = {8},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_7,
  author = {Cryer, Philip E.},
  title = {{Hypoglycemia-associated autonomic failure in diabetes}},
  year = {2001},
  journal = {American Journal of Physiology-Endocrinology and Metabolism},
  volume = {281},
  pages = {E1115-E1121},
  doi = {10.1152/ajpendo.2001.281.6.E1115},
  url = {https://doi.org/10.1152/ajpendo.2001.281.6.E1115},
  number = {6},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_8,
  author = {Fruehwald-Schultes, Bernd and Kern, Werner and Deininger, Eva and Wellhoener, Peter and Kerner, Wolfgang and Born, Jan and Fehm, Horst L. and Peters, Achim},
  title = {{Protective Effect of Insulin against Hypoglycemia-Associated Counterregulatory Failure}},
  year = {1999},
  journal = {The Journal of Clinical Endocrinology \& Metabolism},
  volume = {84},
  pages = {1551-1557},
  doi = {10.1210/jcem.84.5.5675},
  url = {https://doi.org/10.1210/jcem.84.5.5675},
  number = {5},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_10,
  author = {Wendt, Sabrina Lyngbye and Ranjan, Ajenthen and Møller, Jan Kloppenborg and Schmidt, Signe and Knudsen, Carsten Boye and Holst, Jens Juul and Madsbad, Sten and Madsen, Henrik and Nørgaard, Kirsten and Jørgensen, John Bagterp},
  title = {{Cross-Validation of a Glucose-Insulin-Glucagon Pharmacodynamics Model for Simulation Using Data From Patients With Type 1 Diabetes}},
  year = {2017},
  journal = {Journal of Diabetes Science and Technology},
  volume = {11},
  pages = {1101-1111},
  doi = {10.1177/1932296817693254},
  url = {https://doi.org/10.1177/1932296817693254},
  number = {6},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_11,
  author = {Rebrin, Kerstin and Sheppard, Norman F. and Steil, Garry M.},
  title = {{Use of Subcutaneous Interstitial Fluid Glucose to Estimate Blood Glucose: Revisiting Delay and Sensor Offset}},
  year = {2010},
  journal = {Journal of Diabetes Science and Technology},
  volume = {4},
  pages = {1087-1098},
  doi = {10.1177/193229681000400507},
  url = {https://doi.org/10.1177/193229681000400507},
  number = {5},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_12,
  author = {Schmidtke, David W. and Freeland, Angela C. and Heller, Adam and Bonnecaze, Roger T.},
  title = {{Measurement and modeling of the transient difference between blood and subcutaneous glucose concentrations in the rat after injection of insulin}},
  year = {1998},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {95},
  pages = {294-299},
  doi = {10.1073/pnas.95.1.294},
  url = {https://doi.org/10.1073/pnas.95.1.294},
  number = {1},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_13,
  author = {Visentin, Roberto and Dalla Man, Chiara and Kudva, Yogish C. and Basu, Ananda and Cobelli, Claudio},
  title = {{Circadian Variability of Insulin Sensitivity: Physiological Input for In Silico Artificial Pancreas}},
  year = {2015},
  journal = {Diabetes Technology \& Therapeutics},
  volume = {17},
  pages = {1-7},
  doi = {10.1089/dia.2014.0192},
  url = {https://doi.org/10.1089/dia.2014.0192},
  number = {1},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{formula_source_14,
  author = {Saad, Ahmed and Dalla Man, Chiara and Nandy, Debashis K. and Levine, James A. and Bharucha, Adil E. and Rizza, Robert A. and Basu, Rita and Carter, Rickey E. and Cobelli, Claudio and Kudva, Yogish C. and Basu, Ananda},
  title = {{Diurnal Pattern to Insulin Secretion and Insulin Action in Healthy Individuals}},
  year = {2012},
  journal = {Diabetes},
  volume = {61},
  pages = {2691-2700},
  doi = {10.2337/db11-1478},
  url = {https://doi.org/10.2337/db11-1478},
  number = {11},
  note = {Literature anchor explicitly attached to an equation in FORMULA\_REGISTRY; not evidence that all SDK extensions reproduce the paper.}
}

@article{dallaman2014,
  author = {Man, Chiara Dalla and Micheletto, Francesco and Lv, Dayu and Breton, Marc and Kovatchev, Boris and Cobelli, Claudio},
  title = {{The UVA/PADOVA Type 1 Diabetes Simulator}},
  year = {2014},
  journal = {Journal of Diabetes Science and Technology},
  volume = {8},
  pages = {26-34},
  doi = {10.1177/1932296813514502},
  url = {https://doi.org/10.1177/1932296813514502},
  number = {1},
  note = {Simulator comparison/background already cited in paper.bib; not a claim of UVA/Padova equivalence.}
}

@article{kovatchev1997,
  author = {Kovatchev, Boris P and Cox, Daniel J and Gonder-Frederick, Linda A and Clarke, William},
  title = {{Symmetrization of the Blood Glucose Measurement Scale and Its Applications}},
  year = {1997},
  journal = {Diabetes Care},
  volume = {20},
  pages = {1655-1658},
  doi = {10.2337/diacare.20.11.1655},
  url = {https://doi.org/10.2337/diacare.20.11.1655},
  number = {11},
  note = {Risk-scale methodology cited in paper.bib.}
}

@article{kovatchev1998,
  author = {Kovatchev, B P and Cox, D J and Gonder-Frederick, L A and Young-Hyman, D and Schlundt, D and Clarke, W},
  title = {{Assessment of risk for severe hypoglycemia among adults with IDDM: validation of the low blood glucose index.}},
  year = {1998},
  journal = {Diabetes Care},
  volume = {21},
  pages = {1870-1875},
  doi = {10.2337/diacare.21.11.1870},
  url = {https://doi.org/10.2337/diacare.21.11.1870},
  number = {11},
  note = {Hypoglycemia risk-index background cited in paper.bib.}
}

@article{heise2017_corrected_context,
  author = {Heise, Tim and Stender-Petersen, Kirstine and Hövelmann, Ulrike and Jacobsen, Jacob Bonde and Nosek, Leszek and Zijlstra, Eric and Haahr, Hanne},
  title = {{Pharmacokinetic and Pharmacodynamic Properties of Faster-Acting Insulin Aspart versus Insulin Aspart Across a Clinically Relevant Dose Range in Subjects with Type 1 Diabetes Mellitus}},
  year = {2017},
  journal = {Clinical Pharmacokinetics},
  volume = {56},
  pages = {649-660},
  doi = {10.1007/s40262-016-0473-5},
  url = {https://doi.org/10.1007/s40262-016-0473-5},
  number = {6},
  note = {Verified replacement reading for the unresolved faster-aspart reference; not proof of historical use or calibration.}
}

@article{johansen1984,
  author = {Johansen, K. and Svendsen, P.Aaby and L�rup, B.},
  title = {{Variations in renal threshold for glucose in Type 1 (insulin-dependent) diabetes mellitus}},
  year = {1984},
  journal = {Diabetologia},
  volume = {26},
  doi = {10.1007/BF00252403},
  url = {https://doi.org/10.1007/BF00252403},
  number = {3},
  note = {Renal threshold source explicitly linked in FORMULA\_REGISTRY.}
}

@article{peng2022,
  author = {Peng, Fei and Li, Xin and Xiao, Fang and Zhao, Ruxing and Sun, Zheng},
  title = {{Circadian clock, diurnal glucose metabolic rhythm, and dawn phenomenon}},
  year = {2022},
  journal = {Trends in Neurosciences},
  volume = {45},
  pages = {471-482},
  doi = {10.1016/j.tins.2022.03.010},
  url = {https://doi.org/10.1016/j.tins.2022.03.010},
  number = {6},
  note = {Circadian physiology review explicitly linked in FORMULA\_REGISTRY.}
}

@article{numpy2020,
  author = {Harris, Charles R. and Millman, K. Jarrod and van der Walt, Stéfan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and van Kerkwijk, Marten H. and Brett, Matthew and Haldane, Allan and del Río, Jaime Fernández and Wiebe, Mark and Peterson, Pearu and Gérard-Marchant, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.},
  title = {{Array programming with NumPy}},
  year = {2020},
  journal = {Nature},
  volume = {585},
  pages = {357-362},
  doi = {10.1038/s41586-020-2649-2},
  url = {https://doi.org/10.1038/s41586-020-2649-2},
  number = {7825},
  note = {Numerical array software used by the SDK.}
}

@article{scipy2020,
  author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and van der Walt, Stéfan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C J and Polat, İlhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Antônio H. and Pedregosa, Fabian and van Mulbregt, Paul and {SciPy 1.0 Contributors} and Vijaykumar, Aditya and Bardelli, Alessandro Pietro and Rothberg, Alex and Hilboll, Andreas and Kloeckner, Andreas and Scopatz, Anthony and Lee, Antony and Rokem, Ariel and Woods, C. Nathan and Fulton, Chad and Masson, Charles and Häggström, Christian and Fitzgerald, Clark and Nicholson, David A. and Hagen, David R. and Pasechnik, Dmitrii V. and Olivetti, Emanuele and Martin, Eric and Wieser, Eric and Silva, Fabrice and Lenders, Felix and Wilhelm, Florian and Young, G. and Price, Gavin A. and Ingold, Gert-Ludwig and Allen, Gregory E. and Lee, Gregory R. and Audren, Hervé and Probst, Irvin and Dietrich, Jörg P. and Silterra, Jacob and Webber, James T and Slavič, Janko and Nothman, Joel and Buchner, Johannes and Kulick, Johannes and Schönberger, Johannes L. and de Miranda Cardoso, José Vinícius and Reimer, Joscha and Harrington, Joseph and Rodríguez, Juan Luis Cano and Nunez-Iglesias, Juan and Kuczynski, Justin and Tritz, Kevin and Thoma, Martin and Newville, Matthew and Kümmerer, Matthias and Bolingbroke, Maximilian and Tartre, Michael and Pak, Mikhail and Smith, Nathaniel J. and Nowaczyk, Nikolai and Shebanov, Nikolay and Pavlyk, Oleksandr and Brodtkorb, Per A. and Lee, Perry and McGibbon, Robert T. and Feldbauer, Roman and Lewis, Sam and Tygier, Sam and Sievert, Scott and Vigna, Sebastiano and Peterson, Stefan and More, Surhud and Pudlik, Tadeusz and Oshima, Takuya and Pingel, Thomas J. and Robitaille, Thomas P. and Spura, Thomas and Jones, Thouis R. and Cera, Tim and Leslie, Tim and Zito, Tiziano and Krauss, Tom and Upadhyay, Utkarsh and Halchenko, Yaroslav O. and Vázquez-Baeza, Yoshiki},
  title = {{SciPy 1.0: fundamental algorithms for scientific computing in Python}},
  year = {2020},
  journal = {Nature Methods},
  volume = {17},
  pages = {261-272},
  doi = {10.1038/s41592-019-0686-2},
  url = {https://doi.org/10.1038/s41592-019-0686-2},
  number = {3},
  note = {ODE integration and numerical optimisation software used by the SDK.}
}

@article{matplotlib2007,
  author = {Hunter, John D.},
  title = {{Matplotlib: A 2D Graphics Environment}},
  year = {2007},
  journal = {Computing in Science \& Engineering},
  volume = {9},
  pages = {90-95},
  doi = {10.1109/MCSE.2007.55},
  url = {https://doi.org/10.1109/MCSE.2007.55},
  number = {3},
  note = {Scientific plotting library used by reports.}
}

@article{pinn2019,
  author = {Raissi, M. and Perdikaris, P. and Karniadakis, G.E.},
  title = {{Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations}},
  year = {2019},
  journal = {Journal of Computational Physics},
  volume = {378},
  pages = {686-707},
  doi = {10.1016/j.jcp.2018.10.045},
  url = {https://doi.org/10.1016/j.jcp.2018.10.045},
  note = {Methodological background added for physiology-informed losses; constraints alone do not establish an ODE-residual PINN.}
}

@article{neldermead1965,
  author = {Nelder, J. A. and Mead, R.},
  title = {{A Simplex Method for Function Minimization}},
  year = {1965},
  journal = {The Computer Journal},
  volume = {7},
  pages = {308-313},
  doi = {10.1093/comjnl/7.4.308},
  url = {https://doi.org/10.1093/comjnl/7.4.308},
  number = {4},
  note = {Methodological citation for Nelder-Mead optimisation; parameter fitting is not proof of identifiability.}
}

@misc{glucofm2026v2,
  author = {Li, Zechen and Natarajan, Keerthana and Zhang, Weizhi and Zhou, Menglian and Lee, Simon A. and Zhang, Yuwei and Xu, Maxwell A. and Esmaeilpour, Zeinab and Salim, Flora D. and Malhotra, Mark and Sunden, Lindsey and Patel, Shwetak and Yang, Yuzhe and Metwally, Ahmed A.},
  title = {{GlucoFM: A Dual-Stream Foundation Model for Continuous Glucose Monitoring}},
  year = {2026},
  journal = {arXiv},
  url = {https://arxiv.org/abs/2605.30865v2},
  note = {Version 2 preprint (25 August 2026), explicitly referenced by glucofm.py. IINTS implements an independent method reproduction, not official model weights.}
}

@article{bindingdb_2016,
  author = {Gilson, Michael K. and Liu, Tiqing and Baitaluk, Michael and Nicola, George and Hwang, Linda and Chong, Jenny},
  title = {{BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology}},
  year = {2016},
  journal = {Nucleic Acids Research},
  volume = {44},
  pages = {D1045-D1053},
  doi = {10.1093/nar/gkv1072},
  url = {https://doi.org/10.1093/nar/gkv1072},
  number = {D1},
  note = {measured\_binding\_affinity\_evidence; source recorded in the packaged evidence registry.}
}

@misc{ncbi_clinvar_classification_representation,
  author = {{NCBI ClinVar}},
  title = {{Representation of classifications in ClinVar}},
  url = {https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/},
  note = {genetic\_variant\_context; official resource recorded in source registry.}
}

@article{jumper2021,
  author = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and Žídek, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, Clemens and Kohl, Simon A. A. and Ballard, Andrew J. and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W. and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis},
  title = {{Highly accurate protein structure prediction with AlphaFold}},
  year = {2021},
  journal = {Nature},
  volume = {596},
  pages = {583-589},
  doi = {10.1038/s41586-021-03819-2},
  url = {https://doi.org/10.1038/s41586-021-03819-2},
  number = {7873},
  note = {AlphaFold method underlying the predicted structures displayed in the app.}
}

@article{varadi2024,
  author = {Varadi, Mihaly and Bertoni, Damian and Magana, Paulyna and Paramval, Urmila and Pidruchna, Ivanna and Radhakrishnan, Malarvizhi and Tsenkov, Maxim and Nair, Sreenath and Mirdita, Milot and Yeo, Jingi and Kovalevskiy, Oleg and Tunyasuvunakool, Kathryn and Laydon, Agata and Žídek, Augustin and Tomlinson, Hamish and Hariharan, Dhavanthi and Abrahamson, Josh and Green, Tim and Jumper, John and Birney, Ewan and Steinegger, Martin and Hassabis, Demis and Velankar, Sameer},
  title = {{AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences}},
  year = {2024},
  journal = {Nucleic Acids Research},
  volume = {52},
  pages = {D368-D375},
  doi = {10.1093/nar/gkad1011},
  url = {https://doi.org/10.1093/nar/gkad1011},
  number = {D1},
  note = {AlphaFold DB data provenance; local confidence is not functional effect size.}
}

@article{reichman2025,
  author = {Reichman, Trevor W. and Markmann, James F. and Odorico, Jon and Witkowski, Piotr and Fung, John J. and Wijkstrom, Martin and Kandeel, Fouad and de Koning, Eelco J.P. and Peters, Anne L. and Mathieu, Chantal and Kean, Leslie S. and Bruinsma, Bote G. and Wang, Chenkun and Mascia, Molly and Sanna, Bastiano and Marigowda, Gautham and Pagliuca, Felicia and Melton, Doug and Ricordi, Camillo and Rickels, Michael R.},
  title = {{Stem Cell–Derived, Fully Differentiated Islets for Type 1 Diabetes}},
  year = {2025},
  journal = {New England Journal of Medicine},
  volume = {393},
  pages = {858-868},
  doi = {10.1056/NEJMoa2506549},
  url = {https://doi.org/10.1056/NEJMoa2506549},
  number = {9},
  note = {Clinical context cited in REGENERATIVE\_ISLET\_RESEARCH; does not validate the SDK graft simulator.}
}

@article{carlsson2025,
  author = {Carlsson, Per-Ola and Hu, Xiaomeng and Scholz, Hanne and Ingvast, Sofie and Lundgren, Torbjörn and Scholz, Tim and Eriksson, Olof and Liss, Per and Yu, Di and Deuse, Tobias and Korsgren, Olle and Schrepfer, Sonja},
  title = {{Survival of Transplanted Allogeneic Beta Cells with No Immunosuppression}},
  year = {2025},
  journal = {New England Journal of Medicine},
  volume = {393},
  pages = {887-894},
  doi = {10.1056/NEJMoa2503822},
  url = {https://doi.org/10.1056/NEJMoa2503822},
  number = {9},
  note = {Transplantation context cited in regenerative research documentation; not a cure claim.}
}

@article{balboa2022,
  author = {Balboa, Diego and Barsby, Tom and Lithovius, Väinö and Saarimäki-Vire, Jonna and Omar-Hmeadi, Muhmmad and Dyachok, Oleg and Montaser, Hossam and Lund, Per-Eric and Yang, Mingyu and Ibrahim, Hazem and Näätänen, Anna and Chandra, Vikash and Vihinen, Helena and Jokitalo, Eija and Kvist, Jouni and Ustinov, Jarkko and Nieminen, Anni I. and Kuuluvainen, Emilia and Hietakangas, Ville and Katajisto, Pekka and Lau, Joey and Carlsson, Per-Ola and Barg, Sebastian and Tengholm, Anders and Otonkoski, Timo},
  title = {{Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells}},
  year = {2022},
  journal = {Nature Biotechnology},
  volume = {40},
  pages = {1042-1055},
  doi = {10.1038/s41587-022-01219-z},
  url = {https://doi.org/10.1038/s41587-022-01219-z},
  number = {7},
  note = {Islet maturation context explicitly cited in regenerative documentation.}
}

@article{augsornworawat2023,
  author = {Augsornworawat, Punn and Hogrebe, Nathaniel J. and Ishahak, Matthew and Schmidt, Mason D. and Marquez, Erica and Maestas, Marlie M. and Veronese-Paniagua, Daniel A. and Gale, Sarah E. and Miller, Julia R. and Velazco-Cruz, Leonardo and Millman, Jeffrey R.},
  title = {{Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification}},
  year = {2023},
  journal = {Nature Cell Biology},
  volume = {25},
  pages = {904-916},
  doi = {10.1038/s41556-023-01150-8},
  url = {https://doi.org/10.1038/s41556-023-01150-8},
  number = {6},
  note = {Multi-omics and lineage-specification context in regenerative documentation.}
}

@article{maxquant2008,
  author = {Cox, Jürgen and Mann, Matthias},
  title = {{MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification}},
  year = {2008},
  journal = {Nature Biotechnology},
  volume = {26},
  pages = {1367-1372},
  doi = {10.1038/nbt.1511},
  url = {https://doi.org/10.1038/nbt.1511},
  number = {12},
  note = {MaxQuant output-format provenance; the importer reads results, not a reimplementation of MaxQuant.}
}

@article{diann2020,
  author = {Demichev, Vadim and Messner, Christoph B. and Vernardis, Spyros I. and Lilley, Kathryn S. and Ralser, Markus},
  title = {{DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput}},
  year = {2020},
  journal = {Nature Methods},
  volume = {17},
  pages = {41-44},
  doi = {10.1038/s41592-019-0638-x},
  url = {https://doi.org/10.1038/s41592-019-0638-x},
  number = {1},
  note = {DIA-NN quantification method underlying supported imported tables.}
}

@article{sintov2022,
  author = {Sintov, Elad and Nikolskiy, Igor and Barrera, Victor and Hyoje-Ryu Kenty, Jennifer and Atkin, Alexander S. and Gerace, Dario and Ho Sui, Shannan J. and Boulanger, Kyle and Melton, Douglas A.},
  title = {{Whole-genome CRISPR screening identifies genetic manipulations to reduce immune rejection of stem cell-derived islets}},
  year = {2022},
  journal = {Stem Cell Reports},
  volume = {17},
  pages = {1976-1990},
  doi = {10.1016/j.stemcr.2022.08.002},
  url = {https://doi.org/10.1016/j.stemcr.2022.08.002},
  number = {9},
  note = {Stem-cell-derived islet immune-rejection study linked in regenerative documentation; not evidence of efficacy of an SDK intervention.}
}

@misc{resource_alphafold-db,
  author = {{AlphaFold Protein Structure Database maintainers}},
  title = {{AlphaFold Protein Structure Database — official resource and documentation}},
  url = {https://alphafold.ebi.ac.uk/},
  note = {Desktop registry status: Bundled 3D assets + PAE evidence. pLDDT and PAE describe prediction confidence, not pathogenicity or metabolic severity.}
}

@misc{resource_ensembl-vep-alphamissense,
  author = {{Ensembl VEP + AlphaMissense maintainers}},
  title = {{Ensembl VEP + AlphaMissense — official resource and documentation}},
  url = {https://rest.ensembl.org/},
  note = {Desktop registry status: Recommended next live connector. External evidence requires claim-level human review before publication.}
}

@misc{resource_open-targets,
  author = {{Open Targets Platform maintainers}},
  title = {{Open Targets Platform — official resource and documentation}},
  url = {https://platform.opentargets.org/},
  note = {Desktop registry status: Recommended evidence graph connector. External evidence requires claim-level human review before publication.}
}

@misc{resource_reactome,
  author = {{Reactome maintainers}},
  title = {{Reactome — official resource and documentation}},
  url = {https://reactome.org/},
  note = {Desktop registry status: Recommended pathway connector. External evidence requires claim-level human review before publication.}
}

@misc{resource_rcsb-pdb,
  author = {{RCSB PDB maintainers}},
  title = {{RCSB PDB — official resource and documentation}},
  url = {https://www.rcsb.org/},
  note = {Desktop registry status: Recommended structure validation connector. External evidence requires claim-level human review before publication.}
}

@misc{resource_uniprot,
  author = {{UniProt maintainers}},
  title = {{UniProt — official resource and documentation}},
  url = {https://www.uniprot.org/},
  note = {Desktop registry status: Recommended protein summary connector. External evidence requires claim-level human review before publication.}
}

@misc{resource_human-protein-atlas,
  author = {{Human Protein Atlas maintainers}},
  title = {{Human Protein Atlas — official resource and documentation}},
  url = {https://www.proteinatlas.org/},
  note = {Desktop registry status: Recommended expression evidence connector. External evidence requires claim-level human review before publication.}
}

@misc{resource_gtex,
  author = {{GTEx Portal API maintainers}},
  title = {{GTEx Portal API — official resource and documentation}},
  url = {https://gtexportal.org/},
  note = {Desktop registry status: Partially integrated via expression renders. Expression context informs interpretation but does not automatically set physiology parameters.}
}

@misc{resource_chembl,
  author = {{ChEMBL maintainers}},
  title = {{ChEMBL — official resource and documentation}},
  url = {https://www.ebi.ac.uk/chembl/},
  note = {Desktop registry status: Partially integrated molecule lookup. Chemical identity and literature context do not validate a PK parameter without manual review.}
}

@misc{resource_clinpgx-pharmgkb,
  author = {{ClinPGx / PharmGKB maintainers}},
  title = {{ClinPGx / PharmGKB — official resource and documentation}},
  url = {https://api.pharmgkb.org/},
  note = {Desktop registry status: Recommended cautious connector. External evidence requires claim-level human review before publication.}
}

@misc{resource_opencor-physiome,
  author = {{OpenCOR + Physiome Model Repository maintainers}},
  title = {{OpenCOR + Physiome Model Repository — official resource and documentation}},
  url = {https://models.physiomeproject.org/cellml},
  note = {Desktop registry status: Integrated CellML inspection and OpenCOR validation. Repository curation, imports, units, and biological suitability must be checked per model; OpenCOR validation is not biological validation.}
}

@misc{resource_bindingdb,
  author = {{BindingDB maintainers}},
  title = {{BindingDB — official resource and documentation}},
  url = {https://www.bindingdb.org/rwd/bind/index.jsp},
  note = {Desktop registry status: Integrated read-only UniProt affinity evidence. Kd, Ki, and IC50 are assay-specific and cannot be treated as interchangeable physiological effects.}
}

@misc{resource_string-db,
  author = {{STRING DB maintainers}},
  title = {{STRING DB — official resource and documentation}},
  url = {https://string-db.org/},
  note = {Desktop registry status: Partially integrated via pathway renders. External evidence requires claim-level human review before publication.}
}

@misc{resource_clinvar,
  author = {{ClinVar / NCBI Clinical Tables maintainers}},
  title = {{ClinVar / NCBI Clinical Tables — official resource and documentation}},
  url = {https://www.ncbi.nlm.nih.gov/clinvar/},
  note = {Desktop registry status: Partially integrated via mutation examples. ClinVar assertions can conflict or change and never become a physiological scalar automatically.}
}

@misc{resource_fair4rs,
  author = {{FAIR Principles for Research Software (FAIR4RS) maintainers}},
  title = {{FAIR Principles for Research Software (FAIR4RS) — official resource and documentation}},
  url = {https://www.nature.com/articles/s41597-022-01710-x},
  note = {Desktop registry status: Implemented as project guidance and audit criteria. The SDK is FAIR-oriented; this label is not an external FAIR certification.}
}

@misc{resource_pubmed,
  author = {{PubMed maintainers}},
  title = {{PubMed — official resource and documentation}},
  url = {https://pubmed.ncbi.nlm.nih.gov/},
  note = {Desktop registry status: Official literature portal; structured capture planned. External evidence requires claim-level human review before publication.}
}

@misc{resource_clinicaltrials-gov,
  author = {{ClinicalTrials.gov maintainers}},
  title = {{ClinicalTrials.gov — official resource and documentation}},
  url = {https://clinicaltrials.gov/},
  note = {Desktop registry status: Official registry link; no automated inference. External evidence requires claim-level human review before publication.}
}

@misc{resource_zenodo,
  author = {{Zenodo maintainers}},
  title = {{Zenodo — official resource and documentation}},
  url = {https://zenodo.org/},
  note = {Desktop registry status: Manual deposit only. Manual review is mandatory before any deposit; no credentials or uploads are handled by this connector.}
}

@misc{pride,
  author = {{PRIDE Archive}},
  title = {{PRIDE Archive}},
  url = {https://www.ebi.ac.uk/pride/},
  note = {Proteomics source repository used by the importer workflow.}
}

@misc{proteomexchange,
  author = {{ProteomeXchange}},
  title = {{ProteomeXchange}},
  url = {https://www.proteomexchange.org/},
  note = {Dataset accession and provenance framework.}
}

@misc{pxd001539,
  author = {{PRIDE / ProteomeXchange dataset PXD001539}},
  title = {{PRIDE / ProteomeXchange dataset PXD001539}},
  url = {https://www.ebi.ac.uk/pride/archive/projects/PXD001539},
  note = {Named comparator source in regenerative documentation; actual analysed samples require a run manifest.}
}

@misc{pxd064528,
  author = {{PRIDE / ProteomeXchange dataset PXD064528}},
  title = {{PRIDE / ProteomeXchange dataset PXD064528}},
  url = {https://www.ebi.ac.uk/pride/archive/projects/PXD064528},
  note = {Named comparator source in regenerative documentation; do not assume this dataset was used in every run.}
}

@misc{spectronaut,
  author = {{Spectronaut documentation}},
  title = {{Spectronaut documentation}},
  url = {https://biognosys.com/software/spectronaut/},
  note = {Imported output-format context; not bundled software.}
}

@misc{trial_zimislecel,
  author = {{ClinicalTrials.gov}},
  title = {{ClinicalTrials.gov: NCT04786262}},
  url = {https://clinicaltrials.gov/study/NCT04786262},
  note = {Trial record explicitly linked in regenerative documentation.}
}

@article{sbml_2019_l3v2_core,
  author = {Hucka, Michael and Bergmann, Frank T. and Chaouiya, Claudine and Dräger, Andreas and Hoops, Stefan and Keating, Sarah M. and König, Matthias and Novère, Nicolas Le and Myers, Chris J. and Olivier, Brett G. and Sahle, Sven and Schaff, James C. and Sheriff, Rahuman and Smith, Lucian P. and Waltemath, Dagmar and Wilkinson, Darren J. and Zhang, Fengkai},
  title = {{The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2}},
  year = {2019},
  journal = {Journal of Integrative Bioinformatics},
  volume = {16},
  doi = {10.1515/jib-2019-0021},
  url = {https://doi.org/10.1515/jib-2019-0021},
  number = {2},
  note = {mechanistic\_reference\_model\_interchange; source recorded in the packaged evidence registry.}
}

@article{libroadrunner_2015,
  author = {Somogyi, Endre T. and Bouteiller, Jean-Marie and Glazier, James A. and König, Matthias and Medley, J. Kyle and Swat, Maciej H. and Sauro, Herbert M.},
  title = {{libRoadRunner: a high performance SBML simulation and analysis library}},
  year = {2015},
  journal = {Bioinformatics},
  volume = {31},
  pages = {3315-3321},
  doi = {10.1093/bioinformatics/btv363},
  url = {https://doi.org/10.1093/bioinformatics/btv363},
  number = {20},
  note = {mechanistic\_reference\_model\_execution; source recorded in the packaged evidence registry.}
}

@article{copasi_2006,
  author = {Hoops, Stefan and Sahle, Sven and Gauges, Ralph and Lee, Christine and Pahle, Jürgen and Simus, Natalia and Singhal, Mudita and Xu, Liang and Mendes, Pedro and Kummer, Ursula},
  title = {{COPASI—a COmplex PAthway SImulator}},
  year = {2006},
  journal = {Bioinformatics},
  volume = {22},
  pages = {3067-3074},
  doi = {10.1093/bioinformatics/btl485},
  url = {https://doi.org/10.1093/bioinformatics/btl485},
  number = {24},
  note = {sensitivity\_and\_parameter\_analysis; source recorded in the packaged evidence registry.}
}

@article{opencor_2015,
  author = {Garny, Alan and Hunter, Peter J.},
  title = {{OpenCOR: a modular and interoperable approach to computational biology}},
  year = {2015},
  journal = {Frontiers in Physiology},
  volume = {6},
  doi = {10.3389/fphys.2015.00026},
  url = {https://doi.org/10.3389/fphys.2015.00026},
  note = {cellml\_reference\_validation; source recorded in the packaged evidence registry.}
}

@misc{fmi_3_0_2_standard,
  author = {{Modelica Association Project FMI}},
  title = {{Functional Mock-up Interface Specification 3.0.2}},
  url = {https://fmi-standard.org/docs/3.0.2/},
  note = {device\_physics\_model\_interchange; official resource recorded in source registry.}
}

@misc{fmpy_0_3,
  author = {{Sommer T}},
  title = {{FMPy: Simulate Functional Mock-up Units in Python}},
  url = {https://fmpy.readthedocs.io/en/latest/},
  note = {device\_physics\_execution; official resource recorded in source registry.}
}

@misc{myvariant_query_api,
  author = {{MyVariant.info}},
  title = {{MyVariant.info v1 query API}},
  url = {https://docs.myvariant.info/en/latest/doc/quick_start.html},
  note = {genetic\_variant\_context\_transport; official resource recorded in source registry.}
}

@article{fair2016,
  author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Mercè and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J.G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and ’t Hoen, Peter A.C and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
  title = {{The FAIR Guiding Principles for scientific data management and stewardship}},
  year = {2016},
  journal = {Scientific Data},
  volume = {3},
  pages = {160018},
  doi = {10.1038/sdata.2016.18},
  url = {https://doi.org/10.1038/sdata.2016.18},
  number = {1},
  note = {FAIR research-data framing; not a certification of project compliance.}
}

@misc{resource_ro-crate,
  author = {{RO-Crate 1.2 maintainers}},
  title = {{RO-Crate 1.2 — official resource and documentation}},
  url = {https://www.researchobject.org/ro-crate/},
  note = {Desktop registry status: Integrated academic package export. The export is RO-Crate-compatible metadata; it is not a repository deposit or peer review.}
}

@misc{resource_biomodels,
  author = {{BioModels maintainers}},
  title = {{BioModels — official resource and documentation}},
  url = {https://www.biomodels.org/},
  note = {Desktop registry status: Official model library; import planned. BioModels is migrating to BioStudies; the workbench does not yet import or execute deposited models.}
}

@misc{resource_libroadrunner,
  author = {{libRoadRunner maintainers}},
  title = {{libRoadRunner — official resource and documentation}},
  url = {https://libroadrunner.readthedocs.io/},
  note = {Desktop registry status: Integrated optional SBML execution engine. Execution success is not biological validation; model units and population assumptions require review.}
}

@misc{resource_copasi,
  author = {{COPASI maintainers}},
  title = {{COPASI — official resource and documentation}},
  url = {https://copasi.org/},
  note = {Desktop registry status: Integrated task inspection; explicit CopasiSE execution. IINTS never generates an objective or silently imports fitted parameters into a patient model.}
}

@misc{resource_sed-ml,
  author = {{SED-ML maintainers}},
  title = {{SED-ML — official resource and documentation}},
  url = {https://sed-ml.org/},
  note = {Desktop registry status: Planned standards-based simulation export. No SED-ML file is generated yet; current reproducibility uses IINTS run metadata and RO-Crate.}
}

@misc{resource_sbml,
  author = {{SBML maintainers}},
  title = {{SBML — official resource and documentation}},
  url = {https://sbml.org/},
  note = {Desktop registry status: Integrated local inspection; optional execution. Current IINTS patient models remain Python implementations and are not claimed to be SBML-compatible; external model units and assumptions require explicit review.}
}

@misc{marling_2020_ohiot1dm,
  author = {Marling, Cindy and Bunescu, Razvan},
  title = {{The OhioT1DM Dataset for Blood Glucose Level Prediction: Update 2020}},
  year = {2020},
  journal = {Proceedings of the 5th International Workshop on Knowledge Discovery in Healthcare Data; CEUR Workshop Proceedings},
  volume = {2675},
  pages = {71--74},
  url = {https://ceur-ws.org/Vol-2675/paper11.pdf},
  note = {CGM data preparation, retrospective evaluation and calibration context. Data access is governed by a Data Use Agreement.}
}

@misc{dataset_sample,
  author = {{IINTS-AF}},
  title = {{IINTS Sample CGM (Bundled)}},
  url = {https://github.com/python35/IINTS-SDK},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: bundled. Check original licence and run provenance.}
}

@misc{dataset_diatrend,
  author = {{Dartmouth College / Scientific Data}},
  title = {{DiaTrend Dataset}},
  url = {https://doi.org/10.7303/syn38187184},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: request. Check original licence and run provenance.}
}

@misc{dataset_t1d_uom,
  author = {{University of Manchester / Zenodo}},
  title = {{T1D-UOM Longitudinal Multimodal Dataset}},
  url = {https://doi.org/10.5281/zenodo.15806142},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: manual. Check original licence and run provenance.}
}

@misc{dataset_t1d_granada,
  author = {{University of Granada / Zenodo}},
  title = {{T1DiabetesGranada Dataset}},
  url = {https://doi.org/10.5281/zenodo.10050944},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: request. Check original licence and run provenance.}
}

@misc{dataset_aide_t1d,
  author = {{Jaeb Center for Health Research}},
  title = {{AIDE T1D Public Dataset}},
  url = {https://public.jaeb.org/datasets/},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: public-download. Check original licence and run provenance.}
}

@misc{dataset_azt1d,
  author = {{Mendeley Data}},
  title = {{AZT1D: A Real-World Dataset for Type 1 Diabetes}},
  url = {https://data.mendeley.com/datasets/gk9m674wcx/1},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: manual. Check original licence and run provenance.}
}

@misc{dataset_hupa_ucm,
  author = {{Mendeley Data}},
  title = {{HUPA-UCM Diabetes Dataset}},
  url = {https://data.mendeley.com/datasets/3hbcscwz44/1},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: manual. Check original licence and run provenance.}
}

@misc{dataset_openaps_data_commons,
  author = {{OpenAPS}},
  title = {{OpenAPS Data Commons}},
  url = {https://openaps.org/outcomes/data-commons/},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: request. Check original licence and run provenance.}
}

@misc{dataset_tidepool_bigdata,
  author = {{Tidepool}},
  title = {{Tidepool Big Data Donation}},
  url = {https://www.tidepool.org/bigdata},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: request. Check original licence and run provenance.}
}

@misc{dataset_niddk_central,
  author = {{NIDDK}},
  title = {{NIDDK Central Repository}},
  url = {https://repository.niddk.nih.gov/},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: request. Check original licence and run provenance.}
}

@misc{dataset_t1d_exchange,
  author = {{Jaeb Center / T1D Exchange}},
  title = {{T1D Exchange Clinic Registry}},
  url = {https://datacatalog.med.nyu.edu/dataset/10129},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: request. Check original licence and run provenance.}
}

@misc{dataset_d1namo,
  author = {{Zenodo / AISLab HES-SO}},
  title = {{D1NAMO Open Dataset}},
  url = {https://zenodo.org/records/1421616},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: manual. Check original licence and run provenance.}
}

@misc{dataset_t1dexi,
  author = {{Jaeb Center / Vivli / Public Study Websites}},
  title = {{Type 1 Diabetes Exercise Initiative (T1DEXI)}},
  url = {https://public.jaeb.org/datasets/diabetes},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: manual. Check original licence and run provenance.}
}

@misc{dataset_dclp3_idcl,
  author = {{NIDDK Central Repository / Jaeb Center}},
  title = {{International Diabetes Closed Loop Trial (DCLP3 / iDCL)}},
  url = {https://repository.niddk.nih.gov/studies/dclp3/},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: public-download. Check original licence and run provenance.}
}

@misc{dataset_metabonet,
  author = {{MetaboNet / arXiv}},
  title = {{MetaboNet Consolidated T1D Dataset}},
  url = {https://metabo-net.org/},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: mixed. Check original licence and run provenance.}
}

@misc{dataset_glucose_ml,
  author = {{arXiv / Glucose-ML authors}},
  title = {{Glucose-ML Dataset Collection}},
  url = {https://arxiv.org/abs/2507.14077},
  note = {Dataset catalogue entry, NOT proof of use in training. Access mode recorded by SDK: collection. Check original licence and run provenance.}
}

@misc{python,
  author = {{Python Software Foundation}},
  title = {{Python}},
  url = {https://docs.python.org/3/},
  note = {SDK runtime}
}

@misc{rust,
  author = {{The Rust Project}},
  title = {{Rust}},
  url = {https://www.rust-lang.org/},
  note = {Native command boundary}
}

@misc{tauri,
  author = {{Tauri contributors}},
  title = {{Tauri 2}},
  url = {https://v2.tauri.app/},
  note = {Desktop shell and signed updater}
}

@misc{pyside,
  author = {{The Qt Company}},
  title = {{Qt for Python / PySide6}},
  url = {https://doc.qt.io/qtforpython-6/},
  note = {Earlier/optional desktop interface}
}

@misc{ollama,
  author = {{Ollama}},
  title = {{Ollama documentation}},
  url = {https://docs.ollama.com/},
  note = {Optional local-language-model service}
}

@misc{mistral,
  author = {{Mistral AI}},
  title = {{Mistral AI model documentation}},
  url = {https://docs.mistral.ai/},
  note = {Model-family/runtime context; record exact model ID and digest per experiment}
}

@misc{huggingface,
  author = {{Hugging Face}},
  title = {{Hugging Face Hub documentation}},
  url = {https://huggingface.co/docs/hub/},
  note = {Checkpoint/dataset distribution and model cards}
}

@misc{pytorch,
  author = {{PyTorch contributors}},
  title = {{PyTorch documentation}},
  url = {https://pytorch.org/docs/stable/},
  note = {Neural model implementation}
}

@misc{pandas,
  author = {{pandas contributors}},
  title = {{pandas documentation}},
  url = {https://pandas.pydata.org/docs/},
  note = {Tabular data processing}
}

@misc{plotly,
  author = {{Plotly}},
  title = {{Plotly Python documentation}},
  url = {https://plotly.com/python/},
  note = {Interactive figures}
}

@misc{scienceplots,
  author = {{SciencePlots contributors}},
  title = {{SciencePlots}},
  url = {https://github.com/garrettj403/SciencePlots},
  note = {Plot styles, not journal endorsement}
}

@misc{seaborn,
  author = {{seaborn contributors}},
  title = {{seaborn documentation}},
  url = {https://seaborn.pydata.org/},
  note = {Statistical plot styling}
}

@misc{fpdf2,
  author = {{fpdf2 contributors}},
  title = {{fpdf2 documentation}},
  url = {https://py-pdf.github.io/fpdf2/},
  note = {PDF reports}
}

@misc{pymol,
  author = {{Schrodinger} and {PyMOL contributors}},
  title = {{PyMOL}},
  url = {https://pymol.org/},
  note = {Protein rendering workflow}
}

@misc{openaps,
  author = {{OpenAPS community}},
  title = {{OpenAPS documentation}},
  url = {https://openaps.readthedocs.io/},
  note = {Open-source insulin/COB/IOB algorithm context; not a validation of IINTS safety logic}
}

@misc{simglucose,
  author = {Xie, Jinyu},
  title = {{simglucose}},
  url = {https://github.com/jxx123/simglucose},
  note = {Simulator reference already cited in paper.bib}
}

@misc{raspberry,
  author = {{Raspberry Pi Ltd}},
  title = {{Raspberry Pi documentation}},
  url = {https://www.raspberrypi.com/documentation/},
  note = {Pi/Pico hardware and interface context}
}

@misc{arduino,
  author = {{Arduino}},
  title = {{Arduino documentation}},
  url = {https://docs.arduino.cc/},
  note = {Microcontroller bridge context}
}

@misc{jetson,
  author = {{NVIDIA}},
  title = {{NVIDIA Jetson documentation}},
  url = {https://developer.nvidia.com/embedded/learn},
  note = {Edge-training/deployment environment}
}

@misc{mkdocs,
  author = {{MkDocs contributors}},
  title = {{MkDocs}},
  url = {https://www.mkdocs.org/},
  note = {Documentation build}
}

@misc{material,
  author = {{squidfunk} and {contributors}},
  title = {{Material for MkDocs}},
  url = {https://squidfunk.github.io/mkdocs-material/},
  note = {Documentation theme}
}

@misc{mermaid,
  author = {{Mermaid contributors}},
  title = {{Mermaid documentation}},
  url = {https://mermaid.js.org/},
  note = {Architecture diagrams}
}

@misc{pytest,
  author = {{pytest contributors}},
  title = {{pytest documentation}},
  url = {https://docs.pytest.org/},
  note = {Automated software tests}
}

@misc{hypothesis,
  author = {{Hypothesis contributors}},
  title = {{Hypothesis documentation}},
  url = {https://hypothesis.readthedocs.io/},
  note = {Property-based software tests}
}

@misc{git,
  author = {{Git contributors}},
  title = {{Git documentation}},
  url = {https://git-scm.com/doc},
  note = {Version control}
}

@misc{github,
  author = {{GitHub}},
  title = {{GitHub Actions documentation}},
  url = {https://docs.github.com/en/actions},
  note = {Build and release automation}
}