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README.md

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 # Differentiable T1D Simulators
 
+<p align="center">
+  <img src="media/kanderian_data.png">
+</p>
+
 This repository contains various simulators/dynamical systems for modeling Type 1 Diabetes (T1D) dynamics. 
 We implement our models in Jax and PyTorch, allowing for easy differentiation of the dynamics.
 

differentiable_t1d/dynamics/README.md

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+# Various dynamics models for glucose-insulin dynamics for Type 1 Diabetes
+
+## Implementation of the UVa/Padova 2008 Simulator
+
+See
+> Kovatchev et al., 2009. In silico preclinical trials: a proof of concept in closed-loop control of type 1 diabetes.
+
+Code based on [simglucose](https://github.com/jxx123/simglucose/). We use ICR, CF values from [RL4BG](https://github.com/MLD3/RL4BG/blob/master/bgp/simglucose/params/Quest2.csv).
+
+### Glossary of terms in the simulator
+**Rate of glucose entering the blood from the stomach (oral glucose subsystem)**
+
+| State index | Descriptive name | Units | Description |
+| --- | --- | --- | --- |
+| 0 | q_sto1 | mg | amount of solid glucose in stomach |
+| 1 | q_sto2 | mg | amount of liquid glucose in stomach |
+| 2 | q_gut | mg | amount of glucose in the intestine |
+| --- | Ra | mg/kg/min | rate of glucose absorption per body weight |
+| --- | kmax | 1/min | --- |
+| --- | kmin | 1/min | --- |
+| --- | kabs | 1/min | --- |
+| --- | kgut | 1/min | --- |
+| --- | carbs | mg/min | rate of glucose ingested instantaneously |
+| --- | f | 1 | one over the fraction of the total ingested glucose; i.e. total / D |
+
+**Glucose kinetics**
+
+| State index | Descriptive name | Units | Description |
+| --- | --- | --- | --- |
+| 3 | G_p | mg/kg | glucose mass in plasma per kg of bodyweight |
+| 4 | G_t | mg/kg | glucose mass in tissue per kg of bodyweight |
+| --- | EGP | mg/kg/min | endogenous glucose production |
+| --- | E   | mg/kg/min | renal glucose excretion |
+| --- | Uii | mg/kg/min | insulin independent glucose utilization |
+| --- | Uid | mg/kg/min | insulin dependent glucose utilization |
+| --- | G | mg/dL | plasma glucose concentration |
+| 12  | Gs | mg/kg | glucose concentration in the subcutaneous tissue |
+
+**Insulin kinetics**
+
+| State index | Descriptive name | Units | Description |
+| --- | --- | --- | --- |
+| 5 | I_p | pmol/kg | insulin masses in plasma per kg of bodyweight |
+| 6 | X | pmol/L | insulin in the interstitial fluid |
+| 7 | I_1 | pmol/L | delayed insulin compartment 1 (I tilde in Andy's paper)|
+| 8 | I_d | pmol/L | delayed insulin compartment 2 (X_L in Andy's paper)|
+| 9 | I_l | pmol/kg | insulin masses in liver per kg of bodyweight |
+| --- | I | pmol/L | plasma insulin concentration |
+| --- | insulin | pmol/kg/min | insulin infusion rate per kg of bodyweight |
+| --- | V_I | L/kg | distribution volume of insulin |
+| 10 | I_sc1 | pmol/kg | nonmonomeric insulin in subcutaneous space |
+| 11 | I_sc2 | pmol/kg | monomeric insulin in subcutaneous space |
+| --- | Ra_I | pmol/kg | rate of insulin absorption into plasma |
+
+## Implementation of the Medtronic Virtual Patient (MVP) model
+
+See 
+> Kanderian et al., 2009. Identification of Intraday Metabolic Profiles during Closed-Loop Glucose Control in Individuals with Type 1 Diabetes
+
+We descripbe this model and our implementation is our code comments.