ACoP 2026 tutorial

A Hands-on Tutorial on Stochastic Approximation Expectation-Maximization (SAEM) in Python and Jinkō

Everything you need to follow along: open the notebook, sign in to Jinkō, and run each step with us.

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Supporting material

Open both before the session starts. Each link opens in a new tab.

NPDE diagnostic plots from the SAEM notebook

Python notebook

The SAEM walkthrough as a runnable notebook on Binder. No install needed: it opens in your browser.

Open the notebook

Jinkō ACoP organization

The Jinkō workspace set up for the session, with the models and data used in the tutorial.

Open Jinkō

Optional workshop extension

From publication to model

Choose a publication and implement a scoped model in Jinkō using Kōhai’s paper-to-model functionality or the jinko-task-paper2model skill in an agentic harness of your choice.

Start with one scenario and one figure. Check equations, units, and assumptions, compare your results with the publication, and document gaps. The existing reports assess specific implementations and scopes; they do not guarantee full reproduction in a workshop session.

The selection spans PKPD, PBPK, and QSP, with population modeling connections. The RSV option includes popPK context, but does not cover standalone popPK estimation. Complexity is a teaching estimate from 1 to 5, separate from the reports’ moderate reproduction confidence.

Paper links lead to the original publications. Library references may require Jinkō library access.

First page of Making PBPK models more reproducible in practice

PBPK2024

Elena Domínguez-Romero et al.

Three compartments, reproducible PBPK

Start with blood, liver, and other tissues. Implement an infusion and compare concentration curves to the published example.

Complexity: Introductory (1/5)

Report scope and caveats

Reproduction confidence: moderate. Three concentration targets pass. The report compares author outputs on a reduced time grid.

Making PBPK models more reproducible in practice

Elena Domínguez-Romero, Stanislav Mazurenko, Martin Scheringer, Vítor A P Martins dos Santos, Chris T Evelo, Mihail Anton, John M Hancock, Anže Županič, Maria Suarez-Diez

Library reference (Jinkō access)

Paper

First page of Utilizing Virtual Clinical Trials to Inform Target Coverage That Drives RSV Antiviral Efficacy

PKPD2026

J. Cody Herron et al.

Exposure and antiviral response

Bridge PKPD and QSP with antiviral exposure, viral dynamics, and adult and pediatric virtual populations.

Complexity: Intermediate (3/5)

Report scope and caveats

Reproduction confidence: moderate. Pediatric targets pass; adult targets fail. Missing popPK functions exclude part of the paper. This is not a standalone popPK estimation exercise.

Utilizing Virtual Clinical Trials to Inform Target Coverage That Drives RSV Antiviral Efficacy

J. Cody Herron, Kathryn G. Link, Natalie Meacham, Negar Niki Alami, Daniel W. Brookes, Elaine Thomas, Jan Adams, Sima S. Toussi, Ryan Franke, Cynthia J. Musante, Isabel Najera, Richard Allen, Britton Boras

Library reference (Jinkō access)

Paper

First page of Quantitative Systems Pharmacology Model of Chimeric Antigen Receptor T‐Cell Therapy

QSP2019

Deni Hardiansyah & Chee Meng Ng

CAR-T expansion and cytokines

Connect a living therapy to tumor burden and cytokine response. Start with the two published patient scenarios.

Complexity: Intermediate (3/5)

Report scope and caveats

Reproduction confidence: moderate. Ten of twelve targets pass. Late CAR-T persistence remains unresolved, and an assumed blood volume affects comparison independence.

Quantitative Systems Pharmacology Model of Chimeric Antigen Receptor T‐Cell Therapy

Deni Hardiansyah, Chee Meng Ng

Library reference (Jinkō access)

Paper

First page of A Digital Twin of the Angiotensin II Receptor Blocker Losartan: Physiologically Based Modeling of Blood Pressure Regulation

PBPK2026

Ennie Tensil et al.

Losartan from exposure to response

Connect whole-body parent and metabolite kinetics to aldosterone response in a scoped oral-dose experiment.

Complexity: Advanced (4/5)

Report scope and caveats

Reproduction confidence: moderate. All sixteen curve targets pass. One supplement parameter disagrees with the author implementation. Other studies are outside the report scope.

A Digital Twin of the Angiotensin II Receptor Blocker Losartan: Physiologically Based Modeling of Blood Pressure Regulation

Ennie Tensil, Mariia Myshkina, Matthias König

Library reference (Jinkō access)

Paper

First page of Logic Modeling in Quantitative Systems Pharmacology

QSP2017

Pauline Traynard et al.

Logic models of cell signaling

Translate a trained signaling network into logic-based differential equations and compare responses across perturbations.

Complexity: Advanced (4/5)

Report scope and caveats

Reproduction confidence: moderate. Numerical targets pass, but the scoring point set was selected after comparison. Training and stochastic analyses are outside scope.

Logic Modeling in Quantitative Systems Pharmacology

Pauline Traynard, Luis Tobalina, Federica Eduati, Laurence Calzone, Julio Saez-Rodriguez

Library reference (Jinkō access)

Paper

First page of A Quantitative Systems Pharmacology Model of Human Leucine Metabolism

QSP2026

J. Cody Herron et al.

Human leucine metabolism

Explore a 14-state metabolic model, virtual populations, and treatment effects. Begin with one experiment before expanding the population.

Complexity: Advanced (4/5)

Report scope and caveats

Reproduction confidence: moderate. The selected report passes seven publication targets. Equations rely on author code because the published equation supplement was inaccessible.

A Quantitative Systems Pharmacology Model of Human Leucine Metabolism

J. Cody Herron, Anna Sher, Yingbo Ma, Elisabeth Roesch, Sebastian Miculța‐Câmpeanu, Christopher Rackauckas, Kevin J. Filipski, Rachel Roth Flach, Theodore R. Rieger, Cynthia J. Musante, Richard Allen

Library reference (Jinkō access)

Paper

First page of A Prototype QSP Model of the Immune Response to SARS‐CoV‐2 for Community Development

QSP2021

Wei Dai et al.

Viral dynamics and immune response

Explore interacting innate and adaptive immune processes. Scope the exercise to the baseline patient response.

Complexity: Specialist (5/5)

Report scope and caveats

Reproduction confidence: moderate. Eight targets pass for baseline U1 only. Two paper/code terms differ; parameter sweeps and population simulations are outside scope.

A Prototype QSP Model of the Immune Response to SARS‐CoV‐2 for Community Development

Wei Dai, Rohit Rao, Anna Sher, Nessy Tania, Cynthia J. Musante, Richard Allen

Library reference (Jinkō access)

Paper

First page of An integrated quantitative systems pharmacology virtual population approach for calibration with oncology efficacy endpoints

QSP2025

Nathan Braniff et al.

Oncology virtual populations

Extend the calibration discussion to signaling, tumor dynamics, and population efficacy endpoints using supplied virtual patients.

Complexity: Specialist (5/5)

Report scope and caveats

Reproduction confidence: moderate. Scored targets pass with supplied populations. An endpoint rule was chosen after comparison; unavailable clinical inputs prevent full regeneration.

An integrated quantitative systems pharmacology virtual population approach for calibration with oncology efficacy endpoints

Nathan Braniff, Tanvi Joshi, Tyler Cassidy, Michael Trogdon, Rukmini Kumar, Kamrine Poels, Richard Allen, Cynthia J. Musante, Blerta Shtylla

Library reference (Jinkō access)

Paper