This repository contains the reproducibility package for the case study shown in Fig. 2 of our poster, demonstrating cross-tool interoperability with Jinkō.
Interoperability across modeling tools is a persistent barrier to reproducibility. Standards such as PharmML and SBML help, but adoption is incomplete, leaving models to be re-implemented manually across environments like Monolix, SimBiology, MATLAB, or R—introducing delays and errors.
Jinkō addresses this by providing a language-agnostic canonical representation, exposed through an API-first platform with polyglot import/export. Building on this foundation, we demonstrate how LLM-enabled workflows accelerate parser development, enable import from semi-structured sources (e.g. publications), and generate user-preferred code exports.
In this case study, a published model of AZD5363 was reconstructed from PDF, simulated in Jinkō, and exported to both R and MATLAB. Executions in all three environments reproduced the published trajectories, validating cross-tool reproducibility.
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R/
Exported R script (model.R) and resulting plots. -
MATLAB/
Exported MATLAB script (model.m) and resulting plots.
- 🌐 Jinkō Website
- 📚 Jinkō Documentation
- [1] Yates, James W. T., Phillippa Dudley, Jane Cheng, Celina D’Cruz, and Barry R. Davies. “Validation of a Predictive Modeling Approach to Demonstrate the Relative Efficacy of Three Different Schedules of the AKT Inhibitor AZD5363.” Cancer Chemotherapy and Pharmacology 76, no. 2 (June 20, 2015): 343–56. 10.1007/s00280-015-2795-7
- [2] Swat, M J et al. “Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.” CPT: pharmacometrics & systems pharmacology vol. 4,6 (2015): 316-9. 10.1002/psp4.57
- [3] Bizzotto, R et al. “PharmML in Action: an Interoperable Language for Modeling and Simulation.” CPT: pharmacometrics & systems pharmacology vol. 6,10 (2017): 651-665. 10.1002/psp4.12213
- [4] Terranova, Nadia et al. “The Standard Output: A Tool-Agnostic Modeling Storage Format.” CPT: pharmacometrics & systems pharmacology vol. 7,9 (2018): 543-546. 10.1002/psp4.12339
- [5] Kirouac, Daniel C et al. “Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities.” CPT: pharmacometrics & systems pharmacology vol. 8,4 (2019): 205-210. 10.1002/psp4.12390
How to cite this work
Ponchon J, Prevot E, Coudron M, Villard J, Duteil N, Kahoul R, Gourlet J-B, Cogny F. (2025). Enhancing Model Interoperability and Workflow Integration in Clinical Trial Simulations. Poster, Nova In Silico, Lyon, France. Available at: https://github.com/novainsilico/2025-poster-model-interoperability
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