Model-Informed Development of Bacteriophage Therapy: Bridging In Vitro and In Vivo Efficacy Against Multidrug-resistant Pseudomonas aeruginosa. Jun Seok Cha et al.

Published: 6 November 2025| Version 1 | DOI: 10.17632/w9kd3tnmf3.1
Contributors:
Jun Seok Cha, Kyungnam Kim, Hwa Jeong You, Dasom Kim, Hyun Hee Park, SuJin Heo, Choon Ok Kim, Byung Hak Jin, Dongeun Yong, Dongwoo Chae

Description

Data and scripts that were used for analysis in the paper "Model-Informed Development of Bacteriophage Therapy: Bridging In Vitro and In Vivo Efficacy Against Multidrug-resistant Pseudomonas aeruginosa" by Jun Seok Cha et al.

Files

Steps to reproduce

The codes needed to reproduce the fitgures are stored in the file "code_used_for_analysis.zip" in the folder "Data S12 (Python, R, and mlxtran code for simulating the virus-bacteria dynamics)". First, unzip the folder. Then, follow the instructions below. To reproduce Figure 1: Run the ipynb notebook "code_used_for_analysis/code_python/1.invitro_kinetics.ipynb" To reproduce Figure 2: Run the ipynb notebook "invivo_PKPD.ipynb" To reproduce Figure 4: Run the R script "codes_used_for_analysis\code_r\subpopulation_fractions.r" Run the R script "codes_used_for_analysis\code_r\pkpd_dose_response.r" Run the ipynb notebook "codes_used_for_analysis\code_python\4.invitro_model_and_simulations.ipynb" To reproduce Figure 5: Run the ipynb notebook "codes_used_for_analysis\code_python\3.invitro_validation.ipynb" To reproduce Figure 6: Run the R script "codes_used_for_analysis\code_r\invivo_fit.r" Run the R script "codes_used_for_analysis\code_r\threshold.r" Run the R script "codes_used_for_analysis\code_r\immunity_and_cocktail.r" Run the ipynb notebook "codes_used_for_analysis\code_python\6.invivo_model_and_simulations.ipynb" To reproduce Figure 7: Run the R script "codes_used_for_analysis\code_r\invivo_validation.r" Run the ipynb notebook "codes_used_for_analysis\code_python\7.invivo_model_validation.ipynb" To reproduce Figure S1: Run the ipynb notebook "codes_used_for_analysis\code_python\s1.phage_characterization.ipynb" To reproduce Figure S2: Run the R script "codes_used_for_analysis\code_r\local_sensitivity_analysis.r" Run the ipynb notebook "codes_used_for_analysis\code_python\sensitivity_analysis.ipynb" To reproduce Figure S3-5: Run the ipynb notebook "codes_used_for_analysis\code_python\s3_to_s5.expansion_to_other_strains.ipynb" To reproduce Figure S6: Run the R script "codes_used_for_analysis\code_r\invivo_fit_without_immunity.r" Run the ipynb notebook "codes_used_for_analysis\code_python\s6.invivo_no_immunity.ipynb"

Institutions

  • Yonsei University

Categories

Bacteriophage, Mathematical Modeling in Quantitative Microbiology, Pseudomonas aeruginosa

Funders

Licence