Data for: "A new cancer progression model: from synthetic tumors to real data and back"

Overview

This dataset contains the raw simulation results and configuration parameters supporting the study on intratumor heterogeneity (ITH) and tumor evolution. The data were generated using a stochastic modelling framework that integrates genotypic inheritance, phenotype-driven functional traits, and resource-mediated competition. 

The provided simulations illustrate how ecological feedbacks shape clonal dynamics, capturing the transition from early stochastic expansion to selection-driven evolution as described in the accompanying manuscript.

Data Structure and Contents

The data is organized into four main directories corresponding to the different sections of the paper and its supplementary materials:

nD_exp/: Simulations related to the "Exploration of Evolutionary paradigms" section in the main text exploring the sensitivity of the model to various parameters (competition, growth, mutation rates, and carrying capacity).

TumorFit/: Data related to the "Validation against empirical data" section. This folder contains the synthetic simulation runs used to validate the model's ability to reproduce observed behaviors.

Experiment1/ & Experiment2/: Exploratory experiments detailed in Supplementary Material S3.  Experiment1 is further divided into 2 directories:

ExpansivePhase: Simulations focusing on early-stage tumor growth.

StablePhase: Simulations focusing on later stages under environmental constraints and selection.

Organization of Simulation Runs

Each experiment directory follows a consistent internal structure:

params/: Contains the input configuration files (JSON/text) used to define model parameters for the simulation engine.

results/: Contains the output files, organized according to the following logic:

Subfolders are named according to the specific parameter set used (matching the files in the `params/`directory).

Example: In TumorFit/results the folder params_161 contains all simulation outputs generated with the configuration defined in params_161.json retrievable in TumorFit/params.

Each parameter set includes multiple folders (`sim1 to simN), representing individual stochastic realizations to ensure statistical robustness.

Example: TumorFit/results/params_161  contains 100 folders ("sim1" to "sim100") , each containing the output of a single simulation run.

Each simX subfolder contains a .RData file representing the final state (final condition) of that specific simulation.

seed.txt: This file stores the base seed for each parameter configuration. To ensure reproducibility across multiple realizations, the specific seed for each simulation was set as the base seed + the simulation number.

Example: For params_161, the base seed is 736995. Therefore, sim1 was run with seed 736996, sim2 with seed 736997, and so on.

Technical Usage

Details on how to analyze or reproduce these data are available on the project’s GitHub repository: Insite GitHub

Citation Policy

If you use this dataset or any part of these simulation results in your research, please cite the original research article: 

Daniela Volpatto et al. (2026). A new cancer progression model: from synthetic tumors to real data and back.