Repositories list

• Newsletter-Bibliography

  Public
  LaTeX bibliography of the "This week in Math Onco" newsletter (https://mathematical-oncology.org/newsletter)

  TeX

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 12, 2026Aug 12, 2026

• AI-curation-mathonco

  Public
  Codebase and data for bibliometric analysis on Mathematical Research in Oncology

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 31, 2026Jul 31, 2026

• LungTissueDensityModel

  Public
  Population-based model of NSCLC initiation and progression associated with manuscript.

  Java

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2026Jun 18, 2026

• Mathematical-Biomarkers

  Public
  Code repository for the paper 'Mathematical Biomarkers of Adaptive Therapy Outcomes in Prostate Cancer'

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 20, 2026May 20, 2026

• IMAT

  Public
  IMO Methods & Tools Lecture Series

  00 forks•99 stars•00 issues•00 pull requests•Updated May 15, 2026May 15, 2026

• Evolutionary-Antifragile-Therapy

  Public
  Evolutionary Antifragile Therapy project

  MATLAB

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 27, 2026Mar 27, 2026

• Valis-GUI

  Public
  GUI to help handle the Valis imaging process (alternative to using command line/terminal).

  Python

  •

  Other

  •22 forks•11 star•00 issues•00 pull requests•Updated Jan 23, 2026Jan 23, 2026

• OncoLens

  Public
  A modeling and visualization application tool used for biological data research, analysis and prediction.

  Python

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Jan 23, 2026Jan 23, 2026

• Contact-Inhibition

  Public
  Repository for the manuscript "Universal principles of cell population growth follow from local contact inhibition"

  Wolfram Language

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 22, 2026Jan 22, 2026

• ER-breast-cancer-evolutionary-double-bind

  Public
  Repository for code & data for "A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind"

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 7, 2026Jan 7, 2026

• Cell-State-Transitions-B-ALL

  Public
  Repository for the manuscript "Cell state transitions drive the evolution of disease progression in B-lymphoblastic leukemia"

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 12, 2025Dec 12, 2025

• ECO_K

  Public
  This repository houses code that runs an inverse game theory algorithm to detect frequency dependent effects and model subpopulation evolution

  MATLAB

  •00 forks•11 star•00 issues•11 pull request•Updated Sep 29, 2025Sep 29, 2025

• RT-NK-evolutionary-double-bind

  Public
  This repository contains the code to reproduce the figures for the manuscript "Evolutionary double-bind treatment using radiotherapy and NK cell-based immunothe…

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 15, 2025Sep 15, 2025

• NSCLC_Distinct_ecologies

  Public
  Code for paper 'Distinct tumor-immune ecologies in NSCLC patients predict progression and define a clinical biomarker of therapy response'

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 13, 2025Sep 13, 2025

• valis

  Public
  Virtual Alignment of pathoLogy Image Series

  Python

  •

  MIT License

  •6767 forks•235235 stars•108108 issues•99 pull requests•Updated Jun 25, 2025Jun 25, 2025

• CellCycle4DataIntegration

  Public
  Cell identity revealed by precise cell cycle state mapping links data modalities

  XSLT

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 17, 2025Mar 17, 2025

• Lenia-in-HAL

  Public
  Repository for Lenia framework, implemented in Hybrid Automata Library (HAL)

  Java

  •

  MIT License

  •00 forks•1111 stars•00 issues•00 pull requests•Updated Feb 17, 2025Feb 17, 2025

• Gattaca

  Public
  Base pair resolution mutation tracking for somatic evolution studies using agent based simulations

  Python

  •

  GNU General Public License v3.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Dec 9, 2024Dec 9, 2024

• NeoPredPipe

  Public
  Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.

  Python

  •

  GNU Lesser General Public License v3.0

  •3131 forks•118118 stars•33 issues•11 pull request•Updated Sep 2, 2024Sep 2, 2024

• HAL

  Public
  HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needs

  Java

  •

  MIT License

  •1313 forks•3838 stars•22 issues•00 pull requests•Updated Aug 19, 2024Aug 19, 2024

• DRL_Personalized_AT

  Public
  Mathematical Model-Driven Deep Learning Enables Personalized Adaptive Therapy

  Jupyter Notebook

  •33 forks•55 stars•00 issues•00 pull requests•Updated Aug 19, 2024Aug 19, 2024

• Mistic

  Public
  Multiplexed image tSNE visualizer

  Python

  •

  MIT License

  •77 forks•5151 stars•11 issue•00 pull requests•Updated Jul 3, 2024Jul 3, 2024

• Mistic_code_live_cell_imaging

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2024Jul 2, 2024

• PARPi_Model

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 9, 2024Apr 9, 2024

• multiMets

  Public
  grows and seeds multiple metastases and treats them with different therapeutic strategies

  Java

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 8, 2024Feb 8, 2024

• onubogu_spatial_analysis_of_recurrent_glioblastoma

  Public
  Code used in Spatial analysis of recurrent glioblastoma reveals perivascular niche organization.

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 23, 2024Jan 23, 2024

• densityDependentSelection

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 5, 2023Jul 5, 2023

• ploidyEvolution

  Public
  A general N-compartment model of ploidy states is developed and analyzed.

  R

  •

  BSD 2-Clause "Simplified" License

  •11 fork•11 star•77 issues•00 pull requests•Updated Feb 7, 2023Feb 7, 2023

• MIEmodel

  Public
  Simplified version of a deterministic framework for modeling whole chromosome missegregations. This model is more amendable to theoretical analysis to investiga…

  R

  •

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Sep 13, 2022Sep 13, 2022

• HomeostaticEpidermis

  Public
  Homeostatic Epidermis – PNAS Full Codebase

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 12, 2022Aug 12, 2022