Repositories list

• Valis-GUI

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

  Python

  •

  Other

  •1•0•0•0•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

  •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

• Newsletter-Bibliography

  Public
  LaTeX bibliography of the "This week in Math Onco" newsletter (<a href="https://mathematical-oncology.org/newsletter" class="Link--inTextBlock" rel="nofollow">https://mathematical-oncology.org/newsletter</a>)

  TeX

  •0•2•0•0•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

  •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

• MathOnco-Bibliometrics

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

  Python

  •1•0•0•0•Updated Jan 10, 2026Jan 10, 2026

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

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

  MATLAB

  •0•0•0•0•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

  •0•0•0•0•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

  •0•1•0•1•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 immunotherapy in prostate cancer," Luddy et. al. 2023

  MATLAB

  •0•0•0•0•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

  •0•0•0•0•Updated Sep 13, 2025Sep 13, 2025

• IMAT

  Public
  IMO Methods &amp; Tools Lecture Series

  0•9•0•0•Updated Sep 9, 2025Sep 9, 2025

• valis

  Public
  Virtual Alignment of pathoLogy Image Series

  Python

  •

  MIT License

  •53•203•103•6•Updated Jun 25, 2025Jun 25, 2025

• CellCycle4DataIntegration

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

  XSLT

  •0•1•0•0•Updated Mar 17, 2025Mar 17, 2025

• Lenia-in-HAL

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

  Java

  •

  MIT License

  •0•10•0•0•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

  •0•2•0•0•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

  •31•114•3•1•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

  •13•38•1•0•Updated Aug 19, 2024Aug 19, 2024

• DRL_Personalized_AT

  Public
  Mathematical Model-Driven Deep Learning Enables Personalized Adaptive Therapy

  Jupyter Notebook

  •3•4•0•0•Updated Aug 19, 2024Aug 19, 2024

• Mistic

  Public
  Multiplexed image tSNE visualizer

  Python

  •

  MIT License

  •7•47•1•0•Updated Jul 3, 2024Jul 3, 2024

• Mistic_code_live_cell_imaging

  Public
  Python

  •0•0•0•0•Updated Jul 2, 2024Jul 2, 2024

• PARPi_Model

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Apr 9, 2024Apr 9, 2024

• multiMets

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

  Java

  •

  MIT License

  •0•0•0•0•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

  •0•0•0•0•Updated Jan 23, 2024Jan 23, 2024

• densityDependentSelection

  Public
  HTML

  •0•0•0•0•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

  •1•1•7•0•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 investigate conditions for missegregation-induced extinction (MIE).

  R

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Sep 13, 2022Sep 13, 2022

• HomeostaticEpidermis

  Public
  Homeostatic Epidermis – PNAS Full Codebase

  Java

  •0•0•0•0•Updated Aug 12, 2022Aug 12, 2022

• Curvogram

  Public
  Method for plotting histograms on a curve using a West Transform

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •2•10•0•0•Updated Apr 26, 2022Apr 26, 2022

• strobl2021_space_modulates_competition_AT

  Public
  This repository contains the code and data for our publication Strobl et al (2022). Spatial structure impacts adaptive therapy by shaping intra-tumoral competition. Commun Med 2, 46, available at: <a href="https://rdcu.be/cL5bi" class="Link--inTextBlock" rel="nofollow">https://rdcu.be/cL5bi</a>.

  Jupyter Notebook

  •3•5•0•0•Updated Apr 25, 2022Apr 25, 2022

• AT_costOfResistance_LVModel

  Public
  This repository contains the code to generate the figures in our research paper: Strobl et al (2020), Turnover modulates the need for a cost of resistance in adaptive therapy published in Cancer Research.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•3•0•0•Updated Mar 22, 2022Mar 22, 2022