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valis
Virtual Alignment of pathoLogy Image SeriesNeoPredPipe
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.HAL
HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needsMistic
Multiplexed image tSNE visualizerEvoFreq
Evolutionary frequency visualization tool of temporal dataCurvogram
Method for plotting histograms on a curve using a West TransformIsoMaTrix
A framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations (MATLAB, Java)Lenia-in-HAL
Repository for Lenia framework, implemented in Hybrid Automata Library (HAL)strobl2021_space_modulates_competition_AT
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: https://rdcu.be/cL5bi.flipflopblood
Whole Blood Simulations of Hematopoietic Stem CellsnonlinearPGG
This repository contains the data and code for the paper "Neighborhood size-effects shape growing population dynamics in evolutionary public goods games"AT_costOfResistance_LVModel
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.CARTecology
Gattaca
Base pair resolution mutation tracking for somatic evolution studies using agent based simulationsimmune-checkpoint-kickstart
The code (MATLAB) for the paper "The Immune Checkpoint Kick Start: Optimization of Neoadjuvant Combination Therapy Using Game Theory" published in JCO Clinical Cancer Informatics.Newsletter-Bibliography
LaTeX bibliography of the "This week in Math Onco" newsletter (https://mathematical-oncology.org/newsletter)ploidyEvolution
A general N-compartment model of ploidy states is developed and analyzed.DRL_Personalized_AT
Learning to Adapt - Deep Reinforcement Learning in Treatment-Resistant Prostate Cancer (https://doi.org/10.1101/2023.04.28.538766)tissue-structure-modulates-evolution
Code repository associated with the paper "Tissue structure modulates evolution: premalignant sweeps precede neutral expansion"multiscaleGBM
PARPi_Model
MIEmodel
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).Love Open Source and this site? Check out how you can help us