IMO

Moffitt Cancer Center's Integrated Mathematical Oncology public facing repositories for published projects.

Tampa, Florida, USA

Pinned Repositories

Curvogram
Method for plotting histograms on a curve using a West Transform
Language:Jupyter Notebook10 2 02
EvoFreq
Evolutionary frequency visualization tool of temporal data
Language:R21 4 53
HAL
HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needs
Language:Java36 8 411
IsoMaTrix
A framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations (MATLAB, Java)
Language:Java9 5 01
Lenia-in-HAL
Repository for Lenia framework, implemented in Hybrid Automata Library (HAL)
Language:Java50
Mistic
Multiplexed image tSNE visualizer
Language:Python31 3 25
NeoPredPipe
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
Language:Python101 9 4428
Newsletter-Bibliography
LaTeX bibliography of the "This week in Math Onco" newsletter (https://mathematical-oncology.org/newsletter)
Language:TeX2 2 00
scRNAseqITH
Single-cell RNA sequencing pipeline for quantifying intratumor heterogeneity
Language:Mathematica51
valis
Virtual Alignment of pathoLogy Image Series
Language:Python113 2 10028

IMO's Repositories

MathOnco/valis
Virtual Alignment of pathoLogy Image Series
Language:Python113 2 10028
MathOnco/NeoPredPipe
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
Language:Python101 9 4428
MathOnco/HAL
HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needs
Language:Java36 8 411
MathOnco/Mistic
Multiplexed image tSNE visualizer
Language:Python31 3 25
MathOnco/EvoFreq
Evolutionary frequency visualization tool of temporal data
Language:R21 4 53
MathOnco/Curvogram
Method for plotting histograms on a curve using a West Transform
Language:Jupyter Notebook10 2 02
MathOnco/IsoMaTrix
A framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations (MATLAB, Java)
Language:Java9 5 01
MathOnco/Lenia-in-HAL
Repository for Lenia framework, implemented in Hybrid Automata Library (HAL)
Language:Java50
MathOnco/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.
Language:Jupyter Notebook43
MathOnco/flipflopblood
Whole Blood Simulations of Hematopoietic Stem Cells
Language:Java3 2 01
MathOnco/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.
Language:Jupyter Notebook2 4 01
MathOnco/CARTecology
Language:Mathematica2 4 02
MathOnco/Gattaca
Base pair resolution mutation tracking for somatic evolution studies using agent based simulations
2 1 0
MathOnco/Newsletter-Bibliography
LaTeX bibliography of the "This week in Math Onco" newsletter (https://mathematical-oncology.org/newsletter)
Language:TeX2 2 00
MathOnco/DRL_Personalized_AT
Learning to Adapt - Deep Reinforcement Learning in Treatment-Resistant Prostate Cancer (https://doi.org/10.1101/2023.04.28.538766)
Language:Jupyter Notebook12
MathOnco/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).
Language:R1 5 01
MathOnco/multiscaleGBM
Language:Java1 4 00
MathOnco/PARPi_Model
Language:Jupyter Notebook1 1 02
MathOnco/ploidyEvolution
A general N-compartment model of ploidy states is developed and analyzed.
Language:R1 5 221
MathOnco/tissue-structure-modulates-evolution
Code repository associated with the paper "Tissue structure modulates evolution: premalignant sweeps precede neutral expansion"
Language:Java12
MathOnco/adaptivePGG
C++ code developed to study the emergence of dimorphic populations in nonlinear public good games
Language:MATLAB0 3 03
MathOnco/multiMets
grows and seeds multiple metastases and treats them with different therapeutic strategies
Language:Java0 3 00
MathOnco/CellCycle4DataIntegration
Cell identity revealed by precise cell cycle state mapping links data modalities
Language:XSLT
MathOnco/densityDependentSelection
Language:HTML
MathOnco/flipflopspatialmodel
MathOnco/gatenbee_2022_immunosuppressive_niche
Code to used to simulate eco-evolutionary tumor-immune dynamics as described in https://www.researchsquare.com/article/rs-799879/v1
Language:Shell1
MathOnco/HomeostaticEpidermis
Homeostatic Epidermis – PNAS Full Codebase
Language:Java0 0
MathOnco/Mistic_code_live_cell_imaging
Language:Python
MathOnco/onubogu_spatial_analysis_of_recurrent_glioblastoma
Code used in Spatial analysis of recurrent glioblastoma reveals perivascular niche organization.
Language:Jupyter Notebook
MathOnco/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks