{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"Newsletter-Bibliography","owner":"MathOnco","isFork":false,"description":"LaTeX bibliography of the \"This week in Math Onco\" newsletter (https://mathematical-oncology.org/newsletter)","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"TeX","color":"#3D6117"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,1,2,0,1,1,1],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-20T17:54:58.229Z"}},{"type":"Public","name":"valis","owner":"MathOnco","isFork":false,"description":"Virtual Alignment of pathoLogy Image Series","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":33,"starsCount":96,"forksCount":23,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-10T06:50:24.437Z"}},{"type":"Public","name":"PARPi_Model","owner":"MathOnco","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,1,0,0,0,4,0,0,0,0,2,0,0,0,0,0,5,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-09T05:27:35.185Z"}},{"type":"Public","name":"Lenia-in-HAL","owner":"MathOnco","isFork":false,"description":"Repository for Lenia framework, implemented in Hybrid Automata Library (HAL)","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-04T15:05:36.970Z"}},{"type":"Public","name":"multiMets","owner":"MathOnco","isFork":false,"description":"grows and seeds multiple metastases and treats them with different therapeutic strategies","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-08T14:42:40.731Z"}},{"type":"Public","name":"HAL","owner":"MathOnco","isFork":false,"description":"HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needs","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":1,"starsCount":34,"forksCount":6,"license":"MIT License","participation":[0,0,0,0,0,3,0,0,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-08T00:55:20.698Z"}},{"type":"Public","name":"NeoPredPipe","owner":"MathOnco","isFork":false,"description":"Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":7,"starsCount":97,"forksCount":27,"license":"GNU Lesser General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-06T05:49:04.216Z"}},{"type":"Public","name":"onubogu_spatial_analysis_of_recurrent_glioblastoma","owner":"MathOnco","isFork":false,"description":"Code used in Spatial analysis of recurrent glioblastoma reveals perivascular niche organization.","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-23T21:08:32.128Z"}},{"type":"Public","name":"DRL_Personalized_AT","owner":"MathOnco","isFork":false,"description":"Learning to Adapt - Deep Reinforcement Learning in Treatment-Resistant Prostate Cancer (https://doi.org/10.1101/2023.04.28.538766)","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-22T01:59:20.817Z"}},{"type":"Public","name":"densityDependentSelection","owner":"MathOnco","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-05T10:25:14.389Z"}},{"type":"Public","name":"ploidyEvolution","owner":"MathOnco","isFork":false,"description":"A general N-compartment model of ploidy states is developed and analyzed.","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":7,"starsCount":1,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-07T21:04:41.952Z"}},{"type":"Public","name":"Mistic_code_live_cell_imaging","owner":"MathOnco","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-02T03:56:41.969Z"}},{"type":"Public","name":"MIEmodel","owner":"MathOnco","isFork":false,"description":"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).","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-09-13T19:59:22.910Z"}},{"type":"Public","name":"Mistic","owner":"MathOnco","isFork":false,"description":"Multiplexed image tSNE visualizer","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":29,"forksCount":5,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-25T16:00:05.238Z"}},{"type":"Public","name":"HomeostaticEpidermis","owner":"MathOnco","isFork":false,"description":"Homeostatic Epidermis – PNAS Full Codebase","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-12T12:38:39.144Z"}},{"type":"Public","name":"Curvogram","owner":"MathOnco","isFork":false,"description":"Method for plotting histograms on a curve using a West Transform","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":10,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-04-26T19:53:29.503Z"}},{"type":"Public","name":"strobl2021_space_modulates_competition_AT","owner":"MathOnco","isFork":false,"description":"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.","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-04-25T19:15:10.680Z"}},{"type":"Public","name":"AT_costOfResistance_LVModel","owner":"MathOnco","isFork":false,"description":"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.","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-03-22T02:52:43.142Z"}},{"type":"Public","name":"gatenbee_2022_immunosuppressive_niche","owner":"MathOnco","isFork":false,"description":"Code to used to simulate eco-evolutionary tumor-immune dynamics as described in https://www.researchsquare.com/article/rs-799879/v1","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-02-04T18:29:16.302Z"}},{"type":"Public","name":"staged-recipes","owner":"MathOnco","isFork":true,"description":"A place to submit conda recipes before they become fully fledged conda-forge feedstocks","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":4604,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-25T19:19:17.284Z"}},{"type":"Public","name":"EvoFreq","owner":"MathOnco","isFork":false,"description":"Evolutionary frequency visualization tool of temporal data","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":1,"issueCount":3,"starsCount":21,"forksCount":3,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-25T04:07:32.618Z"}},{"type":"Public","name":"Gattaca","owner":"MathOnco","isFork":false,"description":"Base pair resolution mutation tracking for somatic evolution studies using agent based simulations","topicNames":[],"topicsNotShown":0,"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-12-20T16:07:51.927Z"}},{"type":"Public","name":"flipflopspatialmodel","owner":"MathOnco","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-31T22:16:50.385Z"}},{"type":"Public","name":"flipflopblood","owner":"MathOnco","isFork":false,"description":"Whole Blood Simulations of Hematopoietic Stem Cells","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-31T21:52:32.250Z"}},{"type":"Public","name":"IsoMaTrix","owner":"MathOnco","isFork":false,"description":"A framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations (MATLAB, Java)","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":9,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-04-29T19:31:19.693Z"}},{"type":"Public","name":"adaptivePGG","owner":"MathOnco","isFork":false,"description":"C++ code developed to study the emergence of dimorphic populations in nonlinear public good games","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-04-08T15:00:33.075Z"}},{"type":"Public","name":"multiscaleGBM","owner":"MathOnco","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-02-09T17:36:07.982Z"}},{"type":"Public","name":"tissue-structure-modulates-evolution","owner":"MathOnco","isFork":false,"description":"Code repository associated with the paper \"Tissue structure modulates evolution: premalignant sweeps precede neutral expansion\"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":2,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-01-16T04:45:29.554Z"}},{"type":"Public","name":"CARTecology","owner":"MathOnco","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Mathematica","color":"#dd1100"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-11-06T17:20:21.537Z"}},{"type":"Public","name":"immune-checkpoint-kickstart","owner":"MathOnco","isFork":false,"description":"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.","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-10-21T21:59:55.661Z"}}],"repositoryCount":39,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"mirror","text":"Mirrors"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}