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pctk Public
A set of scripts and utilities to analyze PhysiCell/hisyBoSS simulations
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citycovid_calibration Public
Forked from sandialabs/citycovid_calibrationCode to calibrate an agent-based disease model (CityCOVID from Argonne National Lab).
Python MIT License UpdatedMar 27, 2025 -
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Introduction-to-Urban-Science-Course-Materials Public
Forked from lmbett/Introduction-to-Urban-Science-Course-MaterialsThis contains slides, code, data and reading materials for the the course.
Python Creative Commons Zero v1.0 Universal UpdatedJan 5, 2025 -
PhysiCelldFBA Public
Forked from MathCancer/PhysiCellPhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!
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scikit-mobility Public
Forked from scikit-mobility/scikit-mobilityscikit-mobility: mobility analysis in Python
Python BSD 3-Clause "New" or "Revised" License UpdatedApr 1, 2023 -
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cobrapy-tutorial Public
A tutorial on cobrapy
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pyfastcore Public
A python implementation of the context-specific model extraction method FastCore by Vlassis et al. (2014).
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corda Public
Forked from resendislab/cordaAn implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Python MIT License UpdatedMay 5, 2022 -
cobrapy Public
Forked from opencobra/cobrapyCOBRApy is a package for constraint-based modeling of biological networks
Python GNU General Public License v2.0 UpdatedApr 22, 2022 -
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chiSIM Public
Forked from Repast/chiSIMChicago Social Interaction Model (chiSIM) framework repository
C++ Other UpdatedJul 22, 2021 -
MMCAcovid19.jl Public
Forked from jtmatamalas/MMCAcovid19.jlMicroscopic Markov Chain Approach to model the spreading of COVID-19
Julia GNU Affero General Public License v3.0 UpdatedApr 26, 2021 -
ECCB2020-T05 Public
Material for the tutorial 05 of ECCB (Computational modelling of cellular processes: regulatory vs metabolic systems)
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PhysiBoSSv2-EMEWS Public
Forked from pradas/PhysiBoSSa-EMEWSEMEWS template for PhysiBoSSa
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EpiCommute Public
Forked from franksh/EpiCommuteSimulate an epidemic metapopulation model with mobility-reducing containment strategies
Python MIT License UpdatedAug 27, 2020 -
python-loader Public
Forked from PhysiCell-Tools/python-loaderPython data loader for PhysiCell digital snapshots
Python BSD 3-Clause "New" or "Revised" License UpdatedFeb 1, 2020 -
cobra_cbm_tutorial Public
This a basic tutorial on Constraint-Based Metabolic Modeling based on python-cobra
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PhysiCell-povwriter Public
Forked from PhysiCell-Tools/PhysiCell-povwriterSimple cutaway POV-Ray
C++ BSD 3-Clause "New" or "Revised" License UpdatedSep 6, 2019 -
csm4cobra Public
A set of functions and scripts to perform context-specific gene deletions in-silico experiments on genome-scale metabolic models
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consistency_analysis Public
Python implementation of the unconnected modules detection method.
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Python, R, and Matlab code relating to the iSIM manuscript
Python GNU General Public License v3.0 UpdatedJan 9, 2019 -
booleannet Public
Forked from smgroves/booleannetBoolean Network Modeling
Python Other UpdatedOct 2, 2018 -
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