Repositories list

• Uganda-phase-1

  Public
  C++

  •2•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• malasim

  Public
  C++

  •

  MIT License

  •1•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• Temple-Malaria-Simulation

  Public
  Spatial individual-based model of malaria with a focus on drug resistance evolution.

  C++

  •3•2•0•0•Updated Oct 9, 2024Oct 9, 2024

• PSU-CIDD-MaSim-Support

  Public
  Various internal scripts used in conjunction with the malaria simulation across projects.

  Python

  •

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

  •4•3•1•0•Updated Feb 6, 2024Feb 6, 2024

• Temple-Kenya

  Public
  Source files used to study malaria in Kenya using spatial individual-based modeling.

  0•0•0•0•Updated Feb 4, 2024Feb 4, 2024

• malariaibm-spatial-BurkinaFaso-2022

  Public
  Complete source code and intermediary files to accompany the manuscript.

  public-healthmalariaburkina-faso+ 2individual-based-modelspaital-modeling

  C++

  •0•0•0•0•Updated Jan 30, 2024Jan 30, 2024

• malariaibm-generation-of-MDR-mutants

  Public
  Repo for malaria individual-based simulation study of which treatment strategies present more risk in generating multi-drug-resistant mutants earlier

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 7, 2024Jan 7, 2024

• malariaibm-spatial-Rwanda-561H

  Public archive
  Complete source code and intermediary files to accompany the manuscript published in Nature Medicine.

  simulationrwandapublic-health+ 3malariaindividual-based-modellingspaital-modeling

  C++

  •0•0•0•0•Updated Dec 15, 2023Dec 15, 2023

• malariaibm-MDA-2018WHOERG

  Public
  repository with code, output, and figures for manuscript on antimalarial drug-resistance evolution during mass drug administration (MDA). This work was commissioned for a WHO Evidence Review Group (ERG) in September 2018.

  C++

  •

  MIT License

  •0•0•0•0•Updated Nov 27, 2023Nov 27, 2023

• tropicalflu-03FL-10years-communityILI-HCMC

  Public
  R

  •0•0•0•0•Updated Oct 3, 2023Oct 3, 2023

• malariaibm-TACT-2023

  Public
  Complete source code and config files to accompany the manuscript published in Nature Communications

  C++

  •0•0•0•0•Updated Sep 6, 2023Sep 6, 2023

• PSU-CIDD-Malaria-Config

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 5, 2023May 5, 2023

• malariaibm-interrupted-feeding-and-recombination

  Public
  C++

  •

  MIT License

  •0•0•0•0•Updated Apr 16, 2023Apr 16, 2023

• malariaibm-movement-BurkinaFaso-2022

  Public archive
  Complete source code and intermediary files to accompany the manuscript published in Scientific Reports.

  burkina-fasoindividual-based-modelspaital-modeling

  C++

  •0•1•0•0•Updated Jan 22, 2023Jan 22, 2023

• PSU-CIDD-GIS

  Public archive
  Various internal GIS tools used in conjunction with the malaria simulation across projects.

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 17, 2022Oct 17, 2022

• malariaibm-spatial-BurkinaFaso-2021

  Public archive
  Complete source code and intermediary files to accompany the manuscript published in PLOS Global Public Health.

  public-healthmalariaindividual-based-modelling+ 2burkina-fasospaital-modeling

  C++

  •1•0•0•0•Updated Jul 29, 2022Jul 29, 2022

• covid19-omicron-origins-recombination

  Public
  Python

  •

  MIT License

  •1•1•0•0•Updated Jul 8, 2022Jul 8, 2022

• covid19-attackrate-RI-MA-CT

  Public
  code for inferring attack rate and vaccination of seropositives in southern New England, first 15 months of pandemic

  C++

  •1•1•0•0•Updated Dec 6, 2021Dec 6, 2021

• covid19-reopening-RI-MA-PA

  Public
  public repository for PSU CIDD (Hanks, Pritchard, Boni) modeling efforts around the coronavirus pandemic

  R

  •1•3•0•0•Updated Nov 22, 2021Nov 22, 2021

• seroepi-02FL-influenza-vietnam-PCA

  Public
  Analysis and data for paper on principal components analysis on human antibody profiles to influenza virus

  MATLAB

  •0•0•0•0•Updated Oct 24, 2021Oct 24, 2021

• bonilab.github.io

  Public
  JavaScript

  •0•0•0•0•Updated Jul 30, 2021Jul 30, 2021

• covid19-vaccine-allocation-RI-MA

  Public
  Model evaluation of SARS-CoV-2 vaccine allocation in Rhode Island and Massachusetts in Spring 2021

  Shell

  •0•1•0•0•Updated May 19, 2021May 19, 2021

• malariaibm-MMC-WP2-partnerdrugresistance

  Public
  C++

  •

  MIT License

  •0•0•0•0•Updated Mar 11, 2021Mar 11, 2021

• PSU-CIDD-MMC

  Public
  Configuration and related files for MMC benchmarking

  MATLAB

  •0•0•0•0•Updated Aug 26, 2020Aug 26, 2020