A shiny app to visualise the trade-offs between school age and neonatal BCG vaccination

Data from Tycho Project (infectious diseases in US) into an SQLite database + demo analysis in Jupyter notebook

A shiny app recreating the models used in the practicals for the Intro to TB modelling course at the 2017 Union Conference

Estimating the contribution of each step of the HIV cascade to new infections

Reportes de vigilancia de VICo

The pebble game: A simple game that can be used to understand epidemics and vaccination

This repository will contain the code for generating (Java) and analysing (R programming language) a simple multi-Agent Based Model (mABM) of patients in a 2D continuous space. The idea is to simulate (i) causal diagrams for interference, (ii) ABMs, and the contagion of a disease thought a social network.

A Susceptible-Infected-Vaccinated Model for Influenza Infection Dynamics.

[OBSOLETE; USE EPICSPATIAL INSTEAD] An epidemic modelling framework for all resolutions of gridded and polygon spatial data

An epidemic modelling framework for all resolutions of gridded and polygon spatial data

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Client for the PDD platform (provided as a browser extension).

Server for the PDD platform.

Disease Modeling Workshop, UNIMAS

The scripts to reproduce the analysis of the HPI prediction paper

Slides and Practicals for the BIDD modelling short course

Parallel computing: Infectious Disease Modeling with OpenMP. Agent based modelling on Undirected Acyclic graphs.

Code to Compute Tropical Sufficient Statistics for Persistent Homology

Code and data for On the Predictability of Infectious Disease Outbreaks by SV Scarpino & G Petri