A Generic Open-Source Software Framework Supporting Scenario Simulations in Bioterrorist Crises

Abstract

Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of the open-source Spatiotemporal Epidemiological Modeler (STEM) simulation and modeling software for agro- or bioterrorist crisis scenarios. STEM, originally designed to enable community-driven public health disease models and simulations, was extended with new features that enable integration of proprietary data as well as visualization of agent spread along supply and production chains. STEM now provides a fully developed open-source software infrastructure supporting critical modeling tasks such as ad hoc model generation, parameter estimation, simulation of scenario evolution, estimation of effects of mitigation or management measures, and documentation. This open-source software resource can be used free of charge. Additionally, STEM provides critical features like built-in worldwide data on administrative boundaries, transportation networks, or environmental conditions (eg, rainfall, temperature, elevation, vegetation). Users can easily combine their own confidential data with built-in public data to create customized models of desired resolution. STEM also supports collaborative and joint efforts in crisis situations by extended import and export functionalities. In this article we demonstrate specifically those new software features implemented to accomplish STEM application in agro- or bioterrorist crisis scenarios.

The Kendrick modelling platform: language abstractions and tools for epidemiology

“…Closer to our approach are computational modelling tools for epidemiology such as FluTe [46], GLEAMviz [47], STEM [48] and FRED [49]. These solutions use dedicated approaches to model the transmission of infectious disease and provide a graphical user interface (GUI) to specify and visualise an epidemiological model.…”

The Kendrick Modelling Platform: Language Abstractions and Tools for Epidemiology

“…Closer to our approach are computational modelling tools for epidemiology such as FluTe [50], GLEAMviz [51], STEM [52] and FRED [53]. These solutions use dedicated approaches to model the transmission of infectious disease and provide a graphical user interface (GUI) to specify and visualise an epidemiological model.…”

“…Contrary to solutions that only focus on stochastic simulations (such as GLEAMviz [51] and STEM [52]) our platform can provide more detailed modelling thanks to the availability of agent-based simulation. Investigation of epidemics at a global scale as provided by GLEAMviz [51], STEM [52] or FRED [53] is also possible in Kendrick. A case study of meta-population model can be found in the additional file S1 provided with this publication.…”

Separation of concerns in epidemiological modelling

“…Epidemiological modellers have used a variety of tools for constructing models: general programming languages, mathematical modelling languages (Matlab, R, etc. ), libraries targeted to epidemiology such as Epipy 3 -a Python tools for epidemiology, GillespieSSA 4 -an R package for generating stochastic simulation using Gillespie's algorithms (Gillespie 1977) or dedicated modelling software as GLEAMviz (Van den Broeck et al 2011), STEM (Falenski et al 2013), FRED (Grefenstette et al 2013) etc. Such tools use different approaches to model the transmission of infectious diseases.…”