GLEAMviz Simulator

GLEAM, the Global Epidemic and Mobility modeler

The GLEAMviz project builds on long-running research on the computational modeling of epidemics at the Computational Epidemiology Lab at the ISI Foundation and the Center for Complex Networks and Systems Research at Indiana University, USA, under the direction of Alessandro Vespignani and Vittoria Colizza.

GLEAM is a Global Epidemic and Mobility modeler for simulating the global spread of epidemics, considering detailed sociodemographic and population mobility data in a spatially structured stochastic disease approach. This system is used to project the spreading of ongoing epidemics, such as the 2009 Influenza A H1N1 virus outbreak, and asses the impact of various intervention scenarios such as travel restrictions or the preventive administration of antivirals or vacinations. The following movie provides an overview of GLEAM.

GLEAMviz Simulator application

Building on this model we developed a fully integrated client-server system, called the GLEAMviz Simulator system, which allows its users to define, submit and visualize simulations of world-wide epidemic outbreaks. The client application, for which I am the lead developer, is used to design the compartmental model of the investigated disease, define the simulation parameters, submit the simulations for execution on the server, and interactively visualize the results retrieved from the server. The following diagram provides an overview of the workflow of a complete simulation setup, execution and visualization process, and the involved GLEAMviz Simulator components.

The following movie provides an overview of the functionality provided by the GLEAMviz system.

This application was initially used in-house as well as by scientists at the European Commission's Joint Research Center. As of July 2010, a publicly accessible version of the complete system has been made available online.

An improved visualization was provided in v2.6, released in November 2010. The following movie provides some examples of how this new visualization shows the number of new cases at the cell-level, instead of the basin-level incidence.

The user can now also select from a number of backdrop maps onto which the visualization is projected, details of which are shown in the following figure. The left option is based on the NASA Blue Marble map, while the other two provide a more neutral base onto which the cell-level cases can be inspected with greater visual accurracy.

Samples of the three backdrop maps from which the user can choose.

Application components

The following images show the principal components of this application, which was developed for the cross-platform Adobe AIR runtime.

The main window with the current and previously executed simulation management interface.

The compartmental model builder, which provides a visual modeling tool for designing arbitrary compartmental models, ranging from simple SIR models to complex compartmentalizations in which, for instance, multiple interventions are considered and/or disease-associated complications.

The simulation wizard provides a sequence of panels that lead the user through the configuration of a simulation.

The interactive visualization of the geotemporal evolution of the epidemic by means of a multi-scale map and a set of incidence curve. The user can select the day using the slider or can hit play to see the spreading unfold as an animation.

Next to this application targetted at epidemiologic scientists and healthcare professionals, we also developed the Epidemic Planet, an interactive exhibit meant to disseminate this research to a broader audience.

GLEAMviz 3.0

GLEAMviz version 3 was released in the spring of 2012. This version provides the Simulation Builder, a new interface for setting up the simulations that integrates the model builder with the simulation wizard.

Simulation Builder interface.

This new version also provided two new visualizations. The first is based on the SPaTo visualization developed by Christian Thiemann. I adapted this visualization to fit the specifics of the infection spreading data generated by GLEAM, and reimplemented it for integration in GLEAMviz. The visualization shows the shortest-path tree among the cities with airports, either using a geographic layout or a concentric layout (with or without logarithmic scaling). Animated transitions are provided when the user changes the layout.

SPaTo visualization: geographic layout

SPaTo visualization: concentric shortest-path tree layout

The second new visualization uses an interactive 3D representation of the world. The incidence spreading is shown as an animated texture, while the initial seedings are shown as 3D arcs.

GLEAMviz 3D Globe visualization

Accompanying this new release I also worked on a new gleamviz.org website and promotional material.

New GLEAMviz.org website

More information:

• gleamviz.org: the GLEAM project home.
• gleamviz.org/simulator: The GLEAMviz Simulator home.

Publications

• The GLEAMviz computational tool, a publicly available software to explore realistic epidemic spreading scenarios at the global scale. Wouter Van den Broeck, Corrado Gioannini, Bruno Goncalves, Marco Quaggiotto, Vittoria Colizza and Alessandro Vespignani. BMC Infectious Diseases 2011, 11:37doi:10.1186/1471-2334-11-37.
• Modeling the critical care demand and antibiotics resources needed during the Fall 2009 wave of influenza A(H1N1) pandemic
  Duygu Balcan, Vittoria Colizza, Andrew C. Singer, Christos Chouaid, Hao Hu, Bruno Gonçalves, Paolo Bajardi, Chiara Poletto, José J. Ramasco, Nicola Perra, Michele Tizzoni, Daniela Paolotti, Wouter Van den Broeck, A.-J. Valleron, and Alessandro Vespignani. PLoS Currents: Influenza. 2009 Dec 4, RRN1133.
• Estimate of Novel Influenza A/H1N1 cases in Mexico at the early stage of the pandemic with a spatially structured epidemic model. Vittoria Colizza, Alessandro Vespignani, Nicola Perra, Chiara Poletto, Bruno Gonçalves, Hao Hu, Duygu Balcan, Daniela Paolotti, Wouter Van den Broeck, Michele Tizzoni, Paolo Bajardi, and José J. Ramasco. PLoS Currents: Influenza. 2009 Nov 11:RRN1129.
• Modeling vaccination campaigns and the Fall/Winter 2009 activity of the new A(H1N1) influenza in the Northern Hemisphere. Paulo Bajardi, Chiara Poletto, Duygu Balcan, Hao Hu, Bruno Goncalves, José J. Ramasco, Daniela Paolotti, Nicola Perra, Michele Tizzoni, Wouter Van den Broeck, Vittoria Colizza and Alessandro Vespignani. Emerging Health Threats Journal 2009, 2:e11. doi: 10.3134/ehtj.09.011.
• Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility. Duygu Balcan, Hao Hu, Bruno Goncalves, Paolo Bajardi, Chiara Poletto, José J. Ramasco, Daniela Paolotti, Nicola Perra, Michele Tizzoni, Wouter Van den Broeck, Vittoria Colizza, and Alessandro Vespignani. BMC Medicine 2009, 7:45.
• More GLEAM publications