In Dan Brown's bestselling thriller, Inferno, world-renowned art historian Robert Langdon raced across southern Europe, trying to prevent the spread of a highly infectious novel virus that threatens to circle the globe in less than a week.
In 2020 not far from the filming locations, Italy became one of the worst affected places by the novel Coronavirus (COVID-19) pandemic.
The Spatiotemporal Epidemiological Modeler (STEM), an Eclipse Technology project and tool to design, simulate, and analyze compartmental models of infectious disease, could play a vital role in understanding a similar pandemic as public health officials struggle to intervene. Unfortunately designing a new disease in STEM can be complicated, it would take over a week just to prepare the model – long after the world’s population is infected. Luckily building on top of existing models for similar diseases can help and new wizards or generation features in STEM further increase efficiency.
In this talk, we introduce and demo STEM 4.0 - including new tools to simplify disease model creation for scientists and public health experts.
Our primary goal in STEM is to create a tool for subject matter experts – epidemiologists and other public health experts. We accomplish this with the following new features: the STEM Model Generator, Graph based simulation engine, Expression Language, Wizards to create projects, graphs, models, scenarios, sequencers or diseases and a Visual Editor. The Model Generator uses EMF and JET to greatly simplify the process of designing and generating the basic disease model plug-in structure and boilerplate. The Expression Language, an Xtext-powered domain specific language, assists scientists implementing the differential equations that drive a compartment model and provides easy access to disease parameters and STEM’s data APIs. Finally the Visual Model Editor, built on GEF and Xtext, allows scientists to visually draw and edit the compartments (states), transitions, and equations that fully define a new STEM disease. These new features combine to help us move toward the goal of making STEM a powerful tool for scientists, leveraging the features of Eclipse tools while hiding complexity.
We will demonstrate the available Sars-CoV-2 models in a live demo and explain, which one works best for a particular purpose. In addition, we’ll talk about how scientists at Germany's Federal Institute for Risk Assessment (BfR), a STEM contributor, use STEM in their workflows to combat food-borne disease outbreaks in Germany. And what other disease models from Ebola to Flu or Malaria exist beyond COVID-19.
So, come and see how the STEM project is using the latest Eclipse technologies to make studying diseases easier for scientists – and doing our part to help save the world!