Why We Need More Open-Source Epidemiological Tools

September 3, 2019

A newer software called STEM offers an accessible, customizable tool for outbreak response and preparedness efforts.

In the middle of an outbreak, having the right tools can make all the difference. Epidemiological resources, such as modeling systems, are useful but can be costly and have limited use across large teams.

A newer tool, though, is changing the game in outbreak response and modeling. The Spatiotemporal Epidemiologic Modeler (STEM) is an open-source software that is available to the global health community. This is not just a rigid instrument against disease, in that it is not pre-set to a specific disease or environment and has the flexibility for hundreds of variations.

“STEM has been used to study variations in transmission of seasonal influenza in Israel by strains; evaluate social distancing measures taken to curb the H1N1 epidemic in Mexico City; study measles outbreaks in part of London and inform local policy on immunization; and gain insights into H7N9 avian influenza transmission in China. A multi-strain dengue fever model explored the roles of the mosquito vector, cross-strain immunity, and antibody response in the frequency of dengue outbreaks,” the authors of a briefing in Health Security wrote.

The latest version was just released this year and allows users to really refine it based on their needs. From Ebola in West Africa to Salmonella in Germany, it has been used by agencies and universities alike. In fact, one of the authors, Nereyda Sevilla, PhD, used it for her doctoral dissertation work to model SARS, H1N1, and pneumonic plague in air travel in order to assess its role as a vector in the transmission of infectious diseases. What makes STEM so helpful to users is not only that it’s open access, but also its wide application and historical usage in tracking multi-strain vector-borne diseases, human behavioral responses, earth science data, pathogens from farm to fork, and so much more.

I was fortunate to chat with Dr. Sevilla, who is an aerospace physiologist, about her experiences working with STEM and also how frontline users can harness its capabilities. "The open-source nature of STEM allowed for collaborations to help solidify my air travel models, which then I was able to contribute back in terms of models and validation for others to use and expand on," she said. "I found that air travel will contribute in the spread of longer lasting diseases like SARS and H1N1, but is not a factor in diseases such as Ebola and pneumonic plague."

Judith Douglas, a graduate of the Bloomberg School of Public Health at Johns Hopkins and a lead technical writer at IBM for more than 10 years, served as lead author of the paper and noted that “the work reported in this paper reflects the power of STEM as an open-source platform available for free for a diverse community of researchers to adapt and use in studying public health threats.”

Overall, STEM offers an accessible, customizable tool for outbreak response and preparedness efforts. Such tools should be more readily available to help guide change, whether it be an outbreak of Ebola in the Democratic Republic of the Congo or a hospital outbreak of Clostridioides difficile.