Thread by @DrEricDing

⚠️CONTACT TRACING APP FROM 2014: I’ve been thinking about pandemics and epidemic contact tracing for years. Back during last big Ebola epidemic, I led a team to develop an app with goal to help CDC and health depts do contact tracing, called Germ Theory.🧵 hackreactor.com/blog/germ-theo…

2) “Ebola highlighted difficulty we have in tracking spread of infectious diseases and retroactively identifying people at risk, once a patient has been diagnosed. Epidemiologist at Harvard SPH @DrEricDing, technologist @jerseygenius, and @HackReactor staff member Ryan Stellar...

3) “have been developing a different, more effective system that combines epidemiology and technology. Stellar worked w/ a team of 5 Hack Reactor students to build an app that could, one day, save lives.”

4) “The idea behind Germ Theory, is to gather location data from users’ phones to identify high-risk areas and compute the likelihood that a given user has been infected. “What makes Germ Theory unique is that it integrates epidemiology risk algorithms," Dr. Feigl-Ding explains.

5) “The app also generates a heat map of areas at high risk for infection, so that users can take precautions. The app is careful not to publicize the identity of specific infected users. There is both a browser-based app and a mobile version.”

6) “A heat map of a hypothetical outbreak in San Francisco, using the Germ Theory app.

"Outbreak and epidemics are inherently tied to social network & geographic networks, whether locally or globally," says Dr. Feigl-Ding, who was previously a whistle blower for Vioxx drug risks

7) ...and led big data projects on obesity in Major League ⚾️, and social networks & health contagion. "As modern viruses now propagate and travel thousands of miles by ✈️ , 🚞, or 🚗 -- we need modern tools for epidemiology. This is the challenge that Germ Theory set to solve."

8) “The app could be an effective tool in fighting a wide range of infectious diseases, such as influenza, pertussis (whooping cough), or measles, and could even be used to locate the source of food poisonings.”

9) “The problem is that there is no app in place to help track and prevent the spread of disease in real time,” notes Gamble. “Say there’s an area of high risk, we wouldn’t be able to identify those areas.”

10) There are a number of technical challenges involved in this, first and foremost that the number of data points in play grows quite rapidly. Hundreds of users will produce millions of data points before long.

11) “We had to cross-reference every single one of those millions of data points to see if they had crossed an infected user,” Meurer describes.

“This becomes a computational job really fast,” says Stellar.

12) The team used Python, which they were not previously familiar, but all became proficient using self-study methods at Hack Reactor. Python is known for computational power. team set up distributed computing framework using Apache Spark, which allows them to scale efficiently.

13) “We’d be able to, with further funding, put more machines on the job,” Meurer explains. “Supriya was able to optimize it to cut our initial algorithm’s computational expense by 95%. We tried to optimize for scalable architecture and high precision.”

14) To find implied data points: “If we want to find where someone was at 4:05 p.m. and we know where they were at 4:00 p.m. and 4:10 p.m.,” Meurer writes in a blog post, “it will return a tuple of the indexes of 4:00 p.m. and 4:10 p.m. from the array of locations.”

15) The app includes a back-end dashboard, perhaps for CDC someday, in which infected users can be tagged.

In addition to Python and Spark, the project employed Node, PostGreSQL, Sequelize, Express, Ionic, Cordova, Bootstrap, Angular, Travis Continuous Integration, and Heroku.

16) ➡️Bottomline: Our Germ Theory contact tracing app was a bold idea at the time. However, when pitched, tech investors mostly laughed at the premise that Ebola or some pandemic plague would ever ravage downtown SF or NYC or DC... ha! 🙁 Nobody laughing now. But that was 2014.

17) Germ Theory is now open source code for all. Today, @jerseygenius and I welcome collaborators, such as @MIT @ycombinator @snowmaker @trvrb and others who are hoping to find ways to build upon our previous 2014 platform to reinvent more modern contact tracing app for #COVID19