Open source software amidst a pandemic
by Samuel Kirby Aguilar
It’s a running joke on the internet that much of the software development community’s response to the pandemic has been limited to joining hackathons only to come up with another tracker. There’s some truth to this. After all, among other reasons for COVID-19 tracking being ineffective, the decentralized nature of tracking in some countries have encouraged the development of different trackers for seemingly every locale.
However, pandemic development efforts (including hackathons!) have produced so much more than trackers. In particular, open source has been instrumental in the global effort against COVID-19.
Share your code
But what exactly is open source? As opensource.com itself puts it, open source refers to anything that can be modified and shared, because its design is publicly accessible. While the term is often used for software, it doesn’t stop there either; more on this later!
So how has open source helped the fight against COVID?
Modeling and other forms of publicly available mathemagic
Earlier into the pandemic’s timeline, the exponential growth of active cases and hospitalizations, particularly in the United States and Italy, created a ventilator crisis. There simply was not enough ventilators to go around. This certainly wasn’t limited to these breathing devices. Because of a lack of foresight about how many of what would be needed, be it space for beds or test kits, many hospitals have failed to meet the rapid progression of the virus.
Penn Medicine’s Predictive Healthcare Team developed CHIME (COVID-19 Hospital Impact Model for Epidemics) as a tool to help hospitals project how many people they’d have to accommodate in the near future. Specifically, the application uses an epidemiological modeling technique that researchers use to study the transmission of an infectious disease. With the said mathematical model, the software takes in user-provided parameters, such as regional population, to provide estimates for hospitalizations, ICU admissions and ventilators required.
CHIME was open-sourced last March 2020 in response to the pandemic. It’s not the only one of its kind either. SORMAS (Surveillance Outbreak Response Management and Analysis System), an open source eHealth system for optimizing monitoring processes for infectious diseases, has also been adapted for COVID-19. It was initially created for the mid-decade Ebola virus epidemic, and has since been adapted for numerous other infectious diseases. It was open-sourced two years after its initial development in 2014.
Perhaps due to it being a relatively new project, CHIME’s impact has only been documented modestly. The documentation only mentions that they “can not list users but have had traffic from over 150 countries.” SORMAS’s website notes its rapid deployment to multiple countries, particularly Ghana and Nigeria, for detection and control of COVID-19. Both countries boast a top 40 spot in case recovery rate by country, with Ghana at #11.
Truckloads of trackers
Despite the saturation of COVID tracking apps, data that comes from carefully monitoring COVID cases per locale has still been absolutely indispensable for the pandemic response. It provides data for aforementioned modeling, and localized responses to the disease. Localeai and its corresponding Coronavirus Tracker API are just a few examples of the many open source tracking projects that allow developers to help through code.
The larger and more well-known trackers, however, are those backed by governments. The Corona Warn App, used for contact tracing in Germany, has seen over 14 million downloads as of July 2020. Although Germany has been struggling with its second wave as of the time of writing, its initial response to the virus was previously praised as the best in Europe.
Hardware too
That’s right, open source isn’t limited to software! There have been many hardware projects that take from the vast knowledge of, well, everyone. While the process is certainly a bit different from coding and making a pull request on GitHub, hardware projects have been making a difference.
These projects often aim to take expensive hospital-grade equipment and make them much cheaper to produce. Such is the case in Josh Perfetto and Jessie Ho’s Chai OpenPCR which sought to provide an affordable, open-source alternative to traditional real-time PCR (Polymerase Chain Reaction) machines. These are used for diagnosing COVID-19, but are quite costly at around $30,000. Although Chai has since ceased production–opting instead to sell a more expensive but more powerful, still openly-sourced alternative in Open qPCR–-the source still remains for anyone who needs it. Notably, the much cheaper pocketPCR by Gaudi Labs also takes an open-source hardware approach to the same problem.
Open-source hardware doesn’t stop at PCR tests. The great demand for ventilators has also given rise to projects such as the Open Lung Emergency Medical Ventilator and the Pandemic Ventilator. While not often talked about in discussions about open source, hardware has been instrumental in the battle against the virus.
Where do I start?
Perhaps the greatest thing about open source is that you can start as soon as you’d like! Look through the issues raised in the GitHub pages of whichever project you’d like to contribute to, and see if you can start making some pull requests. For instance, SORMAS is currently being maintained actively. Many projects are also available and need your help to localize it to your community. You can also find open-source initiatives like awesome-coronavirus and opencovid19 to look for projects that are more your speed.
The role of computer scientists and developers during this pandemic is a crucial one. Lives are put at stake, with the burden partially but undeniably on the hands of those who code for a living. Unlike many other professions, however, ours is one that is innately collaborative, almost democratic. Even for the college code monkey, making a difference could be one pull request away. For the non-coding monkeys out there, contributions aren’t strictly code either. Open-source hardware projects are built upon research and insight from both experts and people who just want to help.
Now is the best time to put open source to work.
