How open-source software is tackling COVID-19 coronavirus

Many open-source projects are taking on the challenge of conquering COVID-19.
Written by Steven Vaughan-Nichols, Senior Contributing Editor

In Linux and open-source circles, we're fond of saying we've changed the world. And, well, we have changed the world. But, now, we, along with everyone else, face a new challenge: COVID-19.

Here are some of the open-source projects taking on the coronavirus.

CHIME: The COVID-19 hospital impact model for epidemics

One of the biggest problems we face is how to plan and deal with the sheer number of patients that our hospitals will shortly have coming their way. This project, from the Predictive Healthcare team at Penn Medicine, is a tool that leverages SIR modeling, an epidemiological model, which computes the theoretical number of people infected with a contagious illness in a closed population over time, can help hospitals deal with capacity planning.

The newly open-sourced CHIME enables hospitals to enter information about their facility and population and then modify assumptions around COVID-19's spread and behavior. Once it has this information, hospital administrators can run a standard SIR model to project the number of new hospital admissions each day, along with the daily hospital census. They can also create best and worst-case scenarios to assist with capacity planning. 

The most important factor in this model is the doubling time. This defines how rapidly a disease spreads. Experiences in other geographical contexts suggest that doubling time may range from three to 13 days or more. You can enter your own doubling time estimate in an online version of CHIME and see what happens 

The US, according to Our World in Data, has a four-day doubling rate. That does not bode well for our future. Dr. Liz Specht estimated even at a doubling rate of six, "all hospital beds in the US will be filled by about May 10." But, at least with Chime, we can make what plans we can for dealing with this tsunami of cases. 

Pfizer open-sources software tools

Pfizer is one of the Big Pharma drug giants. Historically, it and its rivals are as friendly to open source as Steve Ballmer was when he was Microsoft's CEO. Pfizer CEO Albert Bourla is now calling on all the drug companies to join forces to battle the pandemic. 

Bourla said:

"With very little known about this virus, many are working to develop cell-based assays, viral screening, serological assays, and translational models to test potential therapies and vaccines. Pfizer is committed to making the vital tools we develop available on an open source platform to the broader scientific community and to sharing the data and learnings gained with other companies in real time to rapidly advance therapies and vaccines to patients."

We don't have any further details at this time on this proposal. Still, just the fact that Pfizer is opening its code is significant. 

Facebook open-sources COVID19 medical supplies

No, Facebook, isn't doing anything directly with open-source software and the virus. This is a Facebook group devoted to creating an open-source ventilator, and it has widened its reach to open-sourcing other medical supplies. Ventilators are essential for taking care of people struggling to breathe in serious cases of coronavirus. The US has approximately 100,000 ventilators, and we may need many more. Other groups, such as EndCoronavirus, are also working on open-source ventilators. 

Ventilators may look simple. They're not. Still, the need is great and, hopefully, something can be done in time to create a truly useful ventilator. If not, the efforts to open-source other medical aids won't go amiss. 


This is an open-source program for the real-time tracking of pathogen evolution such as COVID-19. It's used to work out a disease's family history, which, in turn, can give us an idea of how it will turn out tomorrow. Previously, it had been used on Ebola; now, armed with coronavirus genetic data from Global Initiative on Sharing All Influenza Data (Gisaid), the project is tracking the coronavirus.

According to a Wired report, researchers using this software were able to establish that the virus was shared around Seattle as early as Jan. 20.  That was when people still thought there had to be a direct connection with a victim from Wuhan to be infected.

Only time will tell how useful any of these projects will turn out to be. That said, some of them may prove essential in the weeks and months ahead as we cope with the coronavirus.

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