An open-source artificial pancreas

Dana Lewis said that her keynote at linux.conf.au 2019 would be about her journey of learning about open source and how it could be applied in the healthcare world. She hoped it might lead some attendees to use their talents on solutions for healthcare. Her efforts and those of others in the community have led to a much better quality of life for a number of those who suffer from a chronic, time-consuming disease.

She began with a well-known joke in hacker circles ("there are 10 kinds of people in the world ..."), but she added a twist. Beyond those who know binary and those who don't, there are also another 10 kinds of people: those who can produce their own insulin and those who can't. Lewis has type 1 diabetes, so she "just" needs to add insulin to her system because her pancreas does not produce it, but it is not quite that simple. Getting diagnosed with a chronic disease is "like getting struck by lightning", she said; there is no time to prepare and you know that everything will be different from that point forward.

Ups and downs

There is more to it than just eating right, exercising, and adding insulin. Stress, excitement, and adrenaline all factor into her blood sugar levels. She was excited and a bit stressed to give her keynote, which meant that her blood sugar level was going up. It is hard to measure the proper insulin dose to counteract the experience of giving a talk to "a roomful of people really early in a different time zone". It is further complicated by the fact that things that sometimes elevate blood sugar also sometimes lower it.

If you look at the graph of a diabetes patient's blood sugar, it will go up and a down a fair amount. Beyond that, "insulin is not magic"; it takes 60-90 minutes for it to start bringing down blood sugar, while eating makes it rise in as little as 15 minutes. She noted that access to insulin is not a given, though, since there are many parts of the world, especially in developing countries, where it is not available.

Some patients have tools that make diabetes management easier. She has a continuous glucose monitor (CGM) to measure her blood sugar every five minutes and an insulin pump that delivers a configured amount of insulin continuously. Those sound great, she said, and they are, but there is still a lot of manual work required.

A patient has to pull out the CGM and press a button to see the latest reading and the trend, they then need to look at the pump and see what it has been delivering. After that, they need to calculate what action is needed based on the readings and their current and planned activities (e.g. eating, exercising, or giving a talk). They do that "over and over and over and over again" throughout the day. These decisions are not all about insulin either, but also about whether they should eat, what kind of exercise they should do, what they should eat, and so on. It is a lot of work and hard to get right; that is why people's blood sugar graphs have lots of ups and downs

She showed some sample graphs in part because she wanted to point out that it is actually difficult to get access to that data. The only application approved by the US Food and Drug Administration (FDA) to get the glucose readings from her device only works on Windows—and she has a Mac. Meanwhile, the CGM and pump are from different manufacturers, so they don't talk to one another, which is quite common in the medical-device world. That leaves the human in the middle to make all of the decisions and take any required actions.

Alarms

Lewis said that she is "the world's best sleeper"; she sleeps for a long time and deeply. The CGM has an alarm that is meant to wake her when her blood sugar levels are too low, but there is no way to change the volume or sound it makes. Because of "alarm fatigue", where over time the brain stops alerting because it has gotten used to an alarm sound, and her deep sleeping, she can sleep right through the alarm. That made her afraid to go to sleep because she might not hear the alarm and stop the insulin pump from providing more insulin, thus lowering her blood sugar further. You can die from diabetes even if you do everything right, she said; not being able to trust that your device will wake you up when an adjustment is needed is intolerable.

She got so fed up with the problem that she started looking for other ways to create the alarm. In 2013, she and her now-husband, Scott Leibrand, found someone on Twitter who had a way to get information out of the CGM and send it to a server; he used it to monitor his son's blood sugar from afar. They were able to get the code from him and used it to send alarms to her phone when needed. The data was extracted by a Windows program running on an old laptop at her bedside and was sent to an application in the cloud that pushed the alarms out. In the first month, she got many alarms that she actually woke up for; "it was fantastic".

They also created a dashboard on the web that she can easily read and make sense of when she is woken in the middle of the night. It has buttons that she can click to indicate the action that she took, which is helpful for her parents and others who are part of her "secondary line of defense". Brains are a "little weird" when your blood sugar is low, she said, so the dashboard could alert others if she didn't wake up and take the right action (i.e. press the right button) when the alarm went off. She thought the dashboard, which they jokingly called "DIYPS" (for do-it-yourself pancreas system), was the greatest thing ever.

Sleeping through the CGM alarm is a common problem for those suffering from diabetes, she said. Her new open-source awareness meant that she wanted to share her solution with others. They had learned a lot about open source and medical devices, including finding out that the FDA "frowns on distributing code that looks like a medical device", even if it's not a medical device. So they did not end up releasing the code for the dashboard/alarm.

Auto-pancreas

As they started looking around at what others were doing in the open-source diabetes world, though, they found someone who had figured out how to talk to a specific model of insulin pump, which turned out to be the one that she had. With that, they realized that the necessary tools were available to create a closed-loop artificial pancreas. You can take those two dumb devices (CGM and insulin pump), add a Linux system (in their case, a Raspberry Pi), a USB radio to talk to the pump, and a battery—you end up with an artificial pancreas system.

In the manual method, a human needs to take in data, do some calculations on it, and change settings on another device—many times a day. That is a job for a computer, she said. The system is automated, but that does not mean that a human cannot intervene to change things as needed. She showed before and after graphs; the after graph was noticeably flatter, with fewer swings—which is the goal. That was met with much applause from attendees.

The automatic pancreas is not a cure, but it can make a huge difference in people's quality of life. She was helped by multiple people along the way, so she knew the system needed to be released as open source. OpenAPS (open-source artificial pancreas system) is the project that was formed to provide information so that others can build their own devices. Lewis did not return to the FDA "problem" in her talk, but the OpenAPS FAQ notes that the FDA only regulates commercial products that are sold; OpenAPS simply provides information for those who want to build and try the system for themselves.

The DIYPS was an open-loop system, since it simply gave her the information (and recommended action), but she had to make it happen. The newer, closed-loop system took her out of that loop (though she still had the ability to change things if needed); they were able to translate the calculations she normally did into code that could run on every update from the CGM. Their highest goal was safety, so when they started documenting the algorithm at OpenAPS, one of the most important pieces was to document how the system could fail.

There are numerous failure modes (e.g. batteries die, CGM pulled out, pump disconnected, insulin runs out, etc.) but OpenAPS is designed to handle them. When OpenAPS shows the design to new people, who inevitably have a large number of "what if" questions, they are impressed with its safety orientation. That really shouldn't be a surprise, she said, since those who are trying to solve the problem have the disease and have been working out how to deal with it since they were diagnosed. Those who have diabetes "have to figure it out or they don't stay alive".

One thing that developers outside of the project often focus on is how OpenAPS is talking to the insulin pump, she said. The currently targeted pump is an older version of a particular pump brand that has been recalled due to a security vulnerability. But that vulnerability is what allows OpenAPS to talk to the pump over the radio, so it is required that they use this insecure device. That is what allows the loop to be closed.

The software that OpenAPS uses has conservative defaults for various settings. There are also hardware limits on the amount of insulin that can be given, but the software starts with low levels and does not increase them without some action from the user. In addition, while it is monitoring every reading from the CGM, it does not take actions based on one outlying data point; it looks at the trends and is prepared for anomalous or missing data.

The insulin pump has a "basal" rate, which is the base amount of insulin it will dose in the absence of other input. That rate will continue even if blood sugar goes low, which is bad. OpenAPS operates by sending a temporary basal rate adjustment command that only lasts for 30 minutes. If the system is working, another adjustment will be made within that window, but if not, the pump will return to its default state.

She referred interested people to the OpenAPS web site, where there is a plain-language reference design. There have been many non-technical people who have come to the site over the years to try to learn how they can build an artificial pancreas for themselves. In many cases, it takes a lot of convincing to get them to believe that they can do this for themselves. The plain-language description is understandable to those who are already treating their diabetes and the idea is that OpenAPS has just moved that algorithm into a computer. There is also an open-source reference implementation (under the MIT license) available on GitHub.

Results

She has been "looping for four years" and there are now over 1000 people with DIY closed-loop systems in the world including, she said, some in the room. That means that there are over nine million hours of DIY closed-loop experience at this point—using conservative numbers for people and hours. That is significant because many of the "big fancy clinical trials" have 150,000 hours of testing before they are declared ready for use. OpenAPS has learned a lot and its users have chosen to stay with the DIY system for a long time.

"I refuse to let all this beautiful data go to waste", she said. OpenAPS has its own data commons as part of the Open Humans project. OpenAPS users can volunteer their data to be added to the anonymized data set, which she said she does not want companies to ignore when they are working on projects for diabetes. Anyone who has an interest in the data can get access to it and learn from it.

She relayed two anecdotes that she thought encapsulated many of the reasons that people are choosing to use APS. One was a man in Finland whose young son had diabetes; they went from 4.5 manual interventions per day to 0.7/day after using OpenAPS. Each of those interventions is time consuming and burdensome for the caregivers and the child, so getting to less than one a day on average makes a huge difference. Another user had a son with diabetes who needed 420 visits to the school nurse during his 4th-grade year (e.g. before lunch or gym, high or low blood sugar events). Once he was using OpenAPS in his 6th-grade year, that dropped to five visits: three for low blood sugar after gym and two from equipment failures.

The OpenAPS "rig" can communicate with both Android and iOS devices. "You can text your pancreas ... you really can", she said, or use an assistant like "Siri" to send input to the rig. You can also use a smartwatch to enter information, which is her preferred way to do it. Just using three buttons allows her to change the amount of insulin being delivered or to enter the food that she is eating, which is much more discreet than fumbling around with her medical device. That allows her to participate in job interviews, for example, without making her diabetes the focus of the discussion if she needs to provide some input to her pancreas.

As with many open-source projects, lots of great ideas and code have come in from new people. They are often surprised when presenting their new idea or use case that Lewis and other OpenAPS developers are enthusiastic about the idea but not able to make it happen for various reasons—the suggestion that the new person "should go do it" is temporarily astonishing to them. But that is how things work in open source.

The earliest system was based on the first Raspberry Pi, but it made for a bulky system with a large battery; the radio had a short range as well. One potential user said that he needed something smaller for his wife so he started looking into an Intel Edison-based device; he found a radio that would work with it and wrote some code to make it talk to the pump. Another community member had a hardware shop and helped design a board for the rig, which is what she uses today. It is much more compact and uses less power.

Unfortunately, Intel has discontinued the Edison, so she asked anyone who had extra Edisons to contact her or put them up for sale on eBay. The project has gone back to the Raspberry Pi, which has gotten better in the interim. She noted that many of the attendees to LCA had gotten a Raspberry Pi Zero and said that she would be happy to take any that were not needed. By the end of the conference, 11 had been donated, but the organizing committee was also planning to donate any extras that were not handed out; OpenAPS should end up with a nice supply of free computers for users who need them.

There are some naysayers who proclaim that the project is not made up of medical professionals or programmers; "who do you think you are to do this?" That is ridiculous, she said. The algorithm is one that all diabetes patients learn early on: if your blood sugar is going up, add more insulin based on your settings, if it is going down, add less insulin based on your settings. The computer is just able to do it every five minutes. The people who use the system find that any negatives are outweighed by the positives, in terms of quality of life, that it brings.

The most important thing she has learned through this process is that open source is about "the willingness to try"; it is about showing up and asking questions, she said. The OpenAPS project is not made up of doctors, scientists, researchers, and engineers, but it is doing engineering, experimentation, science, and so on every day. The rest of the open-source community has helped immensely along the way as well.

This kind of effort can be applied beyond diabetes. If you know someone with cancer, asthma, cystic fibrosis, or some other rare disease that few people know anything about, start asking them what their biggest problem is; "what is the thing that most annoys you?" A cure is probably at the top of the list, but once you get past that, you may find there is something fairly simple that would help them. For her, it was simply a louder alarm so that she could sleep without worry. Once that was fixed, she (and others) started chipping away at the other problems that existed and ended up with a much bigger and more useful system than they ever envisioned at the beginning.

She closed by noting that there are another 10 types of people: those who will consider using their open-source skills to solve healthcare problems and those who will not. She hopes that her presentation will help to get more people into the first group.

A YouTube video of the keynote is available.

[I would like to thank LWN's travel sponsor, the Linux Foundation, for travel assistance to Christchurch for linux.conf.au.]