Making it possible for researchers to work with #OpenAPS or general Nightscout data – and creating a complex json to csv command line tool that works with unknown schema

This is less of an OpenAPS/DIYPS/diabetes-related post, although that is normally what I blog about. However, since we created the #OpenAPS Data Commons on Open Humans, to allow those of us who desire to donate our diabetes data to research, I have been spending a lot of time figuring out the process from uploading your data to how data is managed and shared securely with researchers. The hardest part is helping researchers figure out how to handle the data – because we PWDs produce a lot of data :) . So this post explains some of the challenges of the data management to get it to a researcher-friendly format. I have been greatly helped over the years by general purpose open-source work from other people, and one of the things that helps ME the most as a non-traditional programmer is plain language posts explaining the thought process by behind the tools and the attempted solution paths. Especially because sometimes the web pages and blog posts pop higher in search than nitty gritty tool documentation without context. (Plus, I’ve been taking my own advice about not letting myself hold me back from trying, even when I don’t know how to do things yet.) So that’s what this post is!

Background/inspiration for the project and the tools I had to build:

We’re using Nightscout, which is a remote data-viewing platform for diabetes data, made with love and open source and freely available for anyone with diabetes to use. It’s one of the best ways to display not only continuous glucose monitor (CGM) data, but also data from our DIY closed loop artificial pancreases (#OpenAPS). It can store data from a number of different kinds and brands of diabetes devices (pumps, CGMs, manual data entries, etc.), which means it’s a rich source of data. As the number of DIY OpenAPS users are growing, we estimate that our real-world use is overtaking the amount of total hours of data from clinical trials of closed loop artificial pancreas systems.  In the #WeAreNotWaiting spirit of moving quickly (rather than waiting years for research teams to collect and analyze their own data) we want to see what we can learn from OpenAPS usage, not only by donating data to help traditional researchers speed up their work, but also by co-designing research studies of the things of most value to the diabetes community.

Step 1: Data from users to Open Humans

I thought Step 1 would be the hardest. However, thanks to Madeleine Ball, John Costik, and others in the Nightscout community, a simple Nightscout Data Transfer App was created that enables people with Nightscout data to pop it into their Open Humans accounts. It’s then very easy to join different projects (like the OpenAPS Data Commons) and share your data with those projects. And as the volunteer administrator of the OpenAPS Data Commons, it’s also easy for me to provide data to researchers.

The biggest challenge at this stage was figuring out how much data to pull from the API. I have almost 3 years worth of DIY diabetes data, and I have numerous devices over time uploading all at once…which makes for large chunks of data. Not everyone has this much data (or 6-7 rigs uploading constantly ;)). Props to Madeleine for the patience in working with me to make sure the super users with large data sets will be able to use all of these tools!

Step 2: Sharing the data with researchers

This was easy. Yay for data-sharing tools like Dropbox.

Step 3: Researchers being able to use the data

Here’s where thing started to get interesting. We have large data files that come in json format from Nightscout. I know some researchers we will be working with are probably very comfortable working with tools that can take large, complex json files. However…not all will be, especially because we also want to encourage independent researchers to engage with the data for projects. So I had the belated realization that we need to do something other than hand over json files. We need to convert, at the least, to csv so it can be easily viewed in Excel.

Sounds easy, right?

According to basic searches, there’s roughly a gazillion ways to convert json to csv. There’s even websites that will do it for you, without making you run it on the command line. However, most of them require you to know the types of data and the number of types, in order to therefore construct headers in the csv file to make it readable and useful to a human.

This is where the DIY and infinite possibility nature of all the kinds of diabetes tools anyone could be using with Nightscout, plus the infinite ways they can self-describe profiles and alarms and methods of entering data, makes it tricky. Just based on an eyeball search between two individuals, I was unable to find and count the hundred+ types of data entry possibilities. This is definitely a job for the computer, but I had to figure out how to train the computer to deal with this.

Again, json to csv tools are so common I figured there HAD to be someone who had done this. Finally, after a dozen varying searches and trying a variety of command line tools, I finally found one web-based tool that would take json, create the schema without knowing the data types in advance, and convert it to csv. It was (is) super slick. I got very excited when I saw it linked to a Github repository, because that meant it was probably open source and I can use it. I didn’t see any instructions for how to use it on the command line, though, so I message the author on Twitter and found out that it didn’t yet exist and was a not-yet-done TODO for him.

Sigh. Given this whole #WeAreNotWaiting thing (and given I’ve promised to help some of the researchers in figuring this out so we can initiate some of the research projects), I needed to figure out how to convert this tool into a command line version.

So, I did.

  • I taught myself how to unzip json files (ended up picking `gzip -cd`, because it works on both Mac and Linux)
  • I planned to then convert the web tool to be able to work on the command line, and use it to translate the json files to csv.

But..remember the big file issue? It struck again. So I first had to figure out the best way to estimate the size and splice or split the json into a series of files, without splitting it in a weird place and messing up the data. That became jsonsplit.sh, a tool to split a json file based on the size you give it (and if you don’t specify, it defaults to something like 100000 records).

FWIW: 100,000 records was too much for the more complex schema of the data I was working with, so I often did it in smaller chunks, but you can set it to whatever size you prefer.

So now “all” I had to do was:

  • Unzip the json
  • Break it down if it was too large, using jsonsplit.sh
  • Convert each of these files from json to csv

Phew. Each of these looks really simple now, but took a good chunk of time to figure out. Luckily, the author of the web tool had done much of the hard json-to-csv work, and Scott helped me figure out how to take the html-based version of the conversion and make it useable in the command line using javascript. That became complex-json2csv.js.

Because I knew how hard this all was, and wanted other people to be able to easily use this tool if they had large, complex json with unknown schema to deal with, I created a package.json so I could publish it to npm so you can download and run it anywhere.

I also had to create a script that would pass it all of the Open Humans data; unzip the file; run jsonsplit.sh, run complex-json2csv.js, and organize the data in a useful way, given the existing file structure of the data. Therefore I also created an “OpenHumansDataTools” repository on Github, so that other researchers who will be using Nightscout-based Open Humans data can use this if they want to work with the data. (And, there may be something useful to others using Open Humans even if they’re not using Nightscout data as their data source – again, see “large, complex, challenging json since you don’t know the data type and count of data types” issue. So this repo can link them to complex-json2csv.js and jsonsplit.sh for discovery purposes, as they’re general purpose tools.) That script is here.

My next TODO will be to write a script to take only slices of data based on information shared as part of the surveys that go with the Nightscout data; i.e. if you started your DIY closed loop on X data, take data from 2 weeks prior and 6 weeks after, etc.

I also created a pull request (PR) back to the original tool that inspired my work, in case he wants to add it to his repository for others who also want to run his great stuff from the command line. I know my stuff isn’t perfect, but it works :) and I’m proud of being able to contribute to general-purpose open source in addition to diabetes-specific open source work. (Big thanks as always to everyone who devotes their work to open source for others to use!)

So now, I can pass researchers json or csv files for use in their research. We have a number of studies who are planning to request access to the OpenAPS Data Commons, and I’m excited about how work like this to make diabetes data more broadly available for research will help improve our lives in the short and long term!

The only thing to fear is fear itself

(Things I didn’t realize were involved in open-sourcing a DIY artificial pancreas: writing “yes you can” style self-help blog posts to encourage people to take the first step to TRY and use the open source code and instructions that are freely available….for those who are willing to try.)

You are the only thing holding yourself back from trying. Maybe it’s trying to DIY closed loop at all. Maybe it’s trying to make a change to your existing rig that was set up a long time ago.  Maybe it’s doing something your spouse/partner/parent has previously done for you. Maybe it’s trying to think about changing the way you deal with diabetes at all.

Trying is hard. Learning is hard. But even harder (I think) is listening to the negative self-talk that says “I can’t do this” and perhaps going without something that could make a big difference in your daily life.

99% of the time, you CAN do the thing. But it primarily starts with being willing to try, and being ok with not being perfect right out of the gate.

I blogged last year (wow, almost two years ago actually) about making and doing and how I’ve learned to do so many new things as part of my OpenAPS journey that I never thought possible. I am not a traditional programmer, developer, engineer, or anything like that. Yes, I can code (some)…because I taught myself as I went and continue to teach myself as I go. It’s because I keep trying, and failing, then trying, and succeeding, and trying some more and asking lots of questions along the way.

Here’s what I’ve learned in 3+ years of doing DIY, technical diabetes things that I never thought I’d be able to accomplish:

  1. You don’t need to know everything.
  2. You really don’t particularly need to have any technical “ability” or experience.
  3. You DO need to know that you don’t know it all, even if you already know a thing or two about computers.
  4. (People who come into this process thinking they know everything tend to struggle even more than people who come in humble and ready to learn.)
  5. You only need to be willing to TRY, try, and try again.
  6. It might not always work on the first try of a particular thing…
  7. …but there’s help from the community to help you learn what you need to know.
  8. The learning is a big piece of this, because we’re completely changing the way we treat our diabetes when we go from manual interventions to a hybrid closed loop (and we learned some things to help do it safely).
  9. You can do this – as long as you think you can.
  10. If you think you can’t, you’re right – but it’s not that you can’t, it’s that you’re not willing to even try.

This list of things gets proved out to me on a weekly basis.

I see many people look at the #OpenAPS docs and think “I can’t do that” (and tell me this) and not even attempt to try.

What’s been interesting, though, is how many non-technical people jumped in and gave autotune a try. Even with the same level of no technical ability, several people jumped in, followed the instructions, asked questions, and were able to spin up a Linux virtual machine and run beta-level (brand new, not by any means perfect) code and get output and results. It was amazing, and really proved all those points above. People were deeply interested in getting the computer to help them, and it did. It sometimes took some work, but they were able to accomplish it.

OpenAPS, or anything else involving computers, is the same way. (And OpenAPS is even easier than most anything else that requires coding, in my opinion.) Someone recently estimated that setting up OpenAPS takes only 20 mouse clicks; 29 copy and paste lines of code; 10 entries of passwords or logins; and probably about 15-20 random small entries at prompts (like your NS site address or your email address or wifi addresses). There’s a reference guide, documentation that walks you through exactly what to do, and a supportive community.

You can do it. You can do this. You just have to be willing to try.

Making it easier to run OpenAPS commands again..and again..and again

Today I built (another) new (really tiny) tool to make it easier for people using OpenAPS rigs to continually update and improve their tools. Woohoo!

When we switched last year to using the “setup scripts” for OpenAPS, this became the tool for setting up new, advanced features like Advanced Meal Assist, Autosensitivity, Autotune, and other things. Which means that people were running the setup scripts multiple times.

It wasn’t bad, because we built in an interactive setup guide to walk people through the process to select which features they did or did not want. But, it took a bit of time to do, and upon your 8th (or 80th) run of the setup script, especially for those of us developing the script, it got tiring. So we decided to automate some output, that could be copied and pasted to speed up running the same set of options on the command line the next time.

Many people, however, in their first setup run-through don’t see that, or don’t remember to copy and paste it.

Last night, it occurred to me that I should add a more explicit note to the docs for people to stop and copy and paste it. But then I had an idea – what if we could stash away the content in another file, so you could find it anytime without having to run the setup script interactively?

Lightbulb. So today, I sat down and gave it a stab. It’s simple-ish code being added in (now in dev branch of oref0; docs for it here), but it will save little bits of time that over time add up to a lot of time saved.
showing output from oref0-runagain.shcreating the oref0-runagain.sh

This is how almost all of the iterative OpenAPS development occurs: we repeat something enough times, decide it needs to be automated, and find a way to make it happen. And that’s how the tools and code and documentation continues to get to be better and better!

#WeAreNotWaiting, even with the small stuff, that eventually adds up to make a bigger difference :)

Autotune (automatically assessing basal rates, ISF, and carb ratio with #OpenAPS – and even without it!)

What if, instead of guessing needed changes (the current most used method) basal rates, ISF, and carb ratios…we could use data to empirically determine how these ratios should be adjusted?

Meet autotune.

What if we could use data to determine basal rates, ISF and carb ratio? Meet autotune

Historically, most people have guessed basal rates, ISF, and carb ratios. Their doctors may use things like the “rule of 1500” or “1800” or body weight. But, that’s all a general starting place. Over time, people have to manually tweak these underlying basals and ratios in order to best live life with type 1 diabetes. It’s hard to do this manually, and know if you’re overcompensating with meal boluses (aka an incorrect carb ratio) for basal, or over-basaling to compensate for meal times or an incorrect ISF.

And why do these values matter?

It’s not just about manually dosing with this information. But importantly, for most DIY closed loops (like #OpenAPS), dose adjustments are made based on the underlying basals, ISF, and carb ratio. For someone with reasonably tuned basals and ratios, that’s works great. But for someone with values that are way off, it means the system can’t help them adjust as much as someone with well-tuned values. It’ll still help, but it’ll be a fraction as powerful as it could be for that person.

There wasn’t much we could do about that…at first. We designed OpenAPS to fall back to whatever values people had in their pumps, because that’s what the person/their doctor had decided was best. However, we know some people’s aren’t that great, for a variety of reasons. (Growth, activity changes, hormonal cycles, diet and lifestyle changes – to name a few. Aka, life.)

With autosensitivity, we were able to start to assess when actual BG deltas were off compared to what the system predicted should be happening. And with that assessment, it would dynamically adjust ISF, basals, and targets to adjust. However, a common reaction was people seeing the autosens result (based on 24 hours data) and assume that mean that their underlying ISF/basal should be changed. But that’s not the case for two reasons. First, a 24 hour period shouldn’t be what determines those changes. Second, with autosens we cannot tell apart the effects of basals vs. the effect of ISF.

Autotune, by contrast, is designed to iteratively adjust basals, ISF, and carb ratio over the course of weeks – based on a longer stretch of data. Because it makes changes more slowly than autosens, autotune ends up drawing on a larger pool of data, and is therefore able to differentiate whether and how basals and/or ISF need to be adjusted, and also whether carb ratio needs to be changed. Whereas we don’t recommend changing basals or ISF based on the output of autosens (because it’s only looking at 24h of data, and can’t tell apart the effects of basals vs. the effect of ISF), autotune is intended to be used to help guide basal, ISF, and carb ratio changes because it’s tracking trends over a large period of time.

Ideally, for those of us using DIY closed loops like OpenAPS, you can run autotune iteratively inside the closed loop, and let it tune basals, ISF, and carb ratio nightly and use those updated settings automatically. Like autosens, and everything else in OpenAPS, there are safety caps. Therefore, none of these parameters can be tuned beyond 20-30% from the underlying pump values. If someone’s autotune keeps recommending the maximum (20% more resistant, or 30% more sensitive) change over time, then it’s worth a conversation with their doctor about whether your underlying values need changing on the pump – and the person can take this report in to start the discussion.

Not everyone will want to let it run iteratively, though – not to mention, we want it to be useful to anyone, regardless of which DIY closed loop they choose to use – or not! Ideally, this can be run one-off by anyone with Nightscout data of BG and insulin treatments. (Note – I wrote this blog post on a Friday night saying “There’s still some more work that needs to be done to make it easier to run as a one-off (and test it with people who aren’t looping but have the right data)…but this is the goal of autotune!” And as by Saturday morning, we had volunteers who sat down with us and within 1-2 hours had it figured out and documented! True #WeAreNotWaiting. :))

And from what we know, this may be the first tool to help actually make data-driven recommendations on how to change basal rates, ISF, and carb ratios.

How autotune works:

Step 1: Autotune-prep

  • Autotune-prep takes three things initially: glucose data; treatments data; and starting profile (originally from pump; afterwards autotune will set a profile)
  • It calculates BGI and deviation for each glucose value based on treatments
  • Then, it categorizes each glucose value as attributable to either carb sensitivity factor (CSF), ISF, or basals
  • To determine if a “datum” is attributable to CSF, carbs on board (COB) are calculated and decayed over time based on observed BGI deviations, using the same algorithm used by Advanced Meal Asssit. Glucose values after carb entry are attributed to CSF until COB = 0 and BGI deviation <= 0. Subsequent data is attributed as ISF or basals.
  • If BGI is positive (meaning insulin activity is negative), BGI is smaller than 1/4 of basal BGI, or average delta is positive, that data is attributed to basals.
  • Otherwise, the data is attributed to ISF.
  • All this data is output to a single file with 3 sections: ISF, CSF, and basals.

Step 2: Autotune-core

  • Autotune-core reads the prepped glucose file with 3 sections. It calculates what adjustments should be made to ISF, CSF, and basals accordingly.
  • For basals, it divides the day into hour long increments. It calculates the total deviations for that hour increment and calculates what change in basal would be required to adjust those deviations to 0. It then applies 20% of that change needed to the three hours prior (because of insulin impact time). If increasing basal, it increases each of the 3 hour increments by the same amount. If decreasing basal, it does so proportionally, so the biggest basal is reduced the most.
  • For ISF, it calculates the 50th percentile deviation for the entire day and determines how much ISF would need to change to get that deviation to 0. It applies 10% of that as an adjustment to ISF.
  • For CSF, it calculates the total deviations over all of the day’s mealtimes and compares to the deviations that are expected based on existing CSF and the known amount of carbs entered, and applies 10% of that adjustment to CSF.
  • Autotune applies a 20% limit on how much a given basal, or ISF or CSF, can vary from what is in the existing pump profile, so that if it’s running as part of your loop, autotune can’t get too far off without a chance for a human to review the changes.

(See more about how to run autotune here in the OpenAPS docs.)

What autotune output looks like:

Here’s an example of autotune output.

OpenAPS autotune example by @DanaMLewis

Autotune is one of the things Scott and I spent time on over the holidays (and hinted about at the end of my development review of 2016 for OpenAPS). As always with #OpenAPS, it’s awesome to take an idea, get it coded up, get it tested with some early adopters/other developers within days, and continue to improve it!

A big thank you to those who’ve been testing and helping iterate on autotune (and of course, all other things OpenAPS). It’s currently in the dev branch of oref0 for anyone who wants to try it out, either one-off or for part of their dev loop. Documentation is currently here, and this is the issue in Github for logging feedback/input, along with sharing and asking questions as always in Gitter!

 

 

OpenAPS feature development in 2016

It’s been two years since my first DIY closed loop and almost two years since OpenAPS (the vision and resulting ecosystem to help make artificial pancreas technology, DIY or otherwise, more quickly available to more people living with diabetes) was created.  I’ve spent time here (on DIYPS.org) talking about a variety of things that are applicable to people who are DIY closed looping, but also focusing on things (like how to “soak” a CGM sensorr and how to do “eating soon” mode) that may be (in my opinion) universally applicable.

OpenAPS feature development in 2016

However, I think it’s worth recapping some of the amazing work that’s been done in the OpenAPS ecosystem over the past year, sometimes behind the scenes, because there are some key features and tools that have been added in that seem small, but are really impactful for people living with DIY closed loops.

  1. Advanced meal assist (aka AMA)
    1. This is an “advanced feature” that can be turned on by OpenAPS users, and, with reliable entry of carb information, will help the closed loop assist sooner with a post-meal BG rise where there is mis-timed or insufficient insulin coverage for the meal. It’s easy to use, because the PWD only has to put carbs and a bolus in – then AMA acts based on the observed absorption. This means that if absorption is delayed because you walk home from dinner, have gastroparesis, etc., it backs off and wait until the carbs actually start taking effect (even if it is later than the human would expect).
    2. We also now have the purple line predictions back in Nightscout to visualize some of these predictions. This is a hallmark of the original iob-cob branch in Nightscout that Scott and I originally created, that took my COB calculated by DIYPS and visualized the resulting BG graph. With AMA, there are actually 3 purple lines displayed when there is carb activity. As described here in the OpenAPS docs, the top purple line assumes 10 mg/dL/5m carb (0.6 mmol/L/5m) absorption and is most accurate right after eating before carb absorption ramps up. The line that is usually in the middle is based on current carb absorption trends and is generally the most accurate once carb absorption begins; and the bottom line assumes no carb absorption and reflects insulin only. Having the 3 lines is helpful for when you do something out of the ordinary following a meal (taking a walk; taking a shower; etc.) and helps a human decide if they need to do anything or if the loop will be able to handle the resulting impact of those decisions.
  2. The approach with a “preferences” file
    1. This is the file where people can adjust default safety and other parameters, like maxIOB which defaults to 0 during a standard setup, ultimately creating a low-glucose-suspend-mode closed loop when people are first setting up their closed loops. People have to intentionally change this setting to allow the system to high temp above a netIOB = 0 amount, which is an intended safety-first approach.
    2. One particular feature (“override_high_target_with_low”) makes it easier for secondary caregivers (like school nurses) to do conservative boluses at lunch/snack time, and allow the closed loop to pick up from there. The secondary caregiver can use the bolus wizard, which will correct down to the high end of the target; and setting this value in preferences to “true” allows the closed loop to target the low end of the target. Based on anecdotal reports from those using it, this feature sounds like it’s prevented a lot of (unintentional, diabetes is hard) overreacting by secondary caregivers when the closed loop can more easily deal with BG fluctuations. The same for “carbratio_adjustmentratio”, if parents would prefer for secondary caregivers to bolus with a more conservative carb ratio, this can be set so the closed loop ultimately uses the correct carb amount for any needed additional calculations.
  3. Autosensitivity
    1. I’ve written about autosensitivity before and how impressive it has been in the face of a norovirus and not eating to have the closed loop detect excessive sensitivity and be able to deal with it – resulting in 0 lows. It’s also helpful during other minor instances of sensitivity after a few active days; or resistance due to hormone cycles and/or an aging pump site.
    2. Autosens is a feature that has to be turned on specifically (like AMA) in order for people to utilize it, because it’s making adjustments to ISF and targets and looping accordingly from those values. It also have safety caps that are set and automatically included to limit the amount of adjustment in either direction that autosens can make to any of the parameters.
  4. Tiny rigs
    1. Thanks to Intel, we were introduced to a board designer who collaborated with the OpenAPS community and inspired the creation of the “Explorer Board”. It’s a multipurpose board that can be used for home automation and all kinds of things, and it’s another tool in the toolbox of off-the-shelf and commercial hardware that can be used in an OpenAPS setup. It’s enabled us, due to the built in radio stick, to be able to drastically reduce the size of an OpenAPS setup to about the size of two Chapsticks.
  5. Setup scripts
    1. As soon as we were working on the Explorer Board, I envisioned that it would be a game changer for increasing access for those who thought a Pi was too big/too burdensome for regular use with a DIY closed loop system. I knew we had a lot of work to do to continue to improve the setup process to cut down on the friction of the setup process – but balancing that with the fact that the DIY part of setting up a closed loop system was and still is incredibly important. We then worked to create the oref0-setup script to streamline the setup process. For anyone building a loop, you still have to set up your hardware and build a system, expressing intention in many places of what you want to do and how…but it’s cut down on a lot of friction and increased the amount of energy people have left, which can instead be focused on reading the code and understanding the underlying algorithm(s) and features that they are considering using.
  6. Streamlined documentation
    1. The OpenAPS “docs” are an incredible labor of love and a testament to dozens and dozens of people who have contributed by sharing their knowledge about hardware, software, and the process it takes to weave all of these tools together. It has gotten to be very long, but given the advent of the Explorer Board hardware and the setup scripts, we were able to drastically streamline the docs and make it a lot easier to go from phase 0 (get and setup hardware, depending on the kind of gear you have); to phase 1 (monitoring and visualizing tools, like Nightscout); to phase 2 (actually setup openaps tools and build your system); to phase 3 (starting with a low glucose suspend only system and how to tune targets and settings safely); to phase 4 (iterating and improving on your system with advanced features, if one so desires). The “old” documentation and manual tool descriptions are still in the docs, but 95% of people don’t need them.
  7. IFTTT and other tool integrations
    1. It’s definitely worth calling out the integration with IFTTT that allows people to use things like Alexa, Siri, Pebble watches, Google Assistant (and just about anything else you can think of), to easily enter carbs or “modes” for OpenAPS to use, or to easily get information about the status of the system. (My personal favorite piece of this is my recent “hack” to automatically have OpenAPS trigger a “waking up” mode to combat hormone-driven BG increases that happen when I start moving around in the morning – but without having to remember to set the mode manually!)

..and that was all just things the community has done in 2016! :) There are some other exciting things that are in development and being tested right now by the community, and I look forward to sharing more as this advanced algorithm development continues.

Happy New Year, everyone!

Automating “wake up” mode with IFTTT and #OpenAPS to blunt morning hormonal rises

tl;dr – automate a trigger to your #OpenAPS rig to start “wake up” mode (or “eating soon”, assuming you eat breakfast) without you having to remember to do it.

Yesterday morning, I woke up and headed to my desk to start working. Because I’m getting some amazing flat line overnights now, thanks to my DIY closed loop (#OpenAPS), I’m more attuned to the fact that after I wake up and start moving around, my hormones kick in to help wake me up (I guess), and I have a small BG rise that’s not otherwise explained by anything else. (It’s not a baseline basal problem, because it happens after I wake up regardless of it being 6am or 8am or even 10:30am if I sleep in on a weekend. It’s also more pronounced when I feel sleep deprived, like my body is working even harder to wake me up.)

Later in the morning, I took a break to jot down my thoughts in response to a question about normal meal rises on #OpenAPS and strategies to optimize mealtimes. It occurred to me later, after being hyper attuned to my lunch results, that my morning wake-up rise up from 1oo perfectly flat to ~140 was higher than the 131 peak I hit after my lunchtime bowl of potato soup.

Hmm, I thought. I wish there was something I could do to help with those morning rises. I often do a temporary target down to 80 mg/dL (a la “eating soon” mode) once I spot the rise, but that’s after it’s already started and very dependent on me paying attention/noticing the rise.

I also have a widely varied schedule (and travel a lot), so I don’t like the idea of scheduling the temp target, or having recurring calendar events that is yet another thing to babysit and change constantly.

What I want is something that is automatically triggered when I wake up, so whether I pop out of the bed or read for 15 minutes first, it kicks in automatically and I (the non-morning person) don’t have to remember to do one more thing. And the best trigger that I could think of is when I end Sleep Cycle, the sleep tracking app I use.

I started looking online to see if there was an easy IFTTT integration with Sleep Cycle. (There’s not. Boo.) So I started looking to see if I could stick my Sleep Cycle data elsewhere that could be used with IFTTT. I stumbled across this blog post describing Sleep Cycle -> iOS Apple HealthKit -> UP -> Google Spreadsheet -> Zapier -> Add to Google Calendar. And then I thought I would add another IFTTT trigger for when the calendar entry was added, to then send “waking up” mode to #OpenAPS. But I don’t need all of the calendar steps. The ideal recipe for me then might be Sleep Cycle ->  iOS Health Kit -> UP -> IFTTT sends “waking up mode” -> Nightscout -> my rig. However, I then learned that UP doesn’t necessarily automatically sync the data from HealthKit, unless the app is open. Hmm. More rabbit holing. Thanks to the tweet-a-friend option, I talked to Ernesto Ramirez (long time QS guru and now at Fitabase), who found the same blog post I did (above) and when I described the constraints, then pointed me to Hipbone to grab Healthkit sleep data and stuff it into Dropbox.

(Why Sleep Cycle? It is my main sleep tracker, but there’s IFTTT integration with Fitbit, Jawbone Up, and a bunch of other stuff, so if you’re interested in this, figure out how to plug your data into IFTTT, otherwise follow the OpenAPS docs for using IFTTT to get data into Nightscout for OpenAPS, and you’ll be all set. I’m trying to avoid having to go back to my Fitbit as the sleep tracker, since I’m wearing my Pebble and I was tired of wearing 2 things. And for some reason my Pebble is inconsistent and slow about showing the sleep data in the morning, so that’s not reliable for this purpose. )

Here’s how I have enabled this “wake up” mode trigger for now:

  1. If you’re using Sleep Cycle, enable it to write sleep analysis data to Apple HealthKit.
  2. Download the Hipbone app for iPhone, connect it with your Dropbox, and allow Hipbone to read sleep data from HealthKit.
  3. Log in or create an account in IFTTT.com and create a recipe using Dropbox as the trigger, and Maker as the action to send a web request to Nightscout. (Again, see the OpenAPS docs for using IFTTT triggers to post to Nightscout, there’s all kinds of great things you can do with your Pebble, Alexa, etc. thanks to IFTTT.) To start, I made “waking up” soon a temporary target to 80 for 30 minutes.

Guess what? This morning, I woke up, ended sleep cycle, and ~10-11 minutes later got notifications that I had new data in Dropbox and checked and found “waking up” mode showing in Nightscout! Woohoo. And it worked well for not having a hormone-driven BG rise after I started moving around.

First "waking up" mode in #OpenAPS automation success

Ideally, this would run immediately, and not take 10-11 minutes, but it went automatically without me having to open Hipbone (or any other app), so this is a great interim solution for me until we find an app that will run more quickly to get the sleep data from HealthKit.

We keep finding great ways to use IFTTT triggers, so if you have any other cool ones you’ve added to your DIY closed loop ecosystem, please let me know!

Autosensitivity (automatically adjusting insulin sensitivity factor for insulin dosing with #OpenAPS)

There’s a secret behind why #OpenAPS was able to deal so well with my BGs during norovirus. Namely, “autosensitivity”.

Autosensitivity (or “autosens”, for short hand) is an advanced feature that can optionally be enabled in OpenAPS.

We know how hard it is for a PWD (person with diabetes) to pay attention to all the numbers and all the things and realize when something is “off”. This could be a bad pump site, a pump site going bad, hormones from growth, hormones from menstrual cycles, sensitivity from exercise the day before, etc. So at the beginning of the year, Scott and I started brainstorming with the community about automatically detecting when the PWD is more or less sensitive to insulin than normal, and adjusting accordingly. Building on the success we’d had in DIYPS with fixed “sensitivity” and “resistance” modes, we built the feature to assess how sensitive or resistant the body is (compared to normal), rather than just a binary mode that sets a predefined response.

How OpenAPS calculates autosensitivity/how it works

It looks at each BG data point for the last 24 hours and calculates the delta (actual observed change) over the last 5 minutes. It then compares it to “BGI” (blood glucose impact, which is how much BG *should* be dropping from insulin alone), and assesses the “deviations” (differences between the delta and BGI).

When sensitivity is normal and basals are well tuned, we expect somewhere between 45-50% of non-meal deviations to be negative, and the remaining 50-55% of deviations should be positive. (To exclude meal-related deviations, we exclude overly large deviations from the sample.) So if you’re outside of that range, you are probably running sensitive or resistant, and we want to adjust accordingly. The output of the detect-sensitivity code is a single ratio number, which is then used to adjust both the baseline basal rate as well as the insulin sensitivity factor (and, optionally, BG targets).

Autosens is designed to detect to food-free downward drift, due to basal rates being too high for the current state of the body, and will adjust basals downward to compensate. The other meal-assist related portion of the algorithms do a pretty good job of dealing with larger than expected post-meal spikes due to resistance: auto-sensitivity mostly comes into play for resistance when you’re sick or otherwise riding high even without food.

Does this calculate basals?

No. Similar to everything else in OpenAPS, this works from your established basals – meaning the baseline basal rates in your pump are what the sensitivity calculations are adjusting from. If you run a marathon and your sensitivity is normally 40, it might adjust your sensitivity to 60 (meaning 1u of insulin would drop your BG an expected 60mg/dl instead of 40 mg/dl) and temporarily adjust your baseline basal rate of 1u to .6u/hour, for example.

This algorithm is simply saying “there’s something going on, let’s adjust proportionately to deal with the lower-than-usual or higher-than-usual sensitivity, regardless of cause”. It easily detects “your basals are too high and/or your ISF is too low” or “your basals are too low and/or your ISF is too high”, but actually differentiating between the effect of basal and ISF is a bit more difficult to do with a simple algorithm like this, so we’re working on a number of new algorithms and tools (see “oref0 issue 99” for our brainstorming on basal tuning and the subsequent issues linked from there) to tackle this in the future.

#OpenAPS’s autosensitivity adjustments during norovirus

After I got over the worst of the norovirus, I started looking at what OpenAPS was calculating for my sensitivity during this time. I was especially curious what would happen during the 2-3 days when I was eating very little.

My normal ISF is 40, but OpenAPS gradually calculated the shift in my sensitivity all the way to 50. That’s really sensitive, and in fact I don’t remember ever seeing a sensitivity adjustment that dramatic – but makes sense given that I usually don’t go so long without eating. (Usually when I notice I’m a little sensitive, I’ll check and see that autosens has been adjusting based on an estimated 43 or so sensitivity.)

And in later days, as expected when sick, I shifted to being more resistant. So autosens continued to assess the data and began adjusting to an estimated sensitivity of 38 as my body continued fighting the virus.

It is so nice to have the tools to automatically make these assessments and adjustments, rather than having to manually deal with them on top of being sick!

 

Sick days solved with a DIY closed loop #OpenAPS

Ask me about the time I got a norovirus over Thanksgiving.

As expected, it was TERRIBLE. Even though the source of the norovirus was cute, the symptoms aren’t. (You can read about the symptoms from the CDC if you’ve never heard of it before.)

But, unexpectedly, it was only terrible on the norovirus symptoms front. My BGs were astoundingly perfect. So much so that I didn’t think about diabetes for 3 days.

Let me explain.

Since I use an OpenAPS DIY closed loop “artificial pancreas”, I have a small computer rig that automatically reads my CGM and pump and automatically adjusts the insulin dosing on my pump.

OpenAPS temp basal adjustments during day 2 norovirus November 2016
Showing the net basal adjustments made on day 2 of my norovirus – the dotted line is what my basals usually are, so anything higher than that dotted line is a “high” temp and anything lower is a “low” temp of various sorts.
  • When I first started throwing up over the first 8 hours, as is pretty normal for norovirus, I first worried about going low, because obviously my stomach was empty.

Nope. I never went lower than about 85 mg/dl. Even when I didn’t eat at all for > 24 hours and very little over the course of 5 days.

  • After that, I worried about going high as my body was fighting off the virus.

Nope. I never went much higher than a few minutes in the 160s. Even when I sipped Gatorade or gasp, ate two full crackers at the end of day two and didn’t bolus for the carbs.

  • The closed loop (as designed – read the OpenAPS reference design for more details) observed the rising or dropping BGs and adjusted insulin delivery (using temporary basal rates) up or down as needed. I sometimes would slowly rise to 150s and then slowly head back down to the 100s. I only once started dropping slowly toward the 80s, but leveled off and then slowly rose back up to the 110s.

None of this (\/\/\/\/\) crazy spiking and dropping fast that causes me to overreact.

No fear for having to force myself to drink sugar while in the midst of the worst of the norovirus.

No worries, diabetes-wise, at all. In fact, it didn’t even OCCUR to me to test or think about ketones (I’m actually super sensitive and can usually feel them well before they’ll register otherwise on a blood test) until someone asked on Twitter.

Why this matters

I was talking with my father-in-law (an ER doc) and listening to him explain how anti-nausea medications (like Zofran) has reduced ER visits. And I think closed loop technology will similarly dramatically reduce ER visits for people with diabetes when sick with things like norovirus and flu and that sort of thing. Because instead of the first instance of vomiting causing a serious spiral and roller coaster of BGs, the closed loop can respond to the BG fluctuations in a safe way and prevent human overreaction in either direction.

This isn’t what you hear about when you look at various reports and articles (like hey, OpenAPS mentioned in The Lancet this week!) about this type of technology – it’s either general outcome reports or traditional clinical trial results. But we need to show the full power of these systems, which is what I experienced over the past week.

I’m reassured now for the future that norovirus, flu, or anything else I may get will likely be not as hard to deal with as it was for the first 12 years of living with diabetes when getting sick. That’s more peace of mind (in addition to what I get just being able to safely sleep every night) that I never expected to have, and I’m incredibly thankful for it.

(I’m also thankful for the numerous wonderful people who share their stories about how this technology impacts their lives – check out this wonderful video featuring the Mazaheri family to see what a difference this is making in other people’s lives. I’m so happy that the benefits I see from using DIY technology are available to so many other people, too. At latest count, there are (n=1)*174 other people worldwide using DIY closed loop technology, and we collectively have over half a million real-world hours using closed loop technology.)

Half life

I have now lived with diabetes for more than half of my life.

That also means I have now lived less than half of my life without diabetes.

This somehow makes the passing of another year living with diabetes seem much more impactful to me. Maybe not to you, or to someone else with a different experience of living with diabetes and a different timeline of life before and after diagnosis…but to me this is a big one.

I’m happy to have context, though, to help me keep things in perspective. For example, I’ve now lived with a closed loop artificial pancreas (or automated insulin delivery) system for almost two full years.

(That’s almost as significant a marker of a “with” vs. “without” comparison as living “with” vs. “without” diabetes.)

And because I ended up with type 1 diabetes, I found out that doing things for other people and the communities you’re a part of is a powerful way to help yourself, both in the short term and the long term. That’s what drove me to figure out a way to take #DIYPS closed loop and make it something open source. And by doing that, I learned so much more about open source, and have been able to partner with incredible people innovating in hardware and software. These collaborations have resulted in an incredibly rich community of passionate people I like to call #OpenAPS-ers.

While #OpenAPS is by no means a cure, and no artificial pancreas will be a cure, they provide an immeasurably improved quality of life that a lot of us didn’t realize was possible with diabetes. Someone told me he can get the same results for his child living with diabetes, but with #OpenAPS it requires about 85% less work. And given the enormous time and cognitive burden of diabetes, this is a HUGE reduction.

And now doors are opening for us collectively to make even more of a significant impact on the diabetes community, and our fellow patient communities. Yesterday, while at the White House Frontiers conference, NIH Director Dr. Francis Collins was in the audience during my panel. At the end of the day, he stopped me to ask questions about my experiences and perspective on the FDA and what we need from the government. I was able to talk with him about the need for FDA & other parts of the government to help foster and support open source innovation. We talked about the importance of data access for patients, and the need for data visibility on commercially approved medical devices.

This is not just a need of people with diabetes (although it’s certainly very applicable for all of the manufacturers with pipelines full of artificial pancreas products): these are universal needs of people dealing with serious health conditions.

Given what I heard yesterday, it’s working. The #WeAreNotWaiting spirit is infusing our partners in these other areas. We are planting seeds, building relationships, and working in collaboration with those at the FDA, NIH, HHS in addition to those in industry and academia. I know they were working toward these same goals before, but social media has helped raise up our collective voices about the burning need to make things better, sooner, for more people.

So if I have to live the rest of my life at a ratio where more than half of it has been spent living with diabetes, I look forward to continuing to work to get to an 85% reduction in the burden of daily life with diabetes for everyone.

 

What a FDA approved commercial hybrid closed loop artificial pancreas system (670G) means for #OpenAPS

You probably heard that a commercial hybrid closed loop (the 670G) has been approved by the U.S. FDA and, like everyone else, are wondering what that means for #OpenAPS.

First, here’s our initial reaction:

And here are some longer form thoughts:

  • Yes, this is exciting. FDA moved months more quickly then expected (hmm, we are sensing a theme when the #WeAreNotWaiting community is involved ;)) to get this tech approved. And as we’ve experienced (check out this self-reported outcomes study with better outcomes than the pivotal trial for this new device), the results of using a hybrid closed loop are outstanding. It’s disappointing that they won’t be ready to ship until Spring 2017, but…
  • …This means the company has time to work on user guides and usability. As we’ve told every device company we’ve encountered, we (the #OpenAPS community) are happy to share everything we’ve learned. And we have learned a lot, including what it takes to trust a system, how much info is needed to help determine if additional human action is needed, what to do in all kinds of real-world situations, and more. We hope the companies continue to work with people with diabetes who have experience with this technology from both clinical trials and the DIY world, where we’ve racked up 350,000+ hours with this type of technology. Because setting expectations with users for this technology will be key for successful and sustained adoption.

This doesn’t really mean anything for #OpenAPS, though. The first generation of AP technology is similar to #OpenAPS in that it’s a hybrid closed loop that still requires the human to input carbs into the system, but it unfortunately has a set point that can not be adjusted below 120mg/dl.  For many people, this is not a big deal. But for others, this will be a deal breaker. For DIYers, that lack of customization will likely be frustrating. And for many families, the lack of remote data visualization may be another deal breaker. And, like with all new technology and devices, getting this stuff covered by insurance may be an uphill battle. So while optimistically this enables many people in the U.S. to finally access this technology (yay) without having to DIY, it won’t necessarily be truly available to everyone from a cost or access perspective for many years to come. So #OpenAPS and other DIY technology may still be needed from a cost/access perspective to continue to help fill gaps compared to current status quo with basic, non-connected diabetes devices (i.e. standalone pump and CGMs).

I also know that many of the parents of kids with T1D are disappointed, because the initial approval is for kids 14+, and it even notes that the system is not recommended for kids <7 or those taking less than 8u of insulin every day (usually young kids). I asked, suspecting it was related to occlusion, but it sounds more like they just don’t have enough data to say for sure that the system is safe with that small amount of insulin, and they’re working on additional studies to get data in that area.

Ditto, too, for more studies allowing different set points. They stuck with a 120mg/dl set point in order to speed to approval, but fingers crossed they get other studies done and new approvals from FDA before this device ships in the spring – that would be awesome. And I was glad to hear that they do have an “exercise” target of 150. That’s a bit of good…but I’m still hesitant that it is enough. From my personal experience knowing net IOB (here’s why net IOB matters) an hour before and when starting exercise is required information to help me decided whether or not I will need carbs to prevent lows during exercise. I don’t think this device will report on net IOB, but I admittedly haven’t seen the device and hopefully I’ll be proved wrong and the data available will be good enough for this purpose!

So in summary: this is good news. But we still need more FDA approved commercial options, and even with a single “commercial approved option”, it’s still ~6+ months away from reaching the hands of people with diabetes…so we as a #WeAreNotWaiting movement continue to have work to do to help speed up the processes for getting enhanced diabetes technology approved and available on the market, with access to view data the ways we need it.

*(Yes, in the title of the post I called it a commercial hybrid closed loop artificial pancreas system. It’s a hybrid closed loop, as is #OpenAPS, but it’s also on the road/part of the suite of more complex artificial pancreas technology. I realize to many PWDs “artificial pancreas” means a lot of different things. Quite certainly, regardless of definition, an artificial pancreas or hybrid closed loop still requires a lot of work. It’s not a cure by any stretch of the imagination. But it’s easy for the media to describe it as an AP, and I also find it a lot easier to describe the small device accompanying my pump when strangers ask as an “artificial pancreas” followed by an explanation rather than saying “hybrid closed loop”.

If anything, I think having the media broadly categorize it as an AP will encourage the diabetes community to ask more questions about what exactly this tech does, leading to greater understanding and better expectations about what the device will/won’t be able to do. So this may result in a good thing.)