In this presentation we share the results of our reverse engineering of an electronic pipette and a -80ºC freezer, both are staples in biomedical laboratories. We share our methodology and try to incite others to create more open software for biomedicine.
Charles Fracchia & Joel Dapello are from BioBright, a Boston-based company working to make biomedical research more reproducible through data.
Who we are: Biologists who grew tired of using outdated tools
And the most important part: How YOU can help!!
We think this community has the skillz that could really push the state of the art.
First, I’m going to take us on a brief tour of the biolab ecosystem, highlighting some of the key tools and their roles.
How many of you have any experience with biology research? This is pretty representative of your basic bio lab. There are definitely a lot of things -- but by no means an internet of things.
The pipette. This is really the bread and butter of cellular and molecular biology research; Using this fundamental tool, biologists spend much of their time manually transferring small volumes of colorless liquid from tube to tube, in the name of science. Want to clone or edit some DNA? Gonna need one of these. Wanna feed your cells? Probably gonna need one of these. Really, this is one of the most ubiquitous tools in all of biology. While this amazingly simple tool has enable an absurd amount of progress in biology, it has some shortcomings. Namely, it’s a dumb device; it doesn’t know what you pipetted, where you pipetted it to, when you did so.. It’s all on you to keep track of it.
Additionally we have: Lab notebook. The majority of lab work, from the steps of the experiment performed to the results thereof are still captured by hand. In some cases, people use an electronic lab notebook, but the point is the same: logging the fundamental data of “what you do” in the lab is by and large a manual process done in real time alongside the experiment. Vortexers for shaking, mixing, and generally agitating samples The centrifuge for spinning samples down, removing bubbles..
Some other players: Spectrophotometers -- for “quantitative measurement of the reflection or transmission properties of a material as a function of wavelength.” An indispensable tool for measuring the quantity of DNA, RNA, or other contents of a sample, these systems often run on proprietary, archaic software, with interfaces on platforms ranging from windows 95 -> windows 10; it’s really a crap shoot. When working with these often, you’ll just save your spectrography results as an image and paste them into your lab notebook.
The freezer and the incubator.. I mean, come on these are simple right? But really: 10s to 100s of thousands of dollars not to mention months of work are trusted to these devices, and most of them have little to no real safety or reliability insurance. Perhaps your incubator will beep for a while if the temperature dips too low, but for the most part there is no logging, no verification that these ubiquitous stalwarts of the biolab are doing what they should be doing. If your incubator loses power overnight and then comes back on in the morning, you have no idea -- and in your notes, and in the papers you publish, this reality, uncaptured, will not be portrayed. Meanwhile, if your freezer loses power or fails for some reason, tons of reagents and samples can be lost just like that.
And finally, the protocols -- the representation and knowledge transfered in protocols leaves a really leaves a lot to be desired. Many steps are implicit, or require a lot of trial and error to perform correctly,
only continue to add to the cognitive load of the researcher.
Ultimately what this adds up to is a rather cumbersome, imprecise, and low bandwidth experience in the lab. Not collecting enough information!! The tools of the bio lab put the burden on the scientist to interact with and coordinate these disparate, proprietary entities. The biologist must operate many different interfaces, both entering and logging the settings, hand collecting the data and recording the results…. It’s fucking difficult!
And ultimately, we’re never sure if what should have happened, is what actually happened. Which… in science…. Is a huge problem.
But wait!.... We’re hackers right? Maybe can we do something about this? As it turns out…..
It looks like many of these devices can be interfaced with electronically (or otherwise)! Even if their manufacturers did not intend them to be.. Or rather, as is often the case, even as their manufacturer's intended them NOT to be. perhaps, with a little reverse engineering, we can manipulate some of these tools to be a just a bit more helpful to us! Which is exactly what we did. So, without further ado, Charles will talk us through some examples of hacking bio equipment -- starting with the pipette.
Before I get into the details, this hack came about because of my masters at MIT: I wanted to quantify
A great starting point to collect information about what the user is doing, if we could only get at this information...
All electronic pipettes are not created equal
This is not your average tamagotchi reverse engineering talk. This can help doctors draw insights, scientists find cures, engineer cheaper and better medicine Bio is becoming more like healthcare, with silos hindering scientists to create longitudinal research
Talk about healthcare - it’s fucked Biomed research is headed that way - funding models & tech practices
People are creating companies whose business models rely on creating silos
There is a lot of low hanging fruit in the biolab, which can have a huge pay off!! However, currently, the skillz to get at this sort of thing are just not taught to biologists.
Let’s avoid the health care data catastrophe -- we can’t afford silos stifling this field; we need an open infrastracture that enables innovation. We need need to create the proper incentives to avoid
DEFCON 24 BioHacking Village: Reverse Engineering Biomedical Equipment for Fun and Open Science
Reverse engineering biomedical
equipment for fun and open science
Charles Fracchia & Joel Dapello
DEFCON BioHacking Village - Aug 6 2016
What to expect from this talk
1. What is a biolab & its equipment
2. How we reverse engineered two pieces of equipment
3. Call to arms: how YOU can help
Step 2: collect samples from the RS-232 port
Sending random characters through the port yields interesting behavior
“N” → Dumps NVRAM
“T” → Temperature packet
Step 3: reverse temperature encoding
Increase the temperature by known amounts and collect the temperature bytes
Still a bit cryptic, until...
Step 3: reverse temperature encoding
This is very likely to be linear !
Calculate the slope: m = ( 20221 - 20608 ) / ( -87 + 84 ) = 129
Get the Y-intercept: 31444 → 243.75ºC
Hmm, strange: 0 Kelvin → -243.15 not 243.75ºC
Temp ºC ≈ n/129 - 243.75
Step 4: make it easy to use for biologists
Complete with alerts & maintenance/downtime prediction algorithms !
These tools are essential in curing
disease, finding new drugs, etc.
What we need help with
Create a repository of open & interoperable device “drivers”
Create a framework to teach these skills to biologists and doctors
Recruit hackers & reverse engineers to this cause