Pioreactor development log #6 - There is no cloud, only someone else's computer

Aug 27, 2021 Posted by: Cameron Davidson-Pilon

By design, there is no Pioreactor "cloud". That is, all your collected data, the web interface, and computations are hosted locally on the Raspberry Pis. This has a number of benefits for you, the user:

Pioreactor development log #5

Aug 20, 2021 Posted by: Cameron Davidson-Pilon

An important metric in bio-processing is the cell density, or biomass, of a bioreactor. The cell density can be measured directly, but the cost of this is very high. Either you are pulling a sample out and counting cells (slow, manual, and noisy), or passing liquid through a flow cytometer (expensive). A common proxy for cell density is optical density: measuring the amount of light scattering off cells. This approach is fast and inexpensive, but has drawbacks, too:

Pioreactor development log #4

Jul 29, 2021 Posted by: Cameron Davidson-Pilon

In our development boards, we are using the terrific ADS1115 chip to convert our analog optical density signal into digital format that our Raspberry Pi can read. The ADS1115 is a high quality chip: 16-bits (meaning it can output any integer between 0 and 65535), has a programmable gain, and programmable samples-per-second (SPS). Unfortunately, it's also pretty expensive - up to $9 / chip. That's by far the costliest piece on our boards. Fortunately, there is a cheaper chip from the same family: the ADS1015. It's half the price, has 12-bits, and same programming. To make the Pioreactor as affordable as possible, we've done some evaluations and decided to move to the ADS1015. 

Pioreactor development log #2

Jul 29, 2021 Posted by: Cameron Davidson-Pilon

An alternative way to think about culture growth is to consider how long it takes for the culture to double - called the doubling time. The doubling time has a real-world interpretation, unlike the traditional growth rate measure. Compare the following "The growth rate is 0.4 per hour" vs "The doubling time is 1.7 hours." The latter is much easier to understand, and to make predictions from (ex: culture will be 4x in 3.4 hours). However, the relationship between growth rate and doubling time is trivial: doubling_time = ln(2) / growth_rate.

Pioreactor development log #3

Jul 13, 2021 Posted by: Cameron Davidson-Pilon

It was time to grow up. During the months of development, a handful of solutions had been used to solve the following problem: "I have this somewhat-important data point, but don't have access to a datastore to store it in". This problem was almost always present on workers (recall workers, unlike the leader, don't have SQLite installed, and pass all their data to the leader via MQTT). For example, we wanted different processes on a Pioreactor to be aware if a PWM channel was in use, so they don't accidentally use that PWM channel. Another problem was caused by our DAC (digital-to-analog converter) being write-only, but we needed multiple processes to know what the DAC's current state was. 

Pioreactor development log #1

Jun 30, 2021 Posted by: Cameron Davidson-Pilon

My first 3D printer, a Prusa Mini, arrived in hundreds of pieces - designed as a build-it-yourself kit. And while the instructions were excellent, it was still an intimidating task: there were lots of moving parts held together by belts, high temperature hotends, and electrical components. After finishing the last step and powering up the printer, I was greeted with the Prusa Mini's self-test. It was a simple routine that tested the different components: moved the belts, heated and cooled components, and checked sensors. At the end of the routine, I saw 100% green check marks:

How we built a bioreactor on top of the Raspberry Pi

Apr 26, 2021 Posted by: Cameron Davidson-Pilon

The Raspberry Pi is a low-cost, single-board computer that has exploded in both at-home use and in industry. What makes the Raspberry Pi so useful is that it can run Linux, connect to the internet, and has lots of input/outputs - making it very useful for being the "brain" of your system. Makers have put the Raspberry Pi at the center of robots, LED displays, home-automation systems, and more. And in industry, they are being adopted to run subsystems of factories, research tools, and be deployed IoT devices. 

Replication, variance, (and growth rates) in Pioreactors

Mar 02, 2021 Posted by: Cameron Davidson-Pilon

One important property we wanted Pioreactors to have was low variance between units. That is, one Pioreactor should be interchangeable with another. This property means that differences in experiment results are solely the result of biological culture conditions, and not on the Pioreactor construction or materials. In fact, we take inspiration from cloud computing providers: the customer shouldn't have to worry about which hardware they are running on, and the cloud provider can swap out hardware without the user noticing.