Introduction: Farma: a Home Bioreactor for Pharmaceutical Drugs

Overview

Synthetic Biology has rapidly developed from a scientific discipline into a large industry. Many new companies are designing microbes that produce valuable chemicals, such as pharmaceutical drugs and fragrances, in very large fermentation reactors.

Today, we are on the verge of using synthetic microbes within consumer products. How should we incorporate synthetic organisms into our products, clothing, and homes?

Farma brews Arthrospira platensis, also known as Spirulina, that has been modified to produce pharmaceutical drugs. The reactor brews, measures, filters, and dries the Spirulina into a powder. The consumer then fills gel capsules using the accompanying pill maker and consumes the drugs.

Background:

Academics and corporations have recently demonstrated complicated, multi-step metabolic pathways into micro-organisms to produce pharmaceutical drugs. For example, Dr. Christina Smolke's laboratory at Stanford recently engineered yeast to synthesize opiates from glucose. Although the researchers demonstrated small concentrations of opiate production, they recently launched a startup company to improve the process and eventually produce and sell opiates commercially. Another example is Artemisinin, an anti-malarial drug traditionally derived from wormwood trees. In the late 2000s, Amyris engineered yeast to produce Artemisinin and now the world's supply of Artemisinin is predominately produced by yeast. In addition to pharmaceutical drugs, other synthetic biology companies are producing valuable fragrances (ex: essence of rose), cosmetics (ex: palm oil), tastes (ex: vanilla & saffron) , and materials (spider silk).

Much of these advances have been made possible by new genome editing techniques, particular CRISPR, and automated, robotic laboratories. The design, build, test cycle for biology is now cheaper and faster than ever, making trying and improving on new ideas lower cost. As a result, synthetic biology has attracted tremendous interest from the Venture Capital industry, netting over $500 million in investment in 2015 alone.

Most of these existing pursuits can be lumped into the same theme: using microbes to produce expensive substances more cheaply than the current method. Now scientists, entrepreneurs, and students are beginning to explore provocative ideas that could bring synthetic microbes into our daily lives - for example, engineered probiotics and fermented foods, hen-free eggs and cow-free milk, and plants that grow as lights. At the same time, a thriving DIY synthetic biology community is now engineering micro-organisms in kitchens using low-cost, wet-lab tools that are often 3D printing and run using open-source electronics and software. The bottom line of all this is that synthetic biology is coming into our lives, whether we like it or not.

How should the development, accessibility, and commercialization of synthetic biology expand into our daily lives? What should our relationship be with engineered life? I think there's a role for designers and artists to create speculative synthetic biology projects to help both synthetic biologists and the public to discuss what organisms should be designed.

Who am I and how do I fit into all this?

I'm a mechanical engineer and product designer who has recently become fascinated by synthetic biology (and all of bioengineering more generally) while in graduate school. I ended up taking most of my coursework on these topics and researched 3D printed microfluidics and microbial symbiosis. (You can check out some of the projects and publications on my personal website). During my residency at Autodesk's Pier 9, I wanted to explore a near-future synthetic biology scenario that seems particularly plausible: the distributed production of pharmaceutical drugs.

I spoke to friends about the idea before pursuing it got a lot of mixed responses along the lines of:

  • This is awesome! I totally want to grow algae at home (i.e. the San Francisco Kombucha crowd).
  • This is awesome! I want to be able to engineer my own nutrition and drugs (i.e. the Soylent people).
  • Shouldn't individuals / consumers be able to make their own drugs and not rely on big Pharma / bloated healthcare system (i.e. the populist liberal / Silicon Valley libertarian)?
  • I don't really care I'll just buy drugs from companies / dealers.
  • Isn't this like Breaking Bad and everyone will become dependent on drugs (pragmatic realist #1)?
  • This is never going to happen with the FDA / government regulation (cynical realist #1).

I think that decentralized production of drugs and other chemicals is inevitable given the coming accessibility and democratization of synthetic biology. Overall, I think this is a good thing, leading to greater access to drugs, chemicals and materials. I would hope this would develop in a free and open manner, where communities of synthetic biologists design, develop and share organisms for the greater good of all (similar to open-source software). However, I doubt this will happen. Instead, I think it's likely that companies will patent, own, and sell the rights to produce organisms, create and sell synthetic biology projects, and sue individuals who attempt to do it themselves.

Concept:

I wanted to create a project that demonstrates the near-future scenario for distributed drug production that I think is most likely: the corporate design, production and sale of microbes for distributed brewing at home. I wanted to make the project as realistic and plausible as possible, making the audience feel that this type of produce could very well be a real thing. Therefore, I attempted to design a piece that seemed familiar and believable and functioned as closely as possible to the hypothetical device.

Why Spirulina?

I decided to use Spirulina as my drug production organism for a few reasons. First, it's a well known as a green "super food" that people eat as a supplement. Secondly, harvesting Spirulina is simple - the bacteria can be strained from its culture medium using a filter and consumed directly (or alternatively dried and then eaten). Many people grow and harvest their own Spirulina at home. If Spirulina is engineered to produce a drug, you could "take" the drug by eating the organism, eliminating any downstream processing. Finally, Spirulina grows in a highly alkaline environment, making sterilization much easier (most contaminating microbes can't grow in the alkaline media).

And now on the the Instructable...

Step 1: Design Requirements and Engineering

To begin designing the device, I first started researching the design requirements. I broke the research into three categories: (a) Spirulina growth, (b) user requirements, and (c) a feature list.

Spirulina growth requirements:

  1. Spirulina grow best at 30C.
  2. Spirulina require CO2 for photosynthesis.
  3. Spirulina photosynthesize by absorbing light in several photoactive pigments. Therefore, they require sun or artificial light to grow. They also grow best in a 12 hour day/night cycle, similar to natural conditions.
  4. They grow in an alkaline (basic) media that contains a nitrogen source (among other necessary nutrients).

Fortunately, there are several at-home Spirulina system currently on the market that served as a good starting point for addressing these growth requirements. In particular, Spirulina Systems has a starter system that I looked at as a good starting point. I also purchased the starter culture and nutrients from Spirulina Systems (more on that later).

Engineering:

Light requirements

As much as possible. I did a brief literature search to try to determine the light intensity preferred by Spirulina. I had trouble finding one authoritative source (such as a review article on the topic) but I did find severalusefulpapers from which I grokked that the Spirulina like as much light as possible. Two of the studies used light intensities greater than 3000 μmol photons per meter squared per second. (A mol of photons is Avogadro's number of photons).

Do wavelengths matter? Yes. The photosynthetic pigments within Spirulina (including chlorophyll a, beta-cartenoids, and phycocyanin) are excited by narrow frequency bands in the blue and red range (not green). It might be possible to increase production and efficiency by using LEDs at these specific frequencies or alter the nutrient profile (many of the pigments are nutrients) by exposing the Spirulina to particular wavelengths. For this project, I just used warm white light.

Reactor design

After scouring severalresearchpapers, I ended up designing an internally illuminated "airlift" photobioreactor.

Internally illumination - I designed a column light that would sit inside a cylindrical reactor. The column light is simply an aluminum rod wrapped with highest power, warm white LEDs I could find (on Amazon). The light radiates outwards from the center of the column with equal intensity in all directions. Because the light is radiating outwards, the intensity (photons per meter per second) is greatest closer to the light and decreases (by a factor of r^2) away from the light. Therefore, cylindrical internal illumination favors building a tall column with high light intensity on both the inner diameter and outer diameter of the reactor. However, there's an obvious trade off with volume: a tall, narrow reactor will have much less volume (and therefore less Spirulina) then a shorter, fat reactor.

Sizing the reactor - Given this tradeoff between light intensity and volume, I knew I would have to make a few assumptions and rough calculations to pick the diameter and length of the reactor. First, I assumed that the photobioreactor might be able to product 1 g per L per day of Spirulina. I got this number from researching the production rates of internally illuminated photobioreactors in literature. It's obviously a huge assumption, but I had to start somewhere! Secondly, I made another huge assumption: a teaspoon of Spirulina per day would be a sufficient volume for a daily dose of drugs. This is loaded with assumptions to questions that have no answer... particularly the drug concentration a future Spirulina organism might be able to produce (i.e. the % of their biomass that is drug vs. everything else) and the drug requirement for the user. So, I picked 1 teaspoon (Again you have to start somewhere!), which would means I would need a 5 L reactor. To give myself a lot of room for error, I decided that 10-15 L seemed like a good size. Then, I set up a spreadsheet calculation that factored in the dimensions, including the OD of the reactor, ID of the reactor, and length of the reactor and calculated the volume. I then plugged in what I knew about the LED light strip (wattage, luminous efficiency) and calculated the light intensity (photons per square meter per second) at the ID and OD. I played around with the inputs (OD, ID and diameter) and calculated the outputs (Volume, Light intensity) until I was happy. I found that with a 200 mm OD, 60 mm ID, 450mm length, I calculated that the light intensity at the ID would be ~4000 μmol m−2 s−1 and ~1100 at the OD with a total volume of 12.8 L. I also CAD'd up that shape and was happy with the proportions. If you're interested in how I made these calculations, please comment below... I'm also pretty interested in how this problem could mathematically modeled -- I'd love your thoughts on that!

Airlift - Airlift reactors use aeration to additionally mix the contents of the reactor. I found an aquarium sparger in the shape of ring. The sparger would emit air bubbles concentrically around the inner light and up to the top surface, creating an upward current around the inner light tube and then a downward current on the edges of the bioreactor.

User requirements:
What does a future drug home brew device look and feel like? How is it used? What features should it have? To answer some of these questions and inform the product design, I could have done some rapid prototyping and testing, user interviews, and other design research approaches. However, I honestly didn't really have time to do them. Instead, I thought of myself as the hypothetical user and tried to imagine the experience I would want.

I came up with the following user requirements.

  1. An automated experience. Ideally, a daily pill would just pop out of the machine.
  2. In the kitchen. I would want to place the product in the Kitchen, near other appliances.
  3. Diverse drug options. I would want the product to be able to brew up lots of different types of drugs.
  4. Fast production. The existing Spirulina systems take up to 2-3 weeks to begin harvesting. I would want harvesting to begin much sooner.
  5. Feedback on the brewing progress. I would want to know how much Spirulina has grown.

From these user requirements, I created a desired list of features:

  1. Artificial light allows the appliance to be placed away from windows and allows the product to have greater control over growth.
  2. Temperature control at 30C.
  3. Aeration. I decided not to use pure CO2, which should result in higher growth.
  4. Continuous mixing. To ensure the Spirulina receive an equal amount of light.
  5. Spirulina density sensing and "Progress Bar". The system would track the density of the culture and report this density using a progress bar, created by the internal illumination lights.
  6. Automated harvesting. The appliance should be able to sense when the Spirulina should be harvested and then automatically do it.
  7. Filtering and drying the Spirulina
  8. Capacitive touch user interface. The user could operate various parts of the device just by touching them.

This was a pretty ambitious list. I was able to successfully implement 1-4... 5-7 are works-in-progress, and I haven't tried to implement 8, yet.

Step 2: Design Iterations

Before fabricating anything, I went through many iterations of the design in Fusion. In big part of this project for me was trying to imagine what this future product should look and feel like. Going through several iterations in CAD, helped me experiment with forms and materials. Some of the initial forms were inspired by coffee makers and blenders. And I also experimented with the idea of making the bioreactor a mid-century lamp.

Step 3: CAD Design, Materials, and Parts List

Description of the CAD design:


Full CAD model:

Download the Fusion file here. Fair warning: the CAM operations are MESSY at the moment and use the Pier 9 CNC tool library.

Material choices

I used 6061 aluminum for the CNC milled pieces and Corian for the base. I chose 6061 aluminum for its machinability, strength, thermal conductivity (needed for the heat sinks), electrical conductivity (for the capactive touch sensor), and corrosion resistance. Stainless steel is probably a better material choice for the top and bottom plates as it is more corrosion resistant and less reactive to foods. However, given the cost of stainless and that I had never used CAM or CNC milling before this project... I thought it would be best to start with aluminum and work up to stainless.


Parts list

Motors, pumps, and electronics

12V DC Peristaltic pumps(3)

12V DC Heat control PCBs (2)

12V DC Air Pump (1)

12V DC Motor + fan (found in the shop)

Arduino Uno

Adafruit Motor Shield v2

Panel mount USB connector

Panel mount power adapter (found in the shop)

Panel mount toggle switch

Relay board

TIP120 Darlington Transistor

A perf board

1K Ohm resistor

12V DC 30A power supply

14 AWG Power cable


Raw Materials for CNC milling

Corian - (1) 30" x 72" x 12 mm

6061 Aluminum - 1.5" x 10" rectangular aluminum cut into 10" lengths (plates), 0.5" x 3" rectangular aluminum cut into 4" lengths, lots of scrap 1", 2" thick pieces around the shop

Lights, Glass, tubing, and other parts for the photobioreactor

Glass: 200mm OD, medium wall glass (7mm wall thickness), 450 mm long & 60 mm OD, thin wall glass, 450mm long

Strip of warm white LED lights

Alum 6061 Tube for Lights - 2 ft - OD: 1.5, ID: 1.37

18-8 Stainless Steel Threaded Rod, 1/2" - 13, 24" long

18-8 Stainless Steel Flange Nut, 1/2" - 13

Light diffusion film

Tubes, fittings, etc

Bulkhead couplings 4mm OD tube fitting (7)

25' - 4 mm OD silicone tubing

4mm OD Push to Connect Straight connectors (10)

1/4" Push to connect bulkhead coupling (1)

10 ft - 3/16" ID, 1/4" OD silicone tubing for Air

Sanitary Air Filter (1)

1/8" brass ball valve (1)

4mm OD push to connect to 1/8" female NPT(2)

1/4" push to connect elbow (2)

4mm OD push to connect elbow (3)

Gasket material

Fasteners for the base

Bolts for putting together Corian layers 3/8" - 16 - 4.75" (2)

Bolts for front filtering pieces- 10-24 - 4.25" - come in packs of 5

Bolts for rectangular square piece 10-24 - 1"

Nuts for front component pieces - 10-24

Nuts for putting together rings 3/8"

Endmills

Onsrud 65-023 1/8", single flute endmill

Step 4: Making Soft Jaws for CNC Milling on the Haas Mill

What are soft jaws?

Soft jaws are custom, milled vice jaws that are used for workholding. Typically, you would make soft jaws if your piece is is non-rectilinear, i.e. it's curved or has some strange geoemetry that would be difficult to clamp onto using the standard vice jaws.

For my piece, I created soft jaws to clamp the curved aluminum plates.

Material:

I used 2" x 2" aluminum and cut two 8" long segments on the horizontal bandsaw.

Tools:

Haas VF-2SS CNC Mill

Horizontal bandsaw

Dimensions:

A google search revealed the dimensions for the jaws on a Kurt vise.

Screen cast explaining CAM in Fusion:


CAD of Soft Jaws holding the base plate:

Step 5: CNC Milling the Aluminum Plates to Hold the Glass

What are the aluminum plates?

These aluminum plates compressed the glass pieces together to create the reactor.

What were the important features of these parts?

Each plate contained concentric, circular grooves for gaskets. The bottom plate contained I holes to mount bulkhead couplings for water and air and two heat sinks. I mounted cartridge heaters inside these heat sinks to heat the bioreactor and a thermocouple in a 4mm bulkhead coupling to regulate the heating. I milled a funnel into the top plate to allow the user to pour the media and initial starter culture. The top plate also had a threaded 1/2" - 13 hole.

Material:

I used 6061 aluminum. I purchased 10" x 10" x 1.5" stock aluminum pieces for both the top and bottom parts.

Tools:

Haas VF2SS CNC mill

Threading:

After milling, I added a 1/2" - 13 blind thread into the top piece. The threaded rod screwed into this blind thread, compressing the two plates onto the glass pieces.

CAD of the base plate:

Screencast describing the CAM of the base plate:


CAD of the top plate:

Screencast showing the CAM of the top plate:

Step 6: CNC Milling the Aluminum Filtering Mechanisms

What are these pieces?

These pieces are used to filter the Spirulina. The Spirulina is fed into the "dripper" using a peristaltic pump. The liquid then drips onto a filter (not pictured in CAD). The Spirulina is filtered while the remaining liquid drips down onto the collector. Another peristaltic pump recirculates the media back into the reactor.

The top bar is designed to serve as a capacitive touch sensor for the user interface. However, I haven't implemented this feature yet.

Material:

6061 Aluminum.

Tools:

Haas V2SS CNC Mill

Horizontal Bandsaw

Machining Strategy:

I began using 1/2" x 3" x 4" aluminum stock for these pieces. I used this stock to create the dripper and the holder. However, I should have used larger stock. The small stock forced me to first perform a 6 "stock finishing" operations (one for each side) to bring the stock down to the rectangular size of my pieces. For the top bar and collector, I abandoned this strategy and milled them out of scraps of aluminum I found around the shop. I discuss this all in much greater depth in the CAM screencasts below.

CAD model of the filtering pieces:

Screencast describing the CAM for the top bar:


Screencast describing the CAM for the "dripper":


Screencast describing the CAM for the "holder":


Screencast describing the CAM for the "collector":


Step 7: Laser Cutting Gaskets

I used a sheet a 1/16" Buna-N rubber to make gaskets on the Epilog 100W laser cutter. I cut large, flat gaskets to sit between the glass pieces and the aluminum plates and small o-rings to fit around the bulkhead couplings in the bottom canister.

To prep the files, I exported DXFs from Fusion.

While cutting, I used a low frequency (~200) and then made a series of test cuts to find the correct power and speed settings. I didn't write down the power and speed I used, but I believe the power was about 90% and the speed was around 35%.

One tip - cutting rubber on the laser cutter is EXTREMELY smelly. After cutting the rubber, let it sit inside the laser cutter for a few minutes to ventilate. Then, immediately wash the gaskets and the remaining material with water to remove the burnt residue. Your lungs and shop mates will appreciate it!

Step 8: Obtaining the Glass Cylinders

I purchased the glass for my project from Adams & Chittenden, a scientific glass blowing shop in Berkeley, CA. They primarily create custom blown glass pieces used for chemical and biotechnology companies, including glass bioreactors. Check out the gallery on their website: http://www.adamschittenden.com/

My order was fairly simple - two 450 mm glass cylinders of two different diameters: 200 mm (the large exterior glass pieces) and 60 mm (inner glass piece). Glass tubing comes in standard sizes with specific tolerances. For my piece the tolerances were:

450mm long, 200 OD, 7mm thick:

Max OD: 202.6 mm // Min OD: 197.4 mm

Max ID: 190.2 mm // Min ID: 181.8 mm

450 mm long, 60 mm OD, 2.4mm thick:

Max OD: 61.1 mm, Min OD: 58.9 mm

Max ID: 56.9mm, Min ID: 53.5 mm

The tolerance for the tubing length was +/- 1mm, although I gave them special guidance to try to make them as equal as possible. (For example, it would be much better if they were both 449 or 451 rather than having one 450.5 and another 449.5. )

I incorporated all of these tolerances into the design of the aluminum canisters.

Step 9: CNC Milling the Base Out of Corian on the Shopbot

What is this?

The base contains the bioreactor's electronics and fluidics (pumps, valves, etc). It is composed of 12 pieces of flat Corian that were each CNC milled on the Shopbot and bolted together. The aluminum, CNC-milled filtering components also fit into base. Three CNC milled feet fit into the bottom of the base to create a small stand.

Machines:

Omax Waterjet (for cutting the stock material into smaller pieces)

Shopbot CNC Router (for milling the Corian)

Bridgeport Mill

Drill press

Polymer nail gun

Software:

Fusion, OMAX Layout/Make

Material:

Corian, an acrylic blend made by Dupont. It's often used for counter tops. I used "Glacier White". I cut a 30" x 72" sheet of Corian into smaller pieces, which were then milled on the Shopbot.

I also used a 1/4" sheet of particle board as spoiler board.

2D -> 3D Design and Machining strategy:

Corian comes in flat sheets (either 1/2" or 1/4"), yet I wanted the base to have a 3D shape that could contain the electronics, pumps, dryer, tubing, and filtering components. I ended up designing and milling many layers of Corian and then bolting them together into a 3D assembly. I decided not to glue the pieces together so I could quickly assembled or disassembled the pieces as needed.

A few more specific aspects of the base design:

  • I designed the aluminum filtering pieces with the same thickness as one layer of Corian; the filtering pieces fit into the Corian base by sliding in from the outside. I used two long bolts to fasten the filtering components to the Corian base.
  • The base is round except for a small flat section at the back. I needed this small flat section for the panel-mounted components: the valve, the bulkhead coupling for the outlet tubing, a USB-B connection, a power switch, and a 12V DC plug. These panel mounted components required holes that I milled into the Corian stock pieces before milling on the Shopbot.
  • I designed these pieces so they could be milled using 1 operation on the Shopbot (no flip) and with 1 tool (no tool change)... Given that I needed to make 12 different pieces, this seemed like the only feasible method. The bottom piece was the only piece that required a flip.

And, more details on the machining:

  • I started by water jet cutting the material down into smaller stock.
  • Workholding: Before milling the parts, I first nailed the particle board to the MDF table with polymer nail gun and then cut the shape of the stock material into the spoiler board. I cut the particle board such that the waterjet Corian stock material fit snugly into it. I also applied double stick to the entire backside of the Corian piece before setting it into the spoiler board.
  • I used single flute Onsrud endmills (1/8" and 1/4"), which are designed for machining plastics.
  • For the work coordinate system on the Shopbot, I always used the limit switches (machine home) to zero x & y.
  • In the particle board cutout and the CAM setup for each piece, I setup the stock size as 12.5" x 12.5" x the actual thickness of the material (particle board or Corian) with the model (the particle board cutout or the layer) positioned centered in the stock. If you'd like to learn more about this, watch the Screencast below where I explain much more detail or comment below.

Other notes on fabricating the base:

  • I sanded the finished parts using 180, 320, 600 and 1200 grit sand paper.
  • During assembly I had to change some of the parts slightly to make components fit... I hand drilled several holes and also used the Dremel.
  • While machining the base, I also milled a small lid out of Corian to cover the funnel in the top plate.

CAD Model of the Base:

Screencast describing how I CAM'd these pieces:


Step 10: CNC Milling Aluminum Feet for the Base

What is this?

These are the three "feet" that create a stand for the base.

Tools:

Haas V2 CNC Mill

Horizontal bandsaw

Material:

6061 Aluminum. I think I used 1.5" x 4" rectangular stock that was cut down on the horizontal band saw.

CAD model:

Screencast of CAM:


Step 11: Polishing Aluminum Pieces

After CNC milling the aluminum pieces, I polished them using the rotary polishing machine (I actually don't know what this machine is called... but it's pictured above).

Polishing is not for the faint of heart! I probably spent a total of 6 hours polishing all of my pieces. The aluminum gets very hot while polishing and you will get very dirty.

Rouge will cut your polishing time. Use the coarse, red (pictured above) rouge first and then finish with the fine, white (also pictured above) rouge.

Step 12: Dryer: 3D Printed Housing and Water Jet Heatsink

What is this?

I designed a Spirulina dryer that would sit inside of the base and blow hot air onto the Spirulina that has been filtered. The pieces is composed of

  • a DC motor with a fan blade,
  • a 3D printed base which mounts into the Corian base (where there are holes for air intake) and holds the DC motor,
  • a waterjet cut heatsink, which holds a cartridge heater and a thermocouple for temperature regulation,
  • and a 3D printed tube which holds the heatsink and directs the airflow to the filtered Spirulina.

Unfortunately, the dryer didn't work well, and it isn't currently operating. The tube is just not very aerodynamic... when you put the heatsink and tube on top of the fan, the airflow reduces to 0. I guess this is what happens when you design a fairly complex part like this for the first time. I haven't had a change to redesign this, but I hope to!

If want to learn more about this part, check out the Screencast I did of the CAD design (several steps earlier), in which I describe this part in much greater depth.

Materials:

A chunk of 1" thick scrap aluminum for the heatsink.

A cartridge heater.

A thermocouple from the heat regulation PCB

ABS-like Polyjet 3D printed material

Tools:

OMAX waterjet

Bridgeport Mill for facing the 1" thick scrap aluminum down to the correct thickness

Drill press for drilling and reaming the holes to the precise size.

Objet Connex 500

Fabrication steps:

  1. I first designed everything in CAD to fit into the Base.
  2. I milled the aluminum using a face mill on the Bridgeport to bring it the correct thickness.
  3. I then cutout the heatsink on the waterjet (quality = 5)
  4. I then 3D printed the base and the airflow tube. To remove the support material, I used the high-pressure waterjet and several different hand tools.
  5. I then tried to assembled everything. The 3D printed parts were too tight (to fit into the Corian, to fit into eachother, to fit the heatsink in, etc) so I hand-sanded and filed the parts until the parts fit.

CAD model:

Step 13: Corian Lid and Aluminum Light Tube

The home stretch!

The milled the Corian lid at the same time as making the base. To get the 45" angle, I used a 1/2" chamfer endmill. For workholding... I used (LOTS) of double sided tape. For some reason, the pocket toolpath created strange ridges on the part (first image), which I sanded out by hand.

The aluminum tube for the lighting was pretty simple. I took the aluminum tubing I purchased from McMaster, measured it, cut it on the cold saw, and then wrapped LED lights around it. To make sure the ends of the lights stayed on the tube, I used a gratuitous amount of doubled side tape (in addition to the adhesive backing already on the lights).

Step 14: Electrical Design

Micro-controller - operates all of the pumps and individual components:

Arduino Uno

Adafruit Motor Shield v2 (a shield for the Uno)

Relay board - switches to turn on/off the air pump and two temperature control PCBs

I used the SainSmart 4-channel relay module. I learned how to use it here.

2 digital output pins controlled 2 relay switches (one for the air pump, one for a temperature control board). For this board, digital LOW switches the relay ON.

The relay board was powered with 5V from the Arduino and also connected to the common ground.

Temperature regulation board -

The board has a build-in temperature feedback loop that you manually set for a temperature. I set it to 30C. The board comes with a thermocouple. I connected the thermocouple to the 4MM push to connect bulkhead coupling to sense the temperature in the reactor. I connected 12V to KO and the catridge heaters between K1 and ground. Thus, when the chip switched the heating on, it completed the circuit, heating the cartridge heaters.

PWM control of lights using TIP120

I wanted to control the intensity of the LED lights, so I built a super-simple circuit using the TIP120 darlington transistor. I followed the instructions here to build this circuit.

Step 15: Assembly and Wiring

And then I assembled all of the pieces.

It mostly came together well. A few parts didn't fit properly... a problem which was solved by sand paper or the handheld Dremel.

The biggest challenge was assembling the top part (glass, aluminum pieces, threaded rod, heaters, thermocouple) to the bottom part in the final assembly step. It took several attempts to assemble the system correctly (for example, sometimes the threaded rod would poke out a lead from the Arduino).

Step 16: Adding Spirulina and Media

I purchased the starter culture and media from Spirulina Systems.

I used 10L of filtered water and 2L of Spirulina culture. I also added the appropriate amount of Starter nutrients (about half a bag) and chelated iron.

Step 17: Creating Accompanying Pieces: a Pill Maker and Bottles of Drugs

To help convey the narrative - brewing pharmaceutical drugs at home - I create a few accompanying pieces: bottles of starter culture for various pharmaceutical drugs and a gel cap filler.

I sandblasted the letters onto the bottle using a vinyl cut stencil.

The gel cap filler was CNC milled on the Haas Mill.

CAD of Exhibit:

CAD of pill maker:

Screencast discussing how I made the gel cap filler.

Step 18: The Final Installation

Comments

author
Hecco Davva made it! (author)2017-03-31

I made a simply version for my school project. Thanks for inspire. you're amazing

17619476_10155163206479137_2139486056_n.jpg17741329_10155163206474137_433458523_n.jpg17742315_10155163206484137_294245308_n.jpg16443517_10155163206389137_601437546_n.jpg
author
wgpatrick (author)Hecco Davva2017-04-08

Wow. This is incredible! Well done!

author
wgpatrick (author)wgpatrick2017-04-08

If you try it with water or spirulina, I'd love to see photos!

author
Engineering (author)2015-11-25

Legalities aside. Taking anything made in this format unless you can verify the end product is very dangerous, like in deadly dangerous.

Using this design to produce non-medical products on the other hand is interesting.

author
snowdruid (author)Engineering2016-08-18

i think at this point this is a non issue since organisms that actually produce useful substances are regulated and more often then not patented so unless your a bored millionaire or a hardcore bio hacker you wouldn't get your hand on those anyway. also in biotechnology there are two main processes upstream and downstream. upstream deal with production while downstream deals with refining and testing the raw product (obviously a bit simplified). you would never use a product in its raw form !!!

author
wgpatrick (author)Engineering2015-11-25

Hi there ... yeah this is definitely a good point. I'm pretty curious when/if people begin making their own chemicals and drugs at home how they deal with this issue. Or maybe it's not an issue? If this idea is actually commercialized, perhaps the hypothetical company that is producing Farma takes on the liability for the quality of the product (they control the engineering and supply of the organisms). Maybe there's some way to test the culture for improperly produced chemicals.

author
GwyneddS (author)wgpatrick2015-12-19

I would imagine a testing kit would come with every culture, to be sure. Otherwise lawsuits would abound no matter who claims liability

author
HenriqueS17 (author)2016-06-24

Hi Will!

What is the current status of the project?

Do you hold any patent on the design?

author
Szőcs-PuskásT (author)2016-03-29

This work is absolutely amazing!!! Thanks a lot for sharing it. Can I ask approximately how much time it takes to build this bioreactor and roughly how much would it cost to make?

author

It took me about 2-3 weeks to design and 2 weeks total to build, working nearly full time.

author
AmyKarle (author)2016-03-15

hi @wgpatrick! Aprox how much does this bioreactor cost to make?

author
wgpatrick (author)AmyKarle2016-05-19

Hey Amy - this was about a $1000 bucks total... the main costs were the glass tube, corian, and billets of aluminum (probably about 85% of the cost). Everything else was relatively inexpensive.

author
AmyKarle (author)2016-03-15

hi @wgpatrick! Aprox how much does this bioreactor cost to make?

author
kit.haberman (author)2016-02-07

on the down side this could be used to make bio-weapons as well

author
sypher (author)2015-11-29

one of the most hardcore Instructables I have read in a while. I am skeptical of the yield, but I really don't care, this is awesome, and useful.

author
helicase (author)2015-11-21

Hi, I really like your project. Awesome work.
But I've some major concerns... Not on the reactor but on what you are going to do.

First, you are creating an genetically modified organism (GMO) for producing your drug. I'm not sure if you are allowed to do that, here in germany you are not.
You need an certified S1 Lab for that, you don't want to get spirulina into nature by for example waste water and produce your drug. So you have to autoclave everything before disposal.

Anyway, assume it is allowed, I guess you introduce a plasmid for drug production into Spirulina? So you have to keep them under selection, are you going to treat it with antibiotics or are you using a deficiency system? Both ways are expensive, I'm not sure you have any financial benefit form just buying your drug.

Further how do you measure the concentration of your drug? I see danger of getting to less or to much of the drug. Are you sure your spirulina drug it taken up by the body equally to the pharma drug? Because you want to hit the terapeutic window. Is your drug stable in spirulina (wet or dry)?

I think you are facing some hard difficulties here for drug production.

author
lunches55 (author)helicase2015-11-23

Exactly, these concerns are major major hurdles. However, I think it is an interesting concept piece and very forward thinking. Great job! Amazing!

author
wgpatrick (author)lunches552015-11-23

Hey guys -

Thanks for all the feedback. I agree there are a lot of technical challenges from making this idea a reality. I guess its worth reiterating that my main goal with the project is to just demonstrate the concept in order to create public discourse about whether we should build anything like this at all. To render the speculative concept, I decided to not address every technical issue. I hope that makes sense... but it was a choice pretty early on.

That being said! A few responses to your thoughts:

Regarding lab safety: Yes, similar regulation exists here in the US and if I did in genetic modification I would need to work within a biosafety level 1 lab.

Other Regulation: To become a reality, the engineered organisms would have to be certified by the FDA. For example, a genetically modified salmon was just approved by the FDA. There might be other regulatory hurdles; if anyone knows, please comment!

How to modify the Spirulina: I'm not really sure how hard it actually is to engineer Spirulina. I believe its quite routine to modify other cyanobacteria (example: synechococcus elongatus) ... and perhaps the same methods would work for Spirulina. Maybe CRISPR works for Spirulina. There is one start-up company working on genetically modified Spirulina (http://matrixgenetics.com/) but they have not published their methodology.

Antibiotic selection: It's hard to know whether you would need antibiotic selection. One of the main benefits of using Spirulina is that they live in an alkaline environment and there's a low risk of contamination. So I don't think you would need to add antibiotics to reduce the risk of contamination.

Now, I think what you're saying is that you would add the antibiotic resistance marker near the genes of interest (for producing the drug) ... such that it would be unlikely for the Spirulina to evolve away the drug producing phenotype (because losing the drug making phenotype would likely mean losing the antibiotic resistance). That could be totally necessary... I really don't know and I don't think anyone would know if this is a problem until they actually modified the Spirulina with the genes of interest. (If anyone else has any thoughts on this, I'd love to hear them!)

On the concentration: Yeah this definitely seems like a huge issue. Maybe there's some way to engineer a genetic circuit into the Spirulina to control the concentration inside? I don't know... but you raise a very good point.

Drug stability: Again, don't know. I'm not sure what the stability of these drugs are in wet/dry conditions. I haven't looked into this.

author
bkonfuzius (author)wgpatrick2015-11-24

First of all I am a Biotech student. That being said I think what you did is a proof of concept (a quite awesome one).

I understand you are a mechanical engineer? Synthetic biology is interdisciplinary and I suggest that you team up with other people to develop this further.(I am pretty sure that you have done this to some extent already).

I am not sure how much you have heard about iGEM but if you haven't considered it yet I would strongly suggest that you get in touch with the biotech department at your university or the team closest to, because THIS is the spirit!

http://www.igem.my/home/

Now my personal 2 cents about drug production:

Spirulina as a "super-food" is just a rip off. I haven't come across any convincing evidence that you would eventually benifit from it.

People may correct me, but I also believe that there is no pharmaceutical product out there that is produced in spirulina.

The same goes for phototrophic organisms in general. It is just very difficult to achieve considerable yields and carbohydrates are dirt cheap(compared to the final product) even if a micro algae is used, they are usually kept the dark and fed some sugars.

Also, nobody uses antibiotic selection markers anymore in production. helicase was not referring to the avoidance of contamination but to check whether some of your spirulina might spontaneously loose the plasmid and stop producing your product. Traditionally and on lab-experiments you would couple the desired genes with some antibiotic resistance to make sure that cells which have lost the plasmid die.

However, this lack of stability of the engineered strains is the reason while you would prefer to incorporate the genes into the genome.

CRISPR/Cas9 is an awesome and relatively new technology to overcome these issues but using it comes with a number of legal issues.

I will stop now but I hope I made clear why I said it is about teaming up and be one happy interdisciplinary family.

PS: I love the fact that the first application you had in mind was to contest big pharma monopolies!

author
wgpatrick (author)bkonfuzius2015-11-25

Hi there!

Thanks for all the feedback. I really appreciate it.

iGEM rocks! It's an amazing community. I actually attended this year as a judge for the hardware track. For future design projects, I would love to work more closely with synthetic biologists.

Yeah, you're definitely right that metabolic engineering in phototrophic organisms is much less common and more challenging than Yeast or E. coli. And there are few examples of engineering Spirulina.

I picked Spirulina because I thought the organism made the most sense in the narrative of the piece. Particularly, Spirulina is seen as a nutritional supplement, grown at home, and robust to contamination. I also speculated that if the chemical was stable inside the Spirulina organism, then the user could simply consume the organism to receive the drugs... meaning that no downstream processing of the chemical (purifying it from the organisms, etc) would be required (this seems like a hard thing to do at home).

I'm in total agreement that there are a number of technical leaps that would be required for Spirulina to brew drugs at home. With this project, I'm attempting to demonstrate one plausible approach. There might be less technically challenging and more user friendly approaches of making drugs at home... and I think it's important to discuss all the possibilities.

author
bkonfuzius (author)wgpatrick2015-11-26

ups my bad. was a bit in a hurry when i wrote this.

didnt't realize that your profile links to your cv. ;)

also, the link i posted should be http://igem.org/Main_Page not igem.com.

author
Karl EmmanuelS (author)wgpatrick2015-11-24

You don't need GMOs to produce goodies in your reactor.
Yeasts. Fungi and bacterium found in nature can be used to produce lots of goodies like protein, vitamins and natural antibiotics.
A huge plus is that your system can run on its own and is useable for bacterium since agitatin is done by air (bacteria and propellers don't mix well)

author
wgpatrick (author)Karl EmmanuelS2015-11-25

Yeah good point about using non-modified organisms. I guess on the GMO debate, I'm pretty firmly on the pro-GMO side, although I'm interested to see exactly how our foods and products become engineered. As I hope is clear with this project, I see many potential dangers (as well as benefits) of modifying home-brew organisms (yeast, Spirulina, etc).

I've also been fascinated by the possibility of making engineered versions of fermented foods, such as yogurts and Kombucha. Lots of interesting possibilities there from adding in additional nutrients to engineered probiotics.

author
Marcos_El_Malo (author)wgpatrick2015-11-24

This is fascinating work you are doing, and you're right, this needs to be publicly discussed (hopefully rationally, but . . . ).

There isn't any question in my mind that black labs and black clinics will exist if they don't already. Very expensive tech will become cheaper, and perhaps someday we will see an electron microscope on Instructables as well as other sophisticated lab equipment.

Anyway, public debate will (hopefully) lead us to formulate the right policy, something balanced to allow DIYers to create their own synthetic biotics. I don't fear illicit bio-drug labs (nor people using drugs). What I worry about is environmental dangers from shoddy labs using shoddy safety practices. I feel certain that there will be biological disasters in the future. Hopefully they will be localized and not global. (To be clear, I believe this will happen regardless of the strictness or looseness of any regulatory regime.)

Hey, and I want to thank you for something else. While writing this comment, I just had an idea for short story (or element of a larger work). The idea is this: criminal organizations offering STEM scholarships. Maybe building up the educational infrastructure in their spheres of influence.

author
Uuvini (author)Marcos_El_Malo2015-11-25

Homemade electron microscope https://www.youtube.com/watch?v=VdjYVF4a6iU

author
ElizabethC28 (author)2015-11-24

Wow. Amazing! I can see this being used for decentralizing distribution to a point, but once the money speaks, it'll be more effective to produce drugs this way for an area, as opposed to just a one person supply. As someone with chronic illness I can't see keeping up with growing my own meds, but putting farms for anti malarial where outbreaks are, or growing drugs in hospitals, that's useful!

As mentioned below, having the GMO organism escape into the wild is a big risk, havoc would ensue. That's the big minus of growing drugs at home this way. Not everyone has the time or skills to handle such stuff properly, and the sicker the person the better a bottle of pills works. Or just growing the original plants like pot.

You never know where new tech will lead, so it's way up in the air...

author
wgpatrick (author)ElizabethC282015-11-25

Thanks for the feedback! I'm also really curious how much distribution production makes economical sense.

If it's possible, I'm also pretty sure individuals will try to produce their own drugs, even if it's illegal or dangerous (the Breaking Bad scenario)... How could this situation be regulated or control this situation? DNA synthesis is fairly centralized (at least at the moment) - so maybe synthesis companies/organizations can keep track of what people are buying and try to limit people from putting together the necessary genetic elements to produce a drug. But - one can already imagine fairly easy ways of getting around this.

author
stnfre001 (author)2015-11-25

I don't want to get involved in the discussion regarding home made drugs, but the design is great! Really inspiring, the presentation is clean and crisp! If only I had a cnc close to home!

author
wgpatrick (author)stnfre0012015-11-25

Thanks!

author
ferraalb (author)2015-11-24

W-O-W, this is plain science fiction, congrats!!

author
jdenslinger (author)2015-11-24

The first thing that came to mind is "Ooh! Axlotl tanks!" The second being "Oh, right, they're not women" The third, "I wonder how many people would get those references"

But then the fourth thing to come to mind was "Wow, I hope this is step 1 of 1 and he just didn't make any more steps" because usually people divide their projects into steps, not a single monolithic brain dump with pictures. :S

Other than that, wonderful artistry, and I wouldn't mind having something like this converted to an LED lamp or possibly as a biodiesel incubator :D

author
jdenslinger (author)jdenslinger2015-11-24

Apparently instructables.com broke their things.
I didn't realize this was broken into steps until the next project I looked at is also in "view all steps" mode (and I seem to not be able to revert that) AND I can't edit my previous post... not sure why I'm being treated as not-the-author of my own post, so I'll blame instructables web staff for breaking that too :D

author
wpierce3 (author)2015-11-24

People are also looking for ways to set up a system to produce a large enough quantity of spirulina to be able to use it as a food supplement.

A larger build could do that.

Or use it as an air filter by putting outside air into the bottom and allowing it to bubble through in small bubbles cleaning and oxygenating the air.

author
michaelnelson (author)2015-11-24

Awesome engineering and construction! With that being said, it makes a beautiful display, but this won't be very practical in the long run. I've grown phytoplankton (nannochloropsis and tetraselmis) for a couple of years. After a LOT of experimenting, plastic bags are without a doubt the most efficient way (in terms of time, energy and money) for a hobbyist to culture it. Your number one concern is contamination, and with plastic bags you'll have much less worry about it since you have less to sanitize between batches.

author
ThomasK19 (author)2015-11-21

Wow! I better don't ask what you spent in time and money into this project. Are you planing to make a commercial product out of this?

author
wgpatrick (author)ThomasK192015-11-23

I'm not planning on making this a commercial product. My hope is to create public discourse around the use synthetic biology at home.

author
echodog (author)2015-11-21

This is amazing work. Your ability to create this device from the design right up through the machining and assembly is truly incredible. Incredible skills.

I have a couple questions--if I understand correctly, you will be measuring the Spirulina's progress by tracking the density of growth based on the amount of light transmitting through the growth medium? If that is correct, is there a sensor that does this job? I have read through the instructions a couple times, and I'm not seeing mention of that.

author
wgpatrick (author)echodog2015-11-23

That's right. I'm hoping to use a ColorPAL sensor (https://www.pololu.com/product/1608) to measure the optical density of the culture liquid (higher density = more cells). A paper came out this year demonstrating the use of the sensor for continuously measuring algae density in a culture (http://www.mdpi.com/1424-8220/15/3/4766/pdf). I'm hoping to do something similar

author
terrefirmax2 (author)2015-11-22

In Florida most grow houses get tipped off by the power companies- either too much being used or not enough. Govern yourself accordingly. Sounds very interesting.

author
Chronoallusion (author)2015-11-20

This is amazing. I do not think I have the skills.

author
smcmasters1 (author)2015-11-20

Very interesting. Bioengineering is way out of my league, but I still love to read about it. This is an incredible concept and your design is beautiful. I'd have it in my kitchen, that's for damn sure. Great job man. Great job.

author
Jedi_zombie85 (author)2015-11-20

Very interesting more of a physics man myself but always like to dabble in biology, thanks for sharing the information

author
tomatoskins (author)2015-11-12

This is cool! I love the bioengineering field!

About This Instructable

47,357views

689favorites

License:

Bio: I'm friendly, I swear!
More by wgpatrick:How to cut polycarbonate tubing using a table sawA Big, Luxurious Stretch Tent for Burning ManA Big, Luxurious Marquee Sign
Add instructable to: