Marchantia Growth Facility

Problem Statement

Introducing a new chassis to iGEM has many challenges, not least of which is encouraging other teams to try the new standard. The Marchantia Growth Facility (MGF) was proposed to promote the adoption of plant based research by offering a dedicated research focused environment in which to grow the plants, which can be made and modified cheaply and easily. Growth chambers for the cultivation of plants are widely commercially available in a variety of configurations, from the simple cold frame to advanced climate control devices. They are, however, generally unsuitable for growing small lower plants such as marchantia in a synthetic biology setting. The reason for this is two-fold; firstly, commercially produced growth chambers are usually designed to grow higher plants such as wheat and are typically very large pieces of equipment. Furthermore, growth chambers with the ability to perform active climate control are costly and have a much greater feature set than is required for the controlled cultivation of marchantia. Secondly, current low-cost solutions for plant growth devices are generally of the greenhouse type, and are thus incapable of maintaining any active climate control

In light of this, the problem statement for the Marchantia Growth Facility (MGF) was given as follows;

The task is to create a low cost device capable of cultivating marchantia and facilitating research by controlling the light conditions and air flow to the plants. In addition, the device should act to prevent the growth of foreign organisms on the marchantia plates, which could contaminate the specimens and hamper plant growth.

Hardware

As shown below, the MGF consists of a cuboidal chamber, which is divided into four subchambers. Each of the subchambers has an identical fan and lighting unit, all of which are controlled by an arduino microcontroller. The fans are 40*40*10mm in size and run at 5V DC. The lighting unit is powered by five Adafruit V2 Neopixels, which output around 2600 lux at maximum brightness.

Software

The MGF is controlled entirely from the software uploaded to the arduino. An example program is given here, which allows the user to control the behavior of each lane by the hour. This is accomplished by calling a function called "hourSet", which sets the light for a lane to the required colour and intensity and turns the ventilation on or off. The behavior then persists for a block of n hours, where n is set by the user in advance. The program can also encode consecutive behaviours, such as a day/night routine. Control of the NeoPixels is achieved using the Adafruit NeoPixel library for arduino, which must be downloaded and installed on the machine used to program the arduino.

Manufacture

The hardware for the MGF was designed in VCarve Pro to be cut out of 9mm MDF and 3mm acrylic using a CNC router. This file contains all of the design files in VCarve and dxf formats. The design assumes the use of a 3mm cutter, normally positioned to follow the outside of rectangular vectors, and the inside of circular vectors. The exception to this is the pocket sections of the lid, which should be cut to a depth of 5mm inside the pocket vector, and the three line vectors on the base, which should be cut to a depth of 5mm along the line.

Assembly Instructions

Materials required; one complete set of MDF parts, one complete set of acrylic parts, one arduino microcontroller, one project box approx 100mm cubed, sixteen M3*30mm cap head screws, sixteen M4 washers, thirty two M3 nuts, five 40*40*10mm 5V DC fan units, twenty Adafruit flora Neopixels, one stripboard, two 5V 2A regulators with heatsinks, one 9V 15W power supply, one reel red equipment wire, one reel black equipment wire, one reel yellow equipment wire, one box of panel pins, one bottle of wood glue, one bottle of acrylic cement, spray paint (optional).

Please note that the instructions presented in these sections assume a degree of experience in woodwork and soldering, and as such, construction of the MGF is not advised for the novice maker.

Mechanical Assembly

Begin by assembling the outer walls of the chamber onto the chamber base. First, drill holes of the same diameter as your panel pins around three sides of the base and on the back edge of the two side panels, pitched at around 50mm . Then assemble the joint using glue on the mating faces and secure by knocking a pin into each pre-drilled hole. Clamp and wait around four hours until the glue has cured.

Now assemble the inner walls of the chamber as a sandwich with the outer walls. It is important to check the inner walls for a good fit before gluing, as some small adjustments may be necessary. If the interior panels are found to be slightly oversize, they can be reduced to fit using a belt sander. Once glue has been applied, clamp the joint until the glue has cured. This will take longer than the first joints due to the large area being glued, so wait around six hours for the glue to cure.

The inside of the assembly can now be painted, and the dividers installed. It is suggested that if the assembly is painted, the inside face of the lid is also painted at the same time. Depending on the tolerances of the MDF parts, the dividers may require some force to be installed, which can be applied with a wooden mallet without danger to the acrylic. Then rotate the assembly so that the front is facing upwards and glue the front panel onto the dividers using acrylic cement, such that it is flush with the top of the dividers. Once the cement cures, seal the edges of the front panel with a bead of silicone sealer.

Once the silicone sealer has cured, acrylic cladding can be attached to the MGF, starting with the side panels. Mix up a large quantity of epoxy and spread it in one smooth, even layer onto the acrylic. Place the acrylic onto the MGF and clamp until the epoxy cures, making sure that the clamping pressure does not displace the cladding from its original position. Repeat this operation first with the other side panel, and then with the back panel.

Electronic Assembly

Begin by fixing five NeoPixels to the base of each light unit (the panel with the central hole) in a ring around the central hole using epoxy resin, making sure the arrows on the data pads of the NeoPixels follow each other in a ring, as shown below. Once the resin has cured, connect all of the positive terminals together using short lengths of equipment wire. It will help to tin the ends of the equipment wire and put a blob of solder on each pad prior to making each connection. When the positive terminals are connected, connect the ground terminals in the same manner (It is extremely helpful to use different colours of wire for the different terminals, as it allows you to quickly identify the wires after they have been routed to the control box). The data terminals can then be connected in a similar manner, but they should not be connected in a full ring; i.e. one of the links in the rink should be broken, so that there is a start and an end to the chain of pixels. Then solder half a metre of wire to the positive, ground and data terminals of the start pixel and pull all three wires through the central hole.

It is important at this point to test the operation of the NeoPixels, as the solder joints cannot be altered once the diffusion box is assembled. This can be achieved by connecting the NeoPixels to an arduino, one light panel at a time, and running the StrandTest program included with the NeoPixel library. If the pixels do not all light up correctly, check the connections on the solder pads for breaks or fragile joints.

Assemble the fixings by inserting a screw into each of the edge holes from the pixel side and secure with a nut on the bare side. It is important to make sure that the nut is sufficiently tight to hold the screw when the light box is attached to the lid, as it is impossible to tighten it once the light box has been assembled. Similarly, it is advisable to test the NeoPixels before the final assembly is made, which can be achieved using the strandTest program included in the Adafruit NeoPixel library. First edit the default parameters in the program to fit the setup by changing the number of pixels in the strip object (the first argument) to 5, and note the pin assignment of the strip. Then power down the arduino before inserting the wires from the strip into the headers on the board and finally powering the board on. Once all of the light modules have been tested, glue the diffusion frame together using acrylic cement and finish the light box assembly by joining the base to the diffusion box with acrylic cement.

The fan interface control schematic is shown below, and is available as an EAGLECAD file here. Note that the schematic specifies two voltages as power supplies, 9V for the arduino and 5V for the light and fan units. Whilst the 9V supply will draw current on the order of milliamps, the 5V power supply can draw as much as 2 amps at full operation. Caution should therefore be exercised in choosing a power supply, and it is advised that separate 2 amp regulators with appropriate heatsinks are used to provide the current for the fans and for the lights, in order to keep the regulators from overheating.

Final Assembly

Feed the wires from each diffusion box through one of the holes in the lower portion of the MGF lid and insert the screws into the fixing holes. Secure each screw with a washer and a nut, tightening the nut with a spanner to just over finger tight. Then insert the fans into their pockets, taking care to orient them such that they will suck air from the outside of the box, rather than the inside. Then route all of the cables along the channels, securing periodically with masking or electrical tape. Position all of the cables in an upright position and lower the top lid section onto the bottom lid section, guiding the cables through the hole in the top lid section. After the fit of the assembly has been checked, remove the top lid section and apply wood glue to the whole of bottom lid section, taking care to give a margin of at least 10mm around the fans. Then sandwich the two halves of the lid section together as before, clamp and let cure overnight.

The final piece of cladding can now be attached to the lid using epoxy resin, and the control box can be screwed into place using the four mounting holes in the lid cladding. Solder the fan leads and NeoPixel power leads into place in the electronic assembly, and connect the data pins on the arduino. The MGF is now fully operational.

Mini Growth Facility

Problem Statement

Whilst the MGF is easy to construct for those with enough prior experience and the required machinery to do so, it is not suitable for first-time makers who lack a mentor to guide them through its construction. The MiniGF was conceived as a suitable project for first time makers that incorporates most of the capabilities of the MGF.

The problem statement for the mini growth facility was therefore given as follows;

The task is to devise and construct a smaller, simpler growth facility, which can easily be constructed entirely from acrylic sheet with no prior experience in electronics or mechanical fabrication.

Hardware

Much like the MGF, the MiniGF is a cuboidal chamber containing a lighting unit. The difference between the two is that the MiniGF is designed to hold a single specimen, whilst the MGFcan hold up to four specimens at once. This unitary, modular design allows the lab growing the specimens to have as many or as few growth facilities as needed, eliminating the need to construct a large and possibly overpowered growth facility.

Software

As the MiniGF contains many of the elements of the MGF, the method of control is essentially identical. As in the case of the MGF, the behavior of the MiniGF is controlled entirely through the program uploaded to the arduino. An example program is given here , which allows the user to control the lighting condition in the MiniGF by the hour. As in the case of the MGF, the lighting condition can be specified for an arbitrary integer number of hours, after which the condition can change to another state for a length of time specified by the user. The function which commands this behavior is called "HourSetMini", and it is closely related to the "HourSet" function used to program the MGF. The difference between the two is that "HourSetMini" contains no arguments for setting lane number or fan power, as the MiniGF contains neither of these features. Control of the NeoPixels is achieved using the Adafruit NeoPixel library for arduino, which must be downloaded and installed on the machine used to program the arduino.

Manufacture

The hardware for the MiniGF was designed in VCarve Pro to be cut out of 3mm acrylic using a CNC router. This file contains all of the design files in VCarve and dxf formats. The design assumes the use of 3mm acrtlic and a 3mm cutter, normally positioned to follow the outside of rectangular vectors, and the inside of circular vectors. The exception to this is the line vectors on the panels, which sould be cut to a depth of 1.5mm on the line itself. If access to a CNC router is not available, the parts can be cut using a jigsaw and router, and finished on a belt sander.

Assembly Instructions

Materials required; One complete set of acrylic parts, four Adafruit NeoPixels, one reel each of red, black and yellow equipment wire, one Arduino, one bottle of acrylic cement, epoxy resin, one arduino power supply.

Note that these instructions are intended to be performed in the order listed. Failure to perform a step or performing steps out of order increases the likelihood of difficulties arising in construction.

Electrical Assembly

Begin by fixing five NeoPixels to the base of the top panel (the panel with the central hole) in a ring around the central hole using epoxy resin, making sure the arrows on the data pads of the NeoPixels follow each other in a ring. Once the resin has cured, connect all of the positive terminals together using short lengths of equipment wire. It will help to tin the ends of the equipment wire and put a blob of solder on each pad prior to making each connection. When the positive terminals are connected, connect the ground terminals in the same manner, noting that it is extremely helpful to use different colours of wire for the different terminals, as it allows you to quickly identify the wires after they have been routed through the hole. The data terminals can then be connected in a similar manner, but they should not be connected in a full ring; i.e. one of the links in the rink should be broken, so that there is a start and an end to the chain of pixels. Then solder 10cm of wire to the positive, ground and data terminals of the start pixel and pull all three wires through the central hole.

It is important at this point to test the operation of the NeoPixels, as the solder joints cannot be altered once the diffusion box is assembled. This can be achieved by connecting the NeoPixels to an arduino, and running the StrandTest program included with the NeoPixel library. If the pixels do not all light up correctly, check the connections on the solder pads for breaks or fragile joints.

Mechanical Assembly

Place the back panel face down onto a flat, clean surface. Attach one of the side panels to the back panel using acrylic cement along the entire mating edge, taking care to align the grooves on the two panels, and use a square wooden block to support the side panel until the cement cures.

Check the fit of the top panel in the grooves of the back and side panels, then fix the top panel in place with acrylic cement. The second side panel can be fixed to the assembly in the same manner as the first.

The front and base panels can then be assembled onto the MiniGF and secured with acrylic cement in either order.

Final Assembly

Connect the power leads of the NeoPixels to the 5V and GND pins of the pre-programmed arduino, and the data lead to pin 6. The MiniGF is now fully operational.