Team:Valencia UPV/Design

Valencia UPV iGEM 2015

Overview

Where will our project flourish? How will the information be transmitted to the seed? What’s needed in order to have access to the multiplexed products? Do I have to transmit the light pulses by myself? All those questions had to be answered somehow. Sure, it’s easy to create a genetically engineered machine and try it in a LAB, but how will it be done once such machine is ready for the public? Not everyone knows the lab protocols, safety protocols or has the knowledge or economic capacity to reproduce those conditions individually.

So how about leaving all the job to just one device and two simple buttons? That’s what our device pursues, and here its displayed:

This is our device, our lamp, where all the process of transformation and product selection happens. It has been designed to form a closed and isolated environment so that there’s no light interference and no in/out contamination. Additional considerations have been taken so that the seeds can develop appropriately in such environment and product extraction can be performed.

If you wish to see it in your hands, download the Augment app (available for Android and iOS) in your smartphone and print the image that follows this link. Once you’ve done so, scan the image with the Augment app and check our model thanks to the power of augmented reality. If you had been at the 2015 Jamboree and you have our card, scan it, it’s the same image.

Watch the video for a brief description of the device and its usage.

(aqui el video cuando lo acabe)


Considerations

Although we couldn’t develop our project until its final stage of implementation in seeds, the device was designed taking the following assumptions:

  • The biological multiplexing circuit was truly functional inside soy seeds.
  • The seeds could produce four medical products.
  • There is enough room for a sufficient amount of seeds that will be enough as a medical dose.
  • The production cycle lasts 15 hours with two periods of information transmission of 6 hours and two waiting periods of 1.5 hours.

At the Jamboree we presented the device programmed and designed for demonstration, meaning that it didn’t took into account the RTC usage and the control circuit relies entirely on one of the integrated timers of the microcontroller.

Device

Our device measures 41.27x26.27x21 cm (16.25x10.34x8.27 inch). It’s composed of the following parts:

  • Body and battery lid

    • Its the base of the entire model. It contains the batteries compartment (two 4xAA battery holders in parallel) at the bottom and secured in place with a lid and a screw. The battery wires go parallel to the contour of the body in a groove that it’s sealed later. It incorporates a handle and a spout through which a vacuum pump can be connected in order to extract the medicine from the seeds, and serve it to whom it needs it.

  • Caps

    • The device contains two caps. The first one is at the end of the spout, isolating the inside of the device from its outside, hence blocking any form of contamination on, or transmission of, the GM seeds. The second cap is located between the handle and the body. When you add water to the device there’s always a risk of adding too little (seeds won’t reach to the water) or too much (seed would drown). In order to avoid such a problem, we’ve made a hole in the body of the device at the right height which seeds will grasp water but wont drown in it. You will only need to add water and let the excess run out though such hole. Once you’re done setting the device, you only have to plug the second cap there.

  • Cup

    • This is where the seeds will be placed, receive the selection information through light and germinate. Based on the design of a mixer of chocolate milk mixer (Baticao), we designed the bottom of the cup with holes to not just allow water pass through for the seeds reach it, but also so that when the cup is moved up and down the water will wash in and out of the cup. This flow of water will cause the seeds to move and allow shed the light information to the inner hidden seeds that rise up.

  • Inner lid and guidance ring

    • These two parts enclose the electronics and allow the movement of the cup. On one hand, the inner lid holds the red and blue LEDs (eight of each) that will project sufficient light to illuminate as many seeds possible. It also holds the cup to the rest of the structure of the device though hooks in the cup and slots inside the inner lid.

  • Lid and circuit holder

    • This is a critical part of the device. It’s here where the control electronics is located in the circuit holder and where the servo is placed. As mentioned in the previous descriptions, the purpose of the servo is to allow vertical movement of the cup shake the move the seeds thanks to water going in and out of the cup. It will move the cup 1 out of 4 seconds of light pulse emission.

Control electronics

It’s thanks to the control electronics that the information can be transmitted through appropriate timing and activation of the right light pulses. We chose a free design rather than using an open source system as such systems occupy a relative big volume for the amount of space that was available in the device. Also, we had the chance to simulate the circuit with Proteus software in order to check its functionality before implementing the entire circuit in a PCB board, built at our university.

It’s divided in to five different sections that correspond to:

  • Microcontroller

    • We’ve used a PIC microcontroller as we have certain experience in class with the usage and programming of such microcontrollers. We chose the PIC18LF14K50 from a list of microcontrollers that took in consideration several aspects like amount of pins it had (we didn’t wanted a huge chip), communication capability with the RTC, low power capabilities, package type (we only have experience with through hole packages), integrated inside the simulation program, etc. Thanks to this microcontroller, we could control the LED switching in time and a simple user interface for product selection.

    For its programing we used the student edition of MPLAB software and the C18 compiler. Its program its entirely based on interrupts from either the user interface, communications from the RTC or the RTC itself when sends the wake-up signal to the microcontroller.

  • Real Time Clock (RTC)

    • If the microcontroller is the brain of the device, the RTC is the heart of it. It incorporates an alarm function that can be set from the microcontroller. This function is critical, as its set accordingly to wake up the microcontroller from its sleep state. The microcontroller could replace the need of an external RTC, but that will have meant to configure it to wake up every second, perform the math of the amount of elapsed time and go back to sleep. It might not seem like a lot of time to do such task, but because it will do it every second over two periods of 1.5 hours (we assumed it took 10 ms for the wake-up, calculate and go back to sleep) it will add up 108 extra seconds. It doesn’t look a lot an additional 1 minute and 48 seconds, but if the device was to be set for longer periods of information transmission that amount of extra time will increase proportionally and out of the established parameters.

  • Servo control

    • It was the only servo that we could find that was available at the electronic distributors that the university uses and had a description of its performance characteristics. Its powered through a controlled transistor because when it receives no signal it still consumes power (8 mA) and depletes the batteries. That way only when its desired to be used, the servo is powered and then the control signal is sent. Also to mention that it’s an analog position servo because we were interested in leaving the cup at its highest position rather than at any random height. This is achieved though the applied control signal.

  • LED control display

    • It’s a simple two button and four colored LEDs display. Starting with the buttons, they provide functions of selection (Button 1), start and stop of the information transmission, and wake up of the device (Button 2). The four LEDs indicate the medicine that has been chosen and if the device is in standby mode while waiting for user input (one of the LEDs will be blinking in that scenario for thirty seconds before setting the circuit to sleep mode and save power).

  • LED circuit

    • It contains the red and blue LEDs responsible for the transmission of the required information that will make the biological circuit work. It’s composed of eight red and eight blue LEDs and two transistors that will manage the activation of the corresponding LEDs by means of a low current signal from the microcontroller.

What will be next?

Sure, the device fulfills its theoretical purpose, but as every object, it can be improved. This is the list of enhancements that we thought could improve our device at new levels, offering better user experience and more:

  • New user interface
  • A LCD screen could expand the information that the current 4 colored LED layout shows, as well as integrate a simple user interface that will allow additional functions on the device. This functions could include remaining production time, execute a diagnosis of the device, check power supply status, change parameters, etc.
  • Communication capabilities
  • Integrating Wi-Fi capabilities, the user will have control of the device around the globe as well as access to the additional functions described above and even reprogramming of the control circuit from an online database for any future genetic circuit.
  • Longer lasting//Rechargeable power supply
  • Right now the device has been designed for using eight AA batteries working in two groups of four in order to have enough voltage for the voltage regulator and enough capacity to last two transmission cycles. It could be expanded its usage by designing a single battery that could fit inside the geometry of the device, meet the voltage requirements, and have a different composition that will make it last longer than the alkaline batteries. It could also be designed to be rechargeable through a micro-USB port and a cellphone charger or compatible.
  • Integrated vacuum pump
  • Product extraction has to be done with the help of an external vacuum pump. In the following versions of the device it will integrate such component.

How to

Step by step handling instructions

  • First introduce the genetically modified seeds inside the device, add some water, and close the lid. Don't worry if you've added way more water than needed, just remove the containment tap at the side and the excess water will flush away.
  • Secondly, select the option of the medicine from the variety of products that the seeds contain. If there is no LED blinking, press the START button in order to wake-up the device and the red LED of the display will blink. Select the medicine with the help of the SELECT button and the LED display will change colors. You got 30 seconds before the device returns back to its sleep mode. Once you’ve selected the medicine, press START and the process will begin.

    • From this point on the device works by itself, selecting the red and blue light pulses in the appropriate order so that the information is transmitted to the genetic circuit. During the process of pulse emission, the cup will be moved up and down in order to allow water come through the holes and shake all the seeds and allow hidden seeds receive the information.

  • Finally, once the seeds have germinated, the red LED of the display will blink again, indicating that the process has been completed. Now proceed to extract the medicine vacuum pump connected to the spout of the device.

Construction

Most of the device has been constructed by 3D printing at our university except the body of the device do to time limitation. We were recommended to use a technique called thermoforming, which consists on using a sheet of plastic, heat it until it’s malleable, formed to the shape of a prepared mold and cut the excess.

Feel free to download the files that have made possible the construction of such device and to add modifications to it. Leave a comment on our social networks about it.