Final Project

PROJECT IDEA: OPEN ECOTRONs

An Ecotron is a device capable of generating a range of physical and chemical conditions applied to terrestrial or aquatic ecosystems. Its principle is to confine a biological system (natural or artificial, complex or simplified one) in a enclosure sealed in matter but not in energy, and simultaneously measure and control such flows of matter and energy. For For this purpose, the enclosures are equipped with many sensors to obtain precise real-time measurements and different actuators to control and modify the enclosure environmental conditions.

REF: Lawton, J. H., Naeem, S., Woodfin, R. M., Brown, V. K., Gange, A., Godfray, H. J. C., Heads, P. A., Lawler, S., Magda, D., Thomas, C. D., Thompson, L. J. & Young, S. (1993) The Ecotron - a Controlled Environmental Facility for the Investigation of Population and Ecosystem Processes. Phil.Trans. R. Soc. B, 341, 181-194.

The idea is to end up with a generic μCosm/bioreactor/fermentor with a modular design that allows to be adapted by the user to match the specific farming/culturing/fermenting requirements of the chosen biological specie. The device will include sensors and electronic systems to monitor control and automatize all the process, making it more resilient, productive and sustainable in a such easy way that it becomes accessible also for non-experts.

OpenGarden / Open μ-COSM

OpenGarden is about to make a modular chamber with a very well controlled inner weather. That include the daily dynamic changes of the temperature, the humidity and light as basics, but also more sophisticated parameters as the flux of CO2 or the photosynthetic tax of the plants that could be growing inside. OpenGraden will be a cheap DIY “classic” microcosm Ecotron, able to be adapted to the needs of each “user”: mushrooms, mycelium, lichens, moss, orchids, tomatoes, aloe, capsicum peppers, etc...

OpenGrow / Open BioReactor

OpenGrow is about to make a modular bioreactor, following the diy-open-source philosophy and keeping a low-price (a normal commercial one, can cost up to 4000 euros). A bioreactor is nothing else than a enclosed space with controlled liquid environment to make the microorganism that grows inside the “happiest” possible. With this new generic apparatus we could cultivate our own yeast for making bread (or beer), your kefir fungi for yogurt, your bacteria to produce cellulose, glue, plastic, light... or even your favorite microalgae: spirulina, chlorella...etc. The modularity, of this micro-farm will be focused into allowing different configurations of sensors and actuators to control different parameters of the conditions of culturing (pH, temperature, density...) and also in allowing increasing culture volumes. Having that open source apparatus can make us envision the emergence of a world wide community of users. Thus, it could be interesting to create also a on-line website, where the community will share which specifications of the bioreactor makes which microorganism happier. We could even invite the team of users to become a distributed repository of different interesting microorganisms.

Open Brew / Open Fermentor

OpenBrew is the follow-up of the OpenGrow. But now, we are not interested in the microorganism that grows inside but in the liquid media and the fermentation process. It is a project to explore the different ways to elaborate/prepare/ferment different beverages. Specially beer (from different cereals) but also drinks that are developed by similar fermentation process like wine, cider or any other fruit alcohol fermentation. But also Mate or kombucha tea as an non-alcoholic drink. Again, the idea is to end up with a general bioreactor/fermentor with a modular design that allows to be adapted to the special requirements of your beverage preparation. The fermentor, of course, will include some sensors and electronic systems to control and automatize the process, in order to make the fermentation easier, less laboured and accessible to everybody.


Boom

Electronics parts

Partlist exported from /home/nanu/Desktop/Tinyduino.sch

PartValueDevicePackageDescription
C10.1 UFCAP-UNPOLARIZEDFABC1206FAB
C20.1UFCAP-UNPOLARIZEDFABC1206FAB
C3CAP-US1206FABCAP-US1206FABC1206FAB
D13.3vZENER_DIODESOD123SOD123zener diode
D23.3vZENER_DIODESOD123SOD123zener diode
IC1ATTINY44-SSUATTINY44-SSUSOIC14
IC23.3VREGULATORSOT23SOT23
LEDLEDFAB1206LED1206FABLED
R168 ΩRES-US1206FABR1206FABResistor (US Symbol)
R268 ΩRES-US1206FABR1206FABResistor (US Symbol)
R31 kΩRES-US1206FABR1206FABResistor (US Symbol)
R41 kΩRES-US1206FABR1206FABResistor (US Symbol)
R51k ΩRES-US1206FABR1206FABResistor (US Symbol)
R60 ΩRES-US1206FABR1206FABResistor (US Symbol)
R710 kΩRES-US1206FABR1206FABResistor (US Symbol)
R80 ΩRES-US1206FABR1206FABResistor (US Symbol)
S1SW16MM_SWITCH6MM_SWITCH6MM_SWITCHOMRON SWITCH
U$1USB_MINIBUSB_MINIBUSB_MINIB
U$4PINHD-1X10PINHD-1X101X10-BIGPin header 1x10 0.1" spacing
U$5PINHD-1X10PINHD-1X101X10-BIGPin header 1x10 0.1" spacing
Partlist exported from /home/nanu/Desktop/Tinyduino/shield_bioreactor.sch

PartValueDevicePackageDescription
D1DIODESOD123SOD123DIODE
D2DIODESOD123SOD123DIODE
D3DIODESOD123SOD123DIODE
D4DIODESOD123SOD123DIODE
D5DIODESOD123SOD123DIODE
IC17806DT7806DTTO252Positive VOLTAGE REGULATOR
IC2REGULATORSOT23SOT23
J1JACK2.1MMJACK2.1MMJACK_2.1MM
JP1PINHD-1X41X04PIN HEADER
JP2PINHD-1X41X04PIN HEADER
JP3PINHD-1X41X04PIN HEADER
PIN1PINHD-1X10PINHD-1X101X10-BIGPin header 1x10 0.1" spacing
PIN@PINHD-1X10PINHD-1X101X10-BIGPin header 1x10 0.1" spacing
PIN@1PINHD-1X10PINHD-1X101X10-BIGPin header 1x10 0.1" spacing
PIN@2PINHD-1X10PINHD-1X101X10-BIGPin header 1x10 0.1" spacing
R110kRES-US1206FABR1206FABResistor (US Symbol)
R210kRES-US1206FABR1206FABResistor (US Symbol)
R310kRES-US1206FABR1206FABResistor (US Symbol)
R410kRES-US1206FABR1206FABResistor (US Symbol)
R510kRES-US1206FABR1206FABResistor (US Symbol)
R74,7RES-US1206FABR1206FABResistor (US Symbol)
T1NMOSFETTO252TO252MOS FET
T2NMOSFETTO252TO252MOS FET
T3NMOSFETTO252TO252MOS FET
T4NMOSFETSOT23SOT-23MOS FET
T5NMOSFETSOT23SOT-23MOS FET
QuantityMaterialsPriceStore
1Tinyduino15 $-
1Oled Display10 $link
2Peristaltic motor10 $link
1Switch0.5 $Fablab
1Pump Air5 $link
1Temperature senor3 $link
1PH sensor50 $link
1Neopixel7 $link
1Vessel30 $link
1CONTRAXAPAT(2500x1220x15 mm)17.03 $link

Modular Lab

Modular lab was created in week 7

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Vessel

The vessel is the most important part for me of the project after the electronica, since it has to be well built, so as not to have any losses and so that all the rods will be perfected, that is why I have dedicated enough time to do it and I I have helped a few templates to make everything fit to stick it.

The first tests were done on carton to see that the design is correct.

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I have created an auxiliary structure of plywood to glue the pieces perfectly

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I used a special glue for the parts that takes 24 hours to cure and if using ultraviolet light the gluing time is less, so I have put it in the sun.

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So that all the pieces remain perfectly and they do not move I have put a few tools of subjection and to avoid any accident.

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Once the gluing has been completed, I have verified that everything fits snugly with threaded rods that pass through the vessel.

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webpage jekyll webpage jekyll
webpage jekyll webpage jekyll

Electronics and programing

I use a Tyniduino small Arduino created in week 13

I have created a shield that fits the Tinyduino, this shield has several mosfest and voltage regulators to automatically control the leds, air pumps and various sensors, also has a 12 volt input to power all external components.

The Tyniduino is the Attiny84 version since it has more capacity to program it 8k.

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For programming I have used the arduino IDE, programming the sensors so that the information of the bioreactor is displayed in the Oled, I currently have a temperature sensor and a pH sensor.
webpage jekyll webpage jekyll

For programming I have used the arduino IDE, programming the sensors so that the information of the bioreactor is displayed in the Oled, I currently have a temperature sensor and a pH sensor.

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    #include <DigisparkOLED.h>
        #include <Wire.h>
        #include "img0_128x64c1.h"
        #include "digistump_128x64c1.h"
        #include <OneWire.h> 
        #define ONEWIRE_BUSS 0
        OneWire TemperatureSensor(ONEWIRE_BUSS);
        #define SensorPin 0          //pH meter Analog output to Arduino Analog Input 0
        int time=0;
        int ledPin = 5;
        int flag = 0;
        
        void setup() {
        
          oled.begin();
          pinMode(ledsPin, OUTPUT); 
        }
        
        void loop() {
          
          oled.fill(0xFF); //fill screen with color
          delay(1000);
          oled.clear(); //all black
          delay(1000);
          oled.setCursor(0, 0); //top left
          oled.setFont(FONT8X16);
          oled.println(F(getTemp()+ "C")); //wrap strings in F() to save RAM!
          oled.clear(); //all black         
          oled.setCursor(0, 0); //top left         
          oled.setFont(FONT6X8);
          oled.println(F(analogRead(SensorPin)+ "Ph")); //wrap strings in F() to save RAM!
          delay(1000);
          time+=1; 
          if(time<900000)
          { 
            digitalWrite(ledsPin,HIGH);//on       
          }
          if(time>900000)
          { 
            digitalWrite(ledsPin,LOW);//off          
            time=0; 
          }
        }
    
        int getTemp()
        {
            byte i;
            byte data[12];
            int16_t raw;
            float celsius;
         
            TemperatureSensor.reset();       // reset one wire buss
            TemperatureSensor.skip();        // select only device
            TemperatureSensor.write(0x44);   // start conversion
         
            delay(1000);                     // wait for the conversion
         
            TemperatureSensor.reset();
            TemperatureSensor.skip();
            TemperatureSensor.write(0xBE);   // Read Scratchpad
            for ( i = 0; i < 9; i++) {       // 9 bytes
              data[i] = TemperatureSensor.read();
            }
         
            raw = (data[1] << 8) | data[0];
            celsius = (float)raw / 16.0;
            return celsius;
        }

    

final process

I have printed a diffuser for the light, since the spirulina needs sunlight to grow, this diffuser will be on the bottom of the bioreactor.

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webpage jekyll webpage jekyll

Here we can see the bioreactor above the module and the spirulin that has been trapped in the filter and ready to be eaten after squeezing it.

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Spirulina with tomato sauce and rigatoni

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Download

Construction file

Electronics

Next Interaction

This project will have a continuation as it is something that interests me, here in Barcelona I belong to a group of Biohackers DIYBIO Barcelona, which we are working with different artists and people who are interested in the whole world of biology.

We also do experiments to make laboratory machines cheaper, and part of this project is exactly that.

What plans have I thought for my bioreactor, first to change the electronics and create a PiHat for a raspberry PI zero in which I am already working that would have the possibility of controlling more sensors and that will include a web interfaces.

In addition to creating different pieces and being able to create other types of living arrangements.