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Microbiology Sensor/Controller Board: The Sensomatic

Jonathan Cline

jcline@ieee.org

© 2013

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Engineered Biology - Let's Do Something "Simple"

by:

for:

(Contrary to popular belief, lab techs & their time are not "free")

Engineered Biology - Let's Do Something "Simple"

Let's perform a cell culturing experiment and isolate some bacteria for bioengineering targets!

Sounds great!

500px-N2-ase.png Link

Engineered Biology - Let's Do Something "Simple"

Assuming we've got a potential soil sample which might contain the desired bacterial strain..

Then finally begin the real experiment with the target bacteria!


These are lab automation and scalability problems.


Engineered Biology - Let's Do Something "Simple"

Let's Automate this as a bio-protocol and remove the busy-work!

Cory's First Solution (Image Copyright 2012 Cory Tobin)

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"Found out the arduino has all these limitations and does not work here."

Spent months.. to bring up an environment to do the real experiment.

Engineered Biology - Let's Do Something "Simple"

Cory's Second Solution (Image Copyright 2012 Cory Tobin)

"Finally successful, one time through. Same amount of effort to run through again."

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Engineered Biology - Let's Do Something "Simple"

Jonathan Cline's version: The Sensomatic

Achieve simplicity, integration of function, and low cost
Solve a specific problem

Sense and Control:



Engineered Biology - Let's Do Something "Simple"

Jonathan Cline's version: The Sensomatic

img_0012sm.jpg mq5-sensor.jpg LM35.jpg ssr-10636-01_i_ma.jpg




Engineered Biology - User/Software/Hardware Model

Prior Art (non-integrated, single function devices)

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Industry-standard robotic automation systems (like Tecan or Beckman) use proprietary, high-level script commands (shown) and proprietary low level device operations unique to each device.


Engineered Biology - User/Software/Hardware Model

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Engineered Biology - User/Software/Hardware Model

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Device data is stored in the database

Engineered Biology - Data Format

Data storage formats are very important:

Watch out -


Engineered Biology - Data Format

  <?xml version="1.0"?>
  <Experiment Name="JCSG Erbeta+Org1+Org2">
    <ID>351</ID>
    <User>Valerie</User>
    <Container>Corning pZero 3550</Container>
    <DatePrepared>2007-10-04T11:05:38.5170000+02:00</DatePrepared>
    <SetupTemperature>20</SetupTemperature>
    <IncubationTemperature>20</IncubationTemperature>
    <ExperimentPlates>
      <ExperimentPlate PlateNumber="1">
        <ID>406</ID>
        <DateDispensed>10/4/2007 12:45:40 PM</DateDispensed>
        <Wells>
          <Well WellNumber="15">
            <WellVolume>75</WellVolume>
            <WaterVolume>37.5</WaterVolume>
            <Drops>
              <Drop DropNumber="3" ProteinFormulation="Erbeta+Org2" ProteinVolume=
  "0.25" WellVolume="0.25" />
              <Drop DropNumber="2" ProteinFormulation="BufferC" ProteinVolume="0.2
  5" WellVolume="0.25" />
              <Drop DropNumber="1" ProteinFormulation="Erbeta+Org1" ProteinVolume=
  "0.25" WellVolume="0.25" />

Just say No to XML


Engineered Biology - Data Format - Device data


  %YAML 1.1
  --- # Fialab-Microsia
  address:
      syringe: A
      valve: C
      peristaltic: D
      external: B
  valve:
      send: # delay after cmds 100ms - 1 sec
          NP_SET:
              desc: set number of physical ports
              opcode: NP
              args:
                  - 1
                  - numport:4-12
              redundancy: 2 # send cmd twice
              delay: 100 # ms
              recv:
                  ok: ~
                  err: ~
          NP_GET:
              desc: get number of physical ports
              opcode: NP
              args:
                  - 0
              redundancy: 2 # send cmd twice
              delay: 100 # ms
              recv:
                  ok: ~
                  err: ~
  peristaltic:
      send: # delay after cmds 100ms - 1 sec
          SET_SPEED:
              desc: set pump speed
              opcode: G
              args:
                  - 1
                  - speed:0-100
              delay: 100
              recv:
                  ok: ~
                  err: ~       
          SET_DIRECTION:
              desc: set pump direction, direction:1=counterclockwise or 2=clockwise
              opcode: W
              args:
                  - 1
                  - direction:1-2:default=1
              delay: 5000
              recv:
                  ok: ~
                  err: ~        
  syringe:
      send: # delay after cmds 100ms - 1 sec
          INIT_ALL:
              desc: init all (both) pumps
              opcode: _Z0R
              args:
                  - 0
              delay: 100
              recv:
                  ok: ~
                  err: ~       
          SET_INPUT:
              desc: position valve in for given pump
              opcode: /$1IR
              args:
                  - 1
                  - pumpnum:1-2:default=1
              delay: 100
              recv:
                  ok: ~
                  err: ~




Engineered Biology - Competing Method/Prior Art: BioBoard (Noisebridge)

BioBoard

"an Arduino-controlled sensor package that allow users to monitor a range of physiochemical factors related to microbiological processes"

noisebridge-bioboard-450px-NIRprobe6.jpg BioBoardAppNewProject.png