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eVOLVER
  • eVOLVER Documentation Wiki
  • General
    • About Us
    • eVOLVER Community
      • Code of Conduct
  • Getting Started
    • Buying eVOLVER
    • Part Sourcing
    • Unboxing and Setting Up
    • Software Installation
      • DPU Installation
      • Electron App (GUI) Installation
    • Configuring Computer and Networking
      • Router Setup
    • Calibrations
      • Temperature Calibration
      • Optical Density Calibration
      • Pump Calibration
      • Manual Calibration - calibrate.py
  • Upgrade Base eVOLVER Hardware
  • Experiments
    • Starting an Experiment
      • Carboy Media Prep
      • Preparing Vials
      • Setup Waste Carboy
      • Sterilizing Lines
      • Loading Vials and Setting Initial Conditions
      • OD Blank
      • GUI Start Guide
      • Command Line Start Guide
      • Cleaning Up After Experiment
    • Growth Curve
    • Chemostat
    • Turbidostat
    • FAQs
    • Tips and Tricks
  • Guides
    • Use the GUI to Control Parameters
    • Building a Smart Sleeve
    • Making media bottles and splitters
    • Emergency Efflux
    • View the Server Log and Restart Server
    • Updating the eVOLVER Server
    • Change Your conf.yml File
    • Arduino Software Installation
    • Raspberry Pi Configuration
    • Command Line Usage
    • Millifluidics Guides
      • Designing Millifluidics Using Eagle
      • Constructing Laser Cut Millifluidics
      • Constructing Millifluidics via SLA Printing
      • Calibrating IPPs
      • Operating Millifluidics
  • Troubleshooting
    • Troubleshooting Overview
    • Experiment Troubleshooting
      • Contamination
      • Vial Overflow, Pump Failure, and Spills
      • Tubing and Connector Blockage and Bursting
    • Optical Density (OD) Readings
    • Vial Troubleshooting
      • Replacing Photodiodes and LEDs
      • Heating Element
      • Stirring
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      • Motherboard Troubleshooting/Replacement
      • 12V Power Supply Troubleshooting/Replacement
    • GUI Troubleshooting
    • eVOLVER Maintenance
  • Hardware
    • Overview of Hardware Architecture
    • Overview of Fluidics
      • Tubing and connectors
      • Peristaltic Pumps
      • Fluidics box
    • Overview of Millifluidics
      • IPPs (Integrated Peristaltic Pumps)
      • Pressure Regulator
    • Vial Caps
      • Universal Vial Cap Construction Guide (Luer Connectors Only)
      • 5 and 7 Port Nylon Tubing Caps Construction Protocol
    • Smart Sleeve
      • Vial Board
      • 🌪️Stirring
      • Temperature
      • Optical Density
        • OD90 vs OD135
    • Motherboard Layout and Circuitry
      • 🌡️Arduino
      • Sensor/Actuator Board Slots
      • Pulse Width Modulation (PWM) Boards
      • Analog-to-Digital Converter (ADC) Boards
    • Raspberry Pi
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      • Calibration
      • custom_script.py
      • Experiment Data Files
      • eVOLVER.py
    • Arduino
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      • Calibration Files
      • Configuration Files (conf.yml)
    • Known Issues
  • Extensions
    • Adding A New Experimental Parameter
      • Power Supply
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      • Custom Calibration Code
    • Custom Experiments
      • ePACE
        • ATTiny1634 Writing
        • LUX Board Troubleshooting
      • Morbidostat
      • Extractor Column
        • Extractor Volume Maintenance
        • Experiment Start
          • Sterilizing Extractor Fluidics
          • Setting up your experiment
          • Using the extractor script
        • Extractor Analysis
        • Troubleshooting
        • Example protocols
      • Phototroph Growth
        • Setup Phototroph eVOLVER
        • Photo-eVOLVER Smart Sleeves
          • Photo-eVOLVER Smart Sleeve Construction Guide
        • Experiment Guide
    • Custom Fluidics
      • Adding a Third Pump Rack
      • Bubblers / In-Vial Aeration
        • Bubbler Construction Protocol
        • Bubbler Cleaning Protocol
      • Running the slow pumps
    • min-eVOLVER
      • About
      • min-eVOLVER Construction
        • Parts
        • Construction Protocol
      • Fluidics Setup
      • Software Installation and Startup
      • send_command.py
      • Calibrations
      • Starting an Experiment
      • ePACE with min-eVOLVER
        • [v1.1] ePACE with min-eVOLVER
      • Troubleshooting
    • Interfacing with Other Systems
  • Contributing
    • Guidelines for Contribution
    • Reporting a Bug / Hardware Failure
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      • Making a Forum Post
      • How to Edit the Wiki
    • Software Development
    • Hardware Development
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On this page
  • Algorithm
  • Turbidostat Dilution
  • Pumps
  • Dilution Calculation Example
  • Growth Rate
  • Calculation
  • Doubling Time
  • More Info

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  1. Experiments

Turbidostat

Turbidostats are automated culturing systems used to maintain a constant cell density in microbial cultures.

Algorithm

  1. OD is constantly monitored

  2. When OD goes above the an upper OD threshold

  3. A dilution is calculated to bring OD to the lower threshold

    1. Dilutions are capped at 20 seconds to avoid vial overflow

  4. Both influx and efflux pumps are run simultaneously for the calculated length

  5. Efflux pumps are run extra to make sure volume stays constant

    1. The efflux straw sets volume

Turbidostat Dilution

Pumps

  • Influx and efflux are both run at the same time

  • Like chemostat, vial volume is set by efflux straw height

    • Efflux is run extra time to make sure that enough volume is removed

  • Pumps run at roughly 0.75mL/second

  • Pump calibration is important for turbidostat otherwise dilutions will not hit the lower OD threshold accurately

Dilution Calculation Example

Example Dilution

time_in = -(np.log(lower_thresh[x]/average_OD) *VOLUME)/flow_rate[x]

average_OD = 1 # OD
lower_threshold = 0.5 # OD
VOLUME = 25 # mL
flow_rate = 0.75 # mL/second
time_in = -(np.log(0.5/1)*25)/0.75 = 23.1 # seconds

However, the mox dilution is 20 seconds to avoid overflow.

Growth Rate

Calculation

When there is a turbidostat dilution, it fits a line to the log of the OD data since the last growth curve (ie last turbidostat dilution) time. The slope of that line is reported as the growth rate in 1/hr.

Doubling Time

Convert growth rate to doubling time (in hours) via ln(2)/growthrate.

Growth Rate (1/hr)
Doubling Time (hr)

0.2

3.47

0.5

1.39

1.0

0.69

1.5

0.46

2.0

0.35

More Info

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Last updated 3 months ago

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Dilution is calculated in the code and is modeled as a mass balance equation

Calculated in eVOLVER.py in function and stored in your data folder during an experiment.

See and the for information.

here
this
custom_script
GUI start guide