📖
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
    • Server Troubleshooting
    • Vial Platform Troubleshooting
      • 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
    • Chassis
    • Light Blocker / Splash Guard
    • Known Issues
  • Software
    • Overview of Software Architecture
    • DPU
      • Calibration
      • custom_script.py
      • Experiment Data Files
      • eVOLVER.py
    • Arduino
    • Server (Raspberry Pi)
      • Calibration Files
      • Configuration Files (conf.yml)
    • Known Issues
  • Extensions
    • Adding A New Experimental Parameter
      • Power Supply
      • Specific Applications
      • 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
    • Documentation
      • Making a Forum Post
      • How to Edit the Wiki
    • Software Development
    • Hardware Development
Powered by GitBook
On this page

Was this helpful?

Edit on GitHub
Export as PDF
  1. Extensions
  2. Custom Experiments
  3. Extractor Column
  4. Experiment Start

Setting up your experiment

PreviousSterilizing Extractor FluidicsNextUsing the extractor script

Last updated 4 months ago

Was this helpful?

1. Prepare and Organize Your Equipment

  • Gather all necessary vials, slow pumps, tubing, and any other required equipment.

    • Recommended equipment: clean vials, pumps, tubing, 1:1 extractor/non-extractor caps, appropriate media, clean beakers, 10% Bleach, 70% Ethanol

  • Ensure that each extractor vial has a matching non-extractor vial (e.g., vial pair 0 and 4).

2. Connect the Tubing

  • Match each pump with one extractor/non-extractor pair.

  • For each pair, connect the tubing from the pump to the appropriate vials:

    • For example, if using vial pair 0 and 4, connect the pump to suck up liquid from vial 0 and dispense it into vial 4.

3. Check Tubing Pathways

  • Carefully follow the path of the tubing:

    • Ensure the tube is correctly drawing from the extractor vial (e.g., vial 0) and dispensing into the non-extractor vial (e.g., vial 4).

    • Similarly, ensure the tube for the reverse flow (non-extractor to extractor) is correctly set up.

While the tubing set up may look confusing at a glance remember that logically the setup works the same and as long as you understand the job of each pump on the slow pump array and the port to each straw on the cap you can trace back what goes where

When setting up the media influx as well as the vial-to-vial efflux in your Chemostat/Turbidostat vial ensure the media influx line is positioned ABOVE the vial-to-vial influx failure can result in contamination of media bottle.

The two angled straws positioned closer to the cap are your media influx and vial-to-vial efflux

4. Volume and Media Preparation

  • Prepare 20 mL of media for the Chemostat/Turbidostat vials used in the experiment.

  • For extractor columns, use a media volume of 15 mL to prevent the liquid level from reaching the photodiodes/LEDs.

  • Use the pumps/slow pumps to fill lines with media

  • Fill non-extractor lines and vials with media first and using a secondary set of extractor vials with media in them already run the slow pumps second to prevent bubbles from forming in slow pump lines

    • This is important because the initial blank should be based off of filled straws

5. Positioning of Vials

  • Ensure that the vials are placed correctly making sure you account for any added acrylic blocks underneath.

  • Double-check that the liquid levels are BELOW the photodiodes/LEDs.

6. Monitor the Pumping Process

  • Observe the pumping operation closely:

    • Ensure that the correct volumes are being transferred between vials as intended.

    • Monitor for any signs of malfunction or unexpected behavior.

Make sure to observe the straws carefully to ensure they are filled with media. Below is an example of a vial where some straws still have pockets of air.

7. Ensure Cleanliness of Vials

  • Clean vials thoroughly to avoid stains, condensation, or drippage.

  • Make sure there are no residual liquids that can impact the sensor readings.

9. Adjust if Necessary

  • Make adjustments to tubing, pumps, or vial positions if liquid levels are incorrect or if the system does not operate as expected.

9. Start the Experiment

  • Once all the checks and setups are completed, start the experiment with your extractor script.

  • Regularly monitor the system to ensure it is functioning correctly throughout the experiment.

The extractor will perform 2 blanks. One directly after starting the experiment and another 15 minutes into the experiment, the second blank can be changed in the extractor script.

By following these steps, you can ensure a successful setup and operation of the two-column extractor system, minimizing errors and ensuring accurate experimental results.

Vial Top View
Vial Side View
Diagram of extractor fluidics setup.
Close up view between Vial 0 (non-extractor) and Vial 4 (extractor)
Front View of just vials 0 (Left) and 4 (Right) outside of smart sleeve
Side view of just vials 0 and 4 on eVOLVER
Secondary Extractor Vial (Left) Experimental Extractor Vial (Middle) Non-Extractor Vial (Right)
Extractor Vial with straws properly filled (Ready for blank)
Acrylic blocks underneath can change the positional height of the vial