A morbidostat is an automated continuous culture machine. With which one can study the emergence of bacterial drug tolerance and resistance over time. Erdal Toprak et al.

This code repository drives the current version of the morbidostat of the NeherLab (Biozentrum, University of Basel). It controls the pumps, optical density measurements (OD), waste pumps and structures them in a cyclic fashion.

Morbidostat user manual

Table of contents

• 1. Starting a morbidostat run
  • 1.1 Classic morbidostat experiments
  • 1.2 Pharmacokinetic, pharmacodynamic experiments (PKPD)
• 2. Displaying experiments
• 3. Optical density (OD) calibration
• 4. Pump calibration
• 5. Additional commands
  • 5.1 Change dilution factor during a run
  • 5.2 Change target OD during a run
  • 5.3 Change cycle time during a run
  • 5.4 Interrupt and resume an experiment during a run
  • 5.5 Stopp an experiment
  • 5.6 Change drug concentration of input bottles during a run
  • 5.7 Change MIC of the strain during a run
  • 5.8 Reset vial concentrations during a run
• 6. Adding changes to version control

1. STARTING A MORBIDOSTAT RUN

Clone the repository onto the computer which is controlling the morbidostat (Or any other computer for using the simulation mode without morbidostat).

Open a terminal and navigate into the python_morbidostat folder:

cd python_morbidostat

Start Ipython:

ipython --pylab

1.1 Classic morbidostat experiments

Set parameters using the example.yml file. (pkpd must be set to False)

Next, run the following command inside the Ipython environment:

run python_src/morbidostat_setup.py --config example.yml

1.2 Pharmacokinetic, pharmacodynamic experiments (PKPD)

Set parameters using the example.yml file. (pkpd must be set to True)

Now also set the additional parameters inside the pkpd_config.yml file.

Next, run the following command inside the Ipython environment:

run python_src/morbidostat_setup.py --config example.yml --pkpd pkpd_config.yml

2. DISPLAYING EXPERIMENTS

1. Open a new terminal shell by a right click on the terminal button on the left.
2. Again navigate to the python_morbidostat folder.
3. Run the following command in the new shell:

./display.sh data/<EXPERIMENT_FOLDER> <ANTIBIOTIC_USED>

3. A figure will open showing the OD of all measured vials and the antibiotic concentration trajectorys. (Red line = Antibiotic concentration, Blue line = OD)
4. To update the graph, type (inside the terminal shell):

morb_monitor.update_all()

5. To change the time window shown in the figure, type:

morb_monitor.data_range = number_of_seconds_you_want_to_see
morb_monitor.update_all()

3. OPTICAL DENSITY (OD) CALIBRATION

Type the following:

cd python_src
ipython --pylab

An Ipython shell will open. In the shell, type:

from morbidostat_experiment import *

The latter imports the necessary functions. Then type:

calibrate_OD()

You will be prompted for the OD of the standard used, enter a number. Following that, confirm that the vial is placed in the correct receptible by pressing enter. Repeat for 1-15. Repeat for all available OD standards (at least 2, best betweeen 10 to 15). After all standards have been measured, press q.

Regression statistics will be printed and a figure should open showing the gauge curves. If figure doesn't open, type:

import matplotlib.pyplot as plt
plt.show()

The routine will save a file OD_calibration.dat in python_src, and a file voltage_measurements_YYYYMMDD.dat in the data directory

4. PUMP CALIBRATION

cd python_src
ipython --pylab

The latter imports the necessary functions. Then type (choose between pump1, pump2, and pump3):

pump_type = 'pump1'

from morbidostat_experiment import *
mymorb = morbidostat()
mymorb.run_all_pumps(pump_type, 200)

Make sure all tubing is filled with liquid and a steady stream of drops enters each vial

Empty all vials.

Set pump time:

dt=200

calibrate_pumps(mymorb, pump_type, dt=dt)

5. ADDITIONAL COMMANDS

These commands can be typed into the terminal shell of the running morbidostat program.

5.1. Change dilution factor during a run:

morb.dilution_factor = x

5.2. Change target OD during a run:

morb.target_OD = x

5.3. Change cycle time during a run:

morb.cycle_dt = x

5.4. Interrupt and resume an experiment during a run:

Useful during media, or antibiotic bottle exchange.

morb.interrupt_experiment()

morb.resume_experiment()

5.5. Stopp an experiment:

morb.stop_experiment()

5.6. Change drug concentration of input bottles during a run:

a. Change the first bottle:

morb.drug_concentrations[0][0] = x

b. Change the second bottle:

morb.drug_concentrations[1][0] = x

c. Change the third bottle:

morb.drug_concentrations[2][0] = x

5.7. Change MIC of the strain during a run:

morb.mics[0] = x

5.8. Reset vial concentrations during a run:

Sets all vial concentrations to 0.

morb.reset_concentrations()

6. ADDING CHANGES TO THE VERSION CONTROL (I.E. AFTER OD CALIBRATION)

Type:

git commit -a -m "A useful message explaining why this change is necessary"