PBR-Scripts

A set of Control Scripts for PSI Bioreactor Client software developed in Department of Adaptive Biotechnologies. These scripts allow automation of both basic and advanced funcionalities not available in standard distribution of the client software.

Getting Started

Put one of the below listed .js files content to PSI Bioreactor Client software protocol scripting part and modify appropriately UserDefinedProtocol section (object).

• PP-GrowthOptimizer Script for automatic quazi-continous characterization and consequent optimization of microorganism cultivated in PBRs based on programatic control of selected PBR parameters. The script is activated on a peristaltic pump scripting protocol. Data postprocessing including growth rates (doubling times) calculation is available here.
• O2-PIcurveMeasurement Script for automatic measurement of oxygen evolution and respiration under different irradiances (PI curve measurements). The script is activated on the oxygen probe (O₂ dissolved) scripting protocol.

Stable releases: v1.0: PP-GrowthOptimizer, O2-PIcurveMeasurement

Examples

• PP-GrowthOptimizer

The pump where the script is activated has to be set to ID 5 by default to allow compatibility with other scripts.

Growth rate (doubling time calculation) based on OD₆₈₀ while diluting according to OD₇₂₀

turbidostatODType: 720
regressionODType: 680

Growth characterization uder different temperatures

controlledParameter: "temperature"
controlledParameterSteps: [ 28, 32, 34, 30, 26, 22 ]

Growth characterization under different lights

controlledParameter: "lights"
controlledParameterSteps: [[ 1100, 25 ], [ 440, 25 ], [ 55, 25 ]]

The lights setting has to be always in pairs, i.e. for each light channel the value has to be specified. Please note the double brackets at the begining and the end of values list

• O2-PIcurveMeasurement

Measurement of O2 evolution/respiration synchronized with turbidostat dilutions

turbidostatSynchronization: true
growthStabilitySynchronization: true
lightStepMultiplierValues: [ 1 ]

Here it's necessary to run PP-GrowthOptimizer script with enabled growth statistics

growthStatistics: true

Measurement of O2 evolution/respiration synchronized with turbidostat dilutions and when the culture gets stable

turbidostatSynchronization: true
lightStepMultiplierValues: [ 1 ]

Measurement O2 evolution/respiration in triplicate

lightStepMultiplierValues: [ 1, 1, 1 ]

Measurement of PI-curve

lightStepMultiplierValues: [ 8, 4, 2, 1, 1/2, 1/4, 1/8, 1/16 ]

This setting enables measurement of PI curve in seven different light intensities defined as multiplier of actual actinic light intensity

Authors

• Jan Červený - Initial work - Department of Adaptive Biotechnologies

See also the list of contributors who participated in this project.

License

Licensed under MIT license

Acknowledgments

Projects supporting development:

• Services and access to state-of-the-art facilities for systems biology across Europe; project „Center for Systems Biology (C4Sys)“
• Innovations for mitigation of global change impacts; project „CzechGlobe 2020 – Development of the Centre of Global Climate Change Impacts Studies“
• Analysis of reaction networks with limiting conditions as a tool for the experimental validation of biochemical and photobiological reactor models; Czech Science Foundation