Introducing the DOTS Platform for Cell Culture! Learn more here.

The Shake Flask

Shake flask cultivations are a widely used for both, microbial and cell culture bioprocesses:

What are shake flasks used for?

Small scale cultivations in the range of 5-1000mL.

When are shake flasks used?

After high-throughput screening in microtiter plates but before bioreactor experiments.

What is cultivated in shake flasks?

  • Bacteria
  • Yeast
  • Filamentous Fungi
  • Plant Cells
  • Microalgae
  • Human Cell Lines (e.g., HEK)
  • Mammalian Cell Lines (e.g., CHO)
  • Insect Cell Lines (e.g., SF9)

What applications are shake flasks used for?

  • Strain/Clone Development/Screening/Characterization
  • Media Development/Optimization/Screening
  • Bioprocess Development/Optimization/Screening
  • Scale Up/Scale Down
  • Small Scale Production
  • Seed Train

The Benefits of Shake Flasks

Already found in most lab spaces, many experiments rely heavily on the usage of shake flasks. Compared to bioreactors, shake flasks are a low-cost, easy-to-use option for use in a small-scale lab setting.

SAVE-MONEY
Save Money

Shakes flasks are inexpensive to buy and maintain.

SAVE-TIME
Speed Up Process Development

Faster setup of experiments frees up time for other things in your day.

EASY-TO-USE
Easy To Use
Shake flasks require little to no technical knowledge compared to more advanced equipment.
SCALE-UP
Increase Throughput

More conditions can be tested in parallel, giving you more insight into your process needs.

REDUCE-FOOTPRINT
Reduce Footprint

Easy to integrate into existing laboratory infrastructure.

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Save Resources

Working in smaller volumes means using less resources, such as media and nutrients.

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Working Volume
Enough culture volume for product and process characterization

Current Shake Flask Challenges

While shake flask play a pivotal role in any modern bioprocess lab and team, they do have some significant disadvantages:

No Monitoring
  • Often shake flask experiments are black-boxes
  • No process information (biomass, pH, DO,substrate, product) available
Manual Sampling
  • Low data density
  • Extensive hands-on time
  • Process interruptions
  • Loss of culture volume
  • Risk of contamination
Shake Flasks are not Bioreactors
  • No real-time data
  • No control (e.g. pH or Fed Batch)
  • Limited scalability

Scientists are forced to choose between bioreactors or flasks. There is no solution that combines the advantages of both...until now!

The Solution: The DOTS Platform

DOTS combines sensors and actuators with a powerful software to create bioreactor-like shake flasks with actionable insights into your bioprocess when and where it matters most. 

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Components of the DOTS Platform

The DOTS Platform consists of 4 components: Multiparameter Sensor (MPS), Sensor Pills, Liquid Injection System (LIS) & DOTS Software.

  • Multiparameter Sensor (MPS)
  • Liquid Injection System (LIS)
  • Sensor Pills
  • Software
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Multiparameter Sensor (MPS)

The Multiparameter Sensor (MPS) enables the optical and non-invasive monitoring of various process parameters. Currently, the MPS can be used to read out DO Sensor pills and for non-invasive fluorescence and biomass monitoring, utilizing backscattered light detection.

Learn More: MPS
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Liduid Injection System (LIS)

sbi’s Liquid Injection System (LIS) facilitates the automated feeding of liquids into shake flask cultures. LIS enables bioreactor-like options in shake flasks: Fed-batch, DO-based feeding, biomass-based feeding, automated promotor induction, and more.

Learn More: LIS
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Sensor Pills

Sensor Pills are the next generation of chemosensors. Each pill contains a chemosensor for a critical process parameter that then can be read out non-invasively by the Multiparameter Sensor. Currently we offer Dissolved Oxygen (DO) Sensor Pills for real-time DO monitoring in shake flasks.

Learn More: Sensor Pills
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DOTS Software

DOTS Software is your tool for easy handling of sensors and actuators, enabling real-time visualization and analysis of multiple parameters in parallel for optimal bioprocess understanding and control.

Learn More: Software

Multiparameter Sensor (MPS)
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Multiparameter Sensor (MPS)

The Multiparameter Sensor (MPS) enables the optical and non-invasive monitoring of various process parameters. Currently, the MPS can be used to read out DO Sensor pills and for non-invasive fluorescence and biomass monitoring, utilizing backscattered light detection.

Learn More: MPS
Liquid Injection System (LIS)
LIS_drop_2

Liduid Injection System (LIS)

sbi’s Liquid Injection System (LIS) facilitates the automated feeding of liquids into shake flask cultures. LIS enables bioreactor-like options in shake flasks: Fed-batch, DO-based feeding, biomass-based feeding, automated promotor induction, and more.

Learn More: LIS
Sensor Pills
multiparameter-sensor-shake-flask-DO-pill-LIS-motion-5

Sensor Pills

Sensor Pills are the next generation of chemosensors. Each pill contains a chemosensor for a critical process parameter that then can be read out non-invasively by the Multiparameter Sensor. Currently we offer Dissolved Oxygen (DO) Sensor Pills for real-time DO monitoring in shake flasks.

Learn More: Sensor Pills
Software
dots-software

DOTS Software

DOTS Software is your tool for easy handling of sensors and actuators, enabling real-time visualization and analysis of multiple parameters in parallel for optimal bioprocess understanding and control.

Learn More: Software

Want to see data for your organism or application?

We have tested over 100 organisms/cell lines for more than 50 different applications with our technology.

Download Microbial Exemplary Data Sets Download Cell Culture Exemplary Data

Customize Your Smart Shake Flask

Choose from an array of parameter-specific sensor-and-software modules to build the smart shake flask that meets your needs. With the MPS, you can continue to expand your shake flask sensing capabilities as new sensors are added in the future.customize

Biomass

MPS

Monitor biomass and growth rates non-invasively through the vessel wall via backscattered light detection. The real-time, high-resolution growth curves provide actionable insights into your strain's growth behavior.

Dissolved Oxygen

SensorPills

When combined with the single-use Dissolved Oxygen Sensor Pill, the MPS continuously detects changes in the DO level of your culture. 

Fluorescence

Fluorescence

An integrated spectrophotometer enables fluorescence monitoring of various wavelengths, also in parallel, and evaluation of fluorescent protein expression.

Parameter-Based Feeding

LIS

Integrate the MPS with sbi's Liquid Injection System (LIS) to precisely feed liquids based on specified parameters (i.e. DO, biomass). These advanced control options elevate your shake flask experiments to a new level of precision and effectiveness.

Environmental Parameters

Environmental

Embedded ambient sensors in the MPS enable the measurement of environmental parameters such as temperature, shaking speed, and humidity, providing comprehensive insights into your bioprocess and indicating shaker openings or other disruptions. 

Application Data & Results

Explore applications in real-world situations. Looking for something specific? Contact us to see data for your organism and application.

Microbial

DO-based feeding with 40% methanol

Pichia pastoris (P. pastoris), 200 rpm/25 mm, 10 % filling volume, 250 ml flask, 37°C

With a DOTS-integrated controller, the methanol feed (carried out with the Liquid Injection System) was adjusted to start repeatedly, always when the DO level, monitored by DO Sensor Pills, reached a preset threshold. By using this feature, methanol was always fed as soon as the cells recovered from the previous shot, enabling ideal cell viability, while keeping promotor activity constant. Biomass was monitored additionally, with the Multiparameter Sensor (MPS).

Cell Culture

CHO DP 12 Cell Culture

CHO Cell, 0.3 million cells / mL, Nalgene flask, 250 mL, 20% filling volume (50 mL), 150 rpm, 50 mm

Biomass for CHO cells demonstrates strong correlation with offline biomass measurements obtained via Total Cell Density (TCD) analysis. The MPS exhibits exceptional reproducibility when comparing data collected from two independent sensors (Flask 1 vs Flask 2), showcasing its consistency and robustness for process monitoring in bioprocess applications.

Want to see data for your organism or application?

We have tested over 100 organisms/cell lines for more than 50 different applications with our technology.

Speak With An Expert

Value of DOTS for your Shake Flask Experiments

Better and faster bioprocessing while saving costs and creating more time for other tasks.

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Medium Throughput & Actionable Insights

More experiments in same time & more knowledge generated from experiments

  • Better Decisions
  • Faster ProjectsHigher
  • Quality Results

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    Run Typical Bioreactor Experiments in Flask & Non-invasive Monitoring

    Less bioreactor runs & less hands-On time per experiment

  • Cost Savings
  • Higher Personal Productivity
  • Lower Contamination Risk

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    Shake Flask Applications

    • Biomass Monitoring
    • Biomass-Based Feeding
    • Liquid Feeding
    • Monitor Environmental Data
    biomass-monitoring
    Online biomass monitoring via backscattered light readings and in multiple, parallel experiments. 

     

    LIS-CGQ-biomass-feeding-shake-flasks-1-1
    Use the interconnectivity of sensors and actuators (LIS) within the DOTS Software to enable feedback controlled feeding in your shake flask experiments. 

     

    biomass-based-feeding-sq
    The Liquid Injection System (LIS) enables automated and non-invasive feeding in shake flasks. 

     

    shake-flasks-shaker-preculture
    DOTS sensors monitor environmental parameters in addition to their sample-centric measurements avoiding the need of additional sensors.

     

    Biomass Monitoring
    biomass-monitoring
    Online biomass monitoring via backscattered light readings and in multiple, parallel experiments. 

     

    Biomass-Based Feeding
    LIS-CGQ-biomass-feeding-shake-flasks-1-1
    Use the interconnectivity of sensors and actuators (LIS) within the DOTS Software to enable feedback controlled feeding in your shake flask experiments. 

     

    Liquid Feeding
    biomass-based-feeding-sq
    The Liquid Injection System (LIS) enables automated and non-invasive feeding in shake flasks. 

     

    Monitor Environmental Data
    shake-flasks-shaker-preculture
    DOTS sensors monitor environmental parameters in addition to their sample-centric measurements avoiding the need of additional sensors.

     

    What Our Customers Are Saying

    "With the DOTS platform I can combine sensors and actuators in a simple way to perform completely new applications like biomass-based feeding in shake flasks. My shake flasks can now operate similar to small-scale bioreactors, keeping the ease and cost-effectiveness of flasks but adding the sensor and control options of bioreactors. This is truly revolutionary for me and my experiments."

    -Christoph Kutzner (Badische Peptide & Proteine, Heidelberg)

    “Using the DOTS Platform, we were able to gain actionable insights from our CHO shake flask cultivations. This allows us to reduce sampling as important data are given online and in real time.”



    --Vivian Ott (Centre for Cell Cultivation Techniques, ZHAW, Switzerland)

    Specifications

    DOTS offers the simplest sensor handling in bioprocessing for a broad variety of parameters and applications.

    Parameters

    • Biomass & growth rate
    • Dissolved Oxygen (DO)
    • Fluorescence
    • Temperature & shaking speed
    • Time-based & parameter-based feeding

    Vessels

    • Shake flasks of all common sizes

     

    Applications

    • Strain development, screening, and characterization

    • Bioprocess optimization

    • Media optimization

    • Growth characterization (including toxicity tests, substrate-/product-inhibitions, and oxygen-limitations)

    • Timing of workflows (such as inoculation, induction, sampling, feeding, or harvesting)

    • Bioreactor-like experiments on shake flask level (e.g., automatized induction, biomass-based fed-batch processes)

    Resources

    compatability-cell-culture-DOTS
    compatabilty-microbial-DOTS
    Overview

    DOTS offers the simplest sensor handling in bioprocessing for a broad variety of parameters and applications.

    Parameters

    • Biomass & growth rate
    • Dissolved Oxygen (DO)
    • Fluorescence
    • Temperature & shaking speed
    • Time-based & parameter-based feeding

    Vessels

    • Shake flasks of all common sizes

     

    Applications

    • Strain development, screening, and characterization

    • Bioprocess optimization

    • Media optimization

    • Growth characterization (including toxicity tests, substrate-/product-inhibitions, and oxygen-limitations)

    • Timing of workflows (such as inoculation, induction, sampling, feeding, or harvesting)

    • Bioreactor-like experiments on shake flask level (e.g., automatized induction, biomass-based fed-batch processes)

    Downloads

    Resources

    Compatibility - Cell Culture
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    Compatibility - Microbial
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    From Estimation To High-Resolution Growth Curves

    Cell Growth Quantifier (CGQ)
    Success Growth Graph

    Customer Success Stories

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    “Incorporating SBI’s pH and DO flow cells into our system removed the need for manual sampling, saving us time, reducing the risk of contamination, and providing information on how the cells are growing even when we are not in the lab. With availability of this more detailed view of our culture, we can make informed improvements to our cell expansion process.”

    -Kitana Manivone Kaiphanliam (Washington State University)
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    Learn More