Vessels and mixing¶

This page provides comprehensive information about the structure and components of the data model, including detailed descriptions of the types and their properties, information on enumerations, and an overview of the ontologies used and their associated prefixes. Below, you will find a graph that visually represents the overall structure of the data model.

Graph

flowchart TB
    vial(Vial)
    plate(Plate)
    stirredtankreactor(StirredTankReactor)
    tubularflowcontinuousreactor(TubularFlowContinuousReactor)
    shaking(Shaking)
    mechanicallyimpelledmixing(MechanicallyImpelledMixing)
    liquidorgasimpelledmixing(LiquidOrGasImpelledMixing)

    click vial "#vial" "Go to Vial"
    click plate "#plate" "Go to Plate"
    click stirredtankreactor "#stirredtankreactor" "Go to StirredTankReactor"
    click tubularflowcontinuousreactor "#tubularflowcontinuousreactor" "Go to TubularFlowContinuousReactor"
    click shaking "#shaking" "Go to Shaking"
    click mechanicallyimpelledmixing "#mechanicallyimpelledmixing" "Go to MechanicallyImpelledMixing"
    click liquidorgasimpelledmixing "#liquidorgasimpelledmixing" "Go to LiquidOrGasImpelledMixing"

Types¶

Vial¶

Vials are sealable containers available in various sizes and materials, playing a crucial role in sample storage and handling, as well as serving as reaction vessels.Plate

vial_size* float

The vial's size, which can be its volume or its dimensions.
Minimum: 0.0

vial_size_unit* string

For describing the vial size, you can use mL (milliliters) as the unit when referring to volume or cm (centimeters) when referring to dimensions.

vial_material* string

Specify the material of the vial, such as glass or plastic, as it can influence the reaction.

closure_type* string

Indicate the type of closure or stopper used for the vial, as it affects sealing and the course of the reaction. If no closure or seal was used for the vial, this should be noted as well.

special_treatment* string

If there are any other specific methods, procedures, characteristics or aspects related to the vial or its preparation for the reaction that are important for reproducibility and are not described by the aforementioned metadata, they should be explained here.

Plate¶

It's crucial to provide detailed information about the plate type, material, well configuration, and other relevant specifications to ensure reproducibility and accuracy of the experimental setup.Stirred Tank Reactor

plate_type* string

The type of plate, such as microtiter plate, deep-well plate, or others.

plate_material* string

The material from which the plate is made, such as plastic (polystyrene), glass, or metal.

number_of_wells* string

The total number of wells or cavities in the plate.

well_shape* string

Descrption: The shape of the wells, such as round, rectangular, square, etc.

well_volume* string

The volume of each well is, usually expressed in µL (microliters).

well_arrangement* string

The arrangement of the wells in the plate, for example, in rows and columns.

supplier* string

Information about the supplier from which the plate was purchased.

lot_number* float

The lot number, also known as a batch number or code, is a unique identifier assigned to a specific batch of a product. This makes it possible to check or track information on production.
Minimum: 0.0

sealing_method* string

Indicate if the wells were sealed with a sealing film or lid. (

sealing_material* string

The material of the sealing film or lid. (

special_treatment* string

If there are any other specific methods, procedures, characteristics or aspects related to the plate or its preparation for the reaction that are important for reproducibility and are not described by the aforementioned metadata, they should be explained here.

StirredTankReactor¶

Stirred Tank Reactors (STRs) are frequently employed as versatile and controlled vessels, allowing for precise regulation of key parameters like temperature, pH, and stirring speed. All relevant specifications or attributes need to be described.Tubular flow/continuous reactor

type* string

There are several types of Stirred Tank Reactors, differing in design and intended use. A detailed description is required.

material* string

Material the reactor is made of, e.g. glass, polypropylene etc.

volume* float

Indicate the total volume capacity of the Stirred Tank Reactor.
Minimum: 0.0

volume_unit* string

The volume is typically expressed in L (liters).

geometry* string

The geometry of the reactor, in particular of interest is the ratio of height to width.

bottom_type* string

Shape of the bottom of the reactor, e.g. a round bottom or a flat bottom.

gas_consumption* string

Common gases that are supplied to the reactor include, e.g., air, oxygen, hydrogen, etc.

gas_supply* string

Gas can be supplied to a Stirred Tank Reactor in various ways, such as through sparging using a tube or an aeration basket, bubbling, or direct injection into the reactor vessel.

gas_supply_rate* float

Specification of the gas supply rate.
Minimum: 0.0

gas_supply_rate_unit* string

The units for the gas supply rate in a Stirred Tank Reactor can be L/min (liters per minute), m³/h (cubic meters per hour), or other volume units per unit of time.

temperature_control* string

The temperature in a Stirred Tank Reactor can be controlled through various methods, typically using external heat sources or cooling systems such as heating jackets, cooling coils, or external temperature control units.

special_treatment* string

If there are any other specific methods, procedures, characteristics or aspects related to the Stirred Tank Reactor or its preparation for the reaction that are important for reproducibility and are not described by the aforementioned metadata, they should be explained here.

TubularFlowContinuousReactor¶

When conducting enzymatic reactions in tubular flow or continuous reactors, it is essential to provide detailed information about the reactor setup, e.g. plug flow reactor, and operating conditions to ensure reproducibility and transparency in reporting the experimental process.

volume* float

Indicate the total volume capacity of the tubular flow/continuous reactor.
Minimum: 0.0

volume_unit* string

The volume is typically expressed in L (liters).

geometry* string

The exact geometry of the tubular flow/continuous reactor.

reactor_type* string

There are several types of tubular flow/continuous reactors, e.g. packed bed reactor, or a plug flow reactor, differing in design and intended use. A detailed description is required.

material* string

Material the reactor is made of, e.g. glass, stainless steel or other materials.

tubing* string

When using tubing in a tubular flow/continuous reactor, various pieces of information can be provided, such as tubing material, diameter, length, connections, etc.

localisation_of_the_catalyst* string

Specify the exact location of the catalyst in the tubular flow/continuous reactor. The biocatalyst is typically present in the liquid phase or immobilized on a support matrix (such as particles or membranes).

special_treatment* string

If there are any other specific methods, procedures, characteristics or aspects related to the tubular flow/continuous reactor or its preparation for the reaction that are important for reproducibility and are not described by the aforementioned metadata, they should be explained here.

Shaking¶

Shaking is an essential method for ensuring uniform mixing and, consequently, recording relevant metadata is crucial for maintaining consistent reaction conditions.Mechanically impelled mixing (stirring)

shaking_type* string

The type of shaking used to mix the reaction (e.g., horizontal, vertical, back-and-forth or circulatory).

deflection* float

Information about the extent of deflection or bending of the agitator from its original position of the horizontal shaking system.
Minimum: 0.0

deflection_unit* string

Units such as mm (millimeters) or μm (micrometers) could be used to describe deflection in relation to the movement of the shaking system.

speed* float

Specify the speed or frequency at which the shaking was conducted.
Minimum: 0.0

speed_unit* string

The shaking speed or frequency could be expressed in units such as rpm (rounds per minute) or Hz (cycles per second).

position* string

Information regarding the orientation of the vessel in the shaking system relative to deflection.

special_treatment* string

If there are any other specific methods, procedures, characteristics or aspects related to the shaking that are important for reproducibility and are not described by the aforementioned metadata, they should be explained here.

MechanicallyImpelledMixing¶

When utilizing mechanically impelled mixing in enzymatic reactions, it is essential to provide information about the mixing method and related parameters.Liquid or gas impelled mixing

stirring_type* string

There are several types of stirring methods used in laboratory and industrial settings, including magnetic stirring (from vessel bottom), mechanical stirring, overhead stirring and other methods.

stirrer_material* string

The specific composition or nature of the material should be indicated, e.g. whether it is made of magnetic material, a PTFE (polytetrafluoroethylene) coating, stainless steel or other relevant features that determine its structural or functional properties within the experimental setup.

supplier* string

If available, details of the specific designation or manufacturer's name of the stirrer should be provided for precise identification.

number_of_stirrers* float

The number of stirrers available in the system.
Minimum: 0.0

distance_between_stirrers* float

Information about the distance, spacing or separation between the stirring rods or impellers within a reaction vessel or container.
Minimum: 0.0

distance_between_stirrers_unit* string

The distance between stirrers can be specified in mm (millimeters), cm (centimeters), or m (meters), depending on the size and scale of the stirring system.

stirrer_blade_pitch_angle* float

The pitch angle at which the blades or paddles of a stirring mechanism are positioned relative to the plane of rotation. It's typically expressed in ° (degrees).
Minimum: 0.0

number_of_stirrer_blades* float

The number of blades on each stirrer.
Minimum: 0.0

stirrer_blade_size* float

The size of the impeller blades in a stirred tank reactor.
Minimum: 0.0

stirrer_blade_size_unit* string

In the case of impellers in a stirred tank reactor, the diameter of the impeller blades is typically specified. This diameter can be measured in millimeters (mm) or centimeters (cm).

stirrer_geometry* string

There are various morphologies or geometries, such as radial impellers, axial impellers, helical ribbon impellers, paddle impellers, and more, depending on its design and intended purpose.

stirrer_speed* float

Specify the speed or frequency at which the stirring was conducted.
Minimum: 0.0

speed_unit* string

The unit for stirring speed can be expressed in RPM (revolutions per minute), Hz (Hertz), or rad/s (radians per second), depending on the measurement instruments and scientific conventions used.

height_of_stirrer_above_vessel_base* float

The vertical distance between the bottom of the vessel or container (where the reaction takes place) and the lowest point of the stirring element or stirrer, which is usually located just above the vessel base.
Minimum: 0.0

height_of_stirrer_above_vessel_base_unit* string

Common units for defining the vertical distance between the bottom of the vessel and the lowest point of the stirrer include: mm (millimeters), cm (centimeters) and m (meters).

power_per_volume* float

The amount of stirring power or energy input into a system per unit volume.
Minimum: 0.0

power_per_volume_unit* string

The units commonly used for expressing the stirring power are W/L (watts per liter) or kW/m³ (kilowatts per cubic meter).

stir_bar_size* float

Minimum: 0.0- Decription: The length, diameter, or volume of the stir bar used in the experiment. Different sizes of stir bars can affect the efficiency of mixing based on the volume of the reaction mixture and the vessel size.

stir_bar_size_unit* float

Minimum: 0.0- Decription: The size of a stir bar can be expressed in various units such as length in cm (centimeters), mm (millimeters), m (meters), in (inches), or ft (feet); diameter in mm (millimeters), cm (centimeters), or μm (micrometers); and cm³ (volume in cubic centimeters) or mL (milliliters). The choice of unit depends on the specific dimensions being measured to describe the stir bar's size accurately within experiments.

stir_bar_shape* string

The shape or configuration of the stir bar, whether it's cylindrical, octagonal, oval, or another shape. Different shapes can interact with the reaction mixture differently, influencing mixing patterns and efficiency.

special_treatment* string

If there are any other specific methods, procedures, characteristics or aspects related to the mechanically impelled mixing (stirring) that are important for reproducibility and are not described by the aforementioned metadata, they should be explained here.

LiquidOrGasImpelledMixing¶

Detailed information about the mixing mode used, whether it involves liquid or gas impelled mixing, is essential for ensuring the reproducibility and understanding of enzymatic reactions.

volume_of_liquid_solid_phase* string

In the context of enzymatic reactions or any chemical processes involving heterogeneous mixtures like a liquid and solid phase, essential parameters for describing the system involve the composition of the phases, the percentage or fraction of the total volume occupied by the liquid-solid phase mixture, and further information.

residence_time* float

The residence time, often denoted as "τ" (tau), refers to the average amount of time a substance or component spends inside a specific system or reactor and is to be specified.
Minimum: 0.0

residence_time_unit* string

The units for residence time can vary depending on the system and the units used for volume and flow rate. Common units include s (seconds), min (minutes), h (hours), or any time-related units.

reynolds_number* string

The Reynolds number (Re) is a dimensionless quantity used in fluid dynamics to predict the flow regime of a fluid within a specific system. It helps to determine whether the flow is laminar, turbulent, or somewhere in between.

passive_mixing* string

The design of the coils and the flow patterns created by the geometry of the tubing can lead to passive mixing as the fluid flows through the reactor without the need for external agitation. More detailed information must be provided to describe the process.

active_T_or_Y_mixer* string

Key features for describing an active Y or T mixer can include inlet ports, mixer chamber, outlet port, control, materials amon others.

pulsing* string

The pulsing process involves periodically injecting or introducing specific components, such as reactants or additives, into a reaction system at regular intervals or in a pulsatile manner. More detailed information must be provided to describe the process.

special_treatment* string

If there are any other specific methods, procedures, characteristics or aspects related to the liquid or gas impelled mixing that are important for reproducibility and are not described by the aforementioned metadata, they should be explained here.