ExperimentMix
ExperimentMix[Objects]⟹Protocol
creates a Protocol to mix the provided sample or container Objects, with optional heating with mixing.
Mixing allows samples to be rolled, homogenized, stirred, sonicated, or vortexed under specific conditions. In addition, it allows for heating and cooling of the sample during mixing. Because ExperimentIncubate and ExperimentMix have access to identical instrumentation, they are functionally equivalent.
Experimental Principles
Figure 1.1: Procedural overview of an incubation. Step 1 (Optional): If desired, the sample is thawed. Step 2: The sample is incubated and/or mixed under the desired conditions. For example, this could be performed using an overhead stirrer and heat plate (as pictured) Step 3: The incubation is completed. If MixUnitlDissolved is desired, the incubation will continue if the sample is not yet fully dissolved. If annealing time is set, the sample will sit at room temperature for the specified time. If ResidualIncubation is set, incubation will continue past the set time while waiting to progress to the next step in the protocol.
Instrumentation
AHP-1200CPV
Figure 2.1.1: The samples are placed inside of the instrument enclosure that is filled with heat-conductive Lab Armour. The instrument is set to the specified temperature until the time is reached.
Thermal-Lok 2510-1104
Figure 2.2.1: The samples are placed inside of the instrument enclosure that is filled with heat-conductive Lab Armour. The instrument is set to the specified temperature until the time is reached.
Cole-Parmer StableTemp Digital Utility Water Baths, 10 liters
Automated Thermal Cycler
Figure 2.4.1: The Automated Thermal Cycler allows programmable 96-well plate-based thermocycling in the temperature range from 4 °C to 105 °C, with a maximum ramp rate of 3.5 °C/sec. Additionally, its automated plate cover can be heated up to 105 °C, which improves thermal contact and minimizes condensation on the plate seal.
Eppendorf Research Plus P1000
Figure 2.5.1: The diagram above lists the available pipette sizes and corresponding tip types that are available in the ECL.
Drum Roller
Figure 2.6.1: The volume to be mixed is placed in the preferred container for use on the bottle/drum roller, and then laid horizontally on the roller cylinders. The roller cylinders are rotated for the specified time at the specified rotations per minute until the the time is reached.
IKA Roller 6 digital
Figure 2.7.1: The volume to be mixed is placed in the preferred container for use on the bottle/drum roller, and then laid horizontally on the roller cylinders. The roller cylinders are rotated for the specified time at the specified rotations per minute until the the time is reached.
Enviro-Genie
Figure 2.8.1: A tube roller allows the agitation of liquids via rolling at set temperatures. A magnetic platform in the instrument provides the foundation for mounting magnetic clip plates, which then lock tubes of different sizes in position. 360-degree rotation of the magnetic platform at 1 to 35 RPM allows the thorough mixing of the liquids inside the tubes while being incubated at the accurately controlled temperature between 22 and 75 Celsius. Chamber air is gently and continuously circulating to ensure the temperature consistency and uniformity of all samples. The instrument can be used for 50mL tubes, 15mL tubes and 2mL tubes with capacities of 6, 6 and 24.
Fisherbrand Nutating Mixer with Precision Low Temperature BOD Refrigerated Incubator
Figure 2.9.1: Samples are nutated inside of a refridgerated incubator such that they can be chiled while they are mixed.
Genie Temp-Shaker 300
Figure 2.10.1: Samples are placed on the instrument platform and held in place by adjustable width restraining bars. An enclosure is placed over the samples while the instrument performs orbital shaking with optional heating.
Burrell Scientific Wrist Action Shaker
Figure 2.11.1: The samples secured using the grippers on the instrument. The MixRate and OscillationAngle of the instrument are set according to user specifications, then the instrument is turned on for the specified time.
LabRAM II Acoustic Mixer
Figure 2.12.1: The LabRAM II uses sound energy to vigorously shake the chosen sample(s). The LabRAM actively monitors the damping characteristics of the mixing vessel to apply a constant G Force when mixing.
20 mm Bottle Vortex Genie
Figure 2.13.1: Samples in 2mL or 15mL Tubes can be vortexed for a specifed time and mix rate (in RPM). The foam insert on the top of the vortex holds the samples in place during the mixing.
35 mm Bottle Vortex Genie
Figure 2.14.1: Samples in bottles that are 35mm (+/- 5mm) in diameter can be vortexed for a specifed time and mix rate (in RPM). The foam insert on the top of the vortex holds the samples in place during the mixing.
Microplate Genie
Microplate Incu-Mixer MP4
Figure 2.16.1: 4 SBS format plates can be vortexed in the MP4 at the same mixing speed (RPM). The cover of the MP4 is temperature controlled and can be set between 25C (Ambient) and 70C. All plates in the MP4 must be set to the same temperature.
Multi Tube Vortex Genie 2
Figure 2.17.1: 50mL, 15mL, and 2mL tubes are snapped into the vortex positions in order to be mixed.
Digital Disruptor Genie
MINISTAR 40 with AHP-1200CPV Hot Plate
Figure 2.19.1: Samples will be mixed via stirring using an impeller that attaches to the IKA MINISTAR 40 unit (top). An appropriate impeller will be chosen depending on the Aperture and InternalDimensions of the container that is being mixed. The sample makes direct contact with the AHP-1200CPV heater/cooler. If the container is not SelfStanding, a thermally conductive tube stand will be used to transfer the heat from the hot plate to the sample (ex. 50mL Tube). The container is physically secured in place using a clamp to prevent movement during mixing.
MINISTAR 40 with C-MAG HS 10 Hot Plate
Figure 2.20.1: Samples will be mixed via stirring using an impeller that attaches to the IKA MINISTAR 40 unit (top). An appropriate impeller will be chosen depending on the Aperture and InternalDimensions of the container that is being mixed. The sample makes direct contact with the C MAG HS 10 hot plate. If the container is not SelfStanding, a thermally conductive tube stand will be used to transfer the heat from the hot plate to the sample (ex. 50mL Tube). The container is physically secured in place using a clamp to prevent movement during mixing.
Branson 1510
Figure 2.21.1: Samples are placed into a tank filed with deionized water. The transducers at the bottom of the sonicator generate vibration energy which agitates particles in a samples.
Branson CPXH 3800
Figure 2.22.1: Samples are placed into a tank filed with deionized water. The transducers at the bottom of the sonicator generate vibration energy which agitates particles in a samples. To improve the performance temperature range from 22°C to 69°C can be applied.
Qsonica Q700MX
Figure 2.23.1: A single plate is placed into a water bath that is connected to the sonification horn. The water bath can be cooled or heated using a recirculating pump during sonication. It is recommended to use PCR plates that have allow greater surface area around each of the wells when performing plate sonication.
SFX550 Sonifer with AHP-1200CPV
Figure 2.24.1: A probe is connected to a sound wave generator. The probe is immersed into a solution, and sound waves are supplied to agitate and disperse the liquid. A variety of probe heads are available with different form factors, accommodating variety of container types from small 2 mL tubes to 2 liter Schott bottles. Sound waves can be supplied discontinuously, as to not to overheat the liquid. Furthermore, temperature feedback and control can be adjusted to ensure that the solution remains at the desired temperature throughout the mixing.
Caron 7000-10-1 Environmental Chamber
Figure 2.25.1: The Caron 7000 can control the temperature and relative humidity of the chamber used to degrade the samples.
Caron 7545-11-2 Environmental Chamber with Photostability
Experiment Options
General
RelativeHumidity
The amount of water vapor present in air that the samples are exposed to during incubation, relative to the amount needed for saturation.
Default Calculation: Automatically set to 70 Percent if using an environmental chamber with relative humidity control.
Pattern Description: Greater than or equal to 0 percent and less than or equal to 100 percent in increments of 1 percent or Null.
LightExposure
The range of wavelengths of light that the incubated samples are exposed to. Only available when incubating the samples in an environmental chamber with UVLight and VisibleLight control.
Default Calculation: Automatically set to UVLight if LightExposureIntensity is in units of Watt/Meter^2, set to VisibleLight if LightExposureIntensity is in units of Lumen/Meter^2, otherwise set to Null.
LightExposureIntensity
The intensity of light that the incubated samples will be exposed to during the course of the incubation. UVLight exposure is measured in Watt/Meter^2 and Visible Light Intensity is measured in Lumen/Meter^2.
Default Calculation: Automatically set to 19 Watt/Meter^2 if LightExposure is set to UVLight and 14500 Lumen/Meter^2 if LightExposure is set to VisibleLight. Otherwise, set to Null.
Programmatic Pattern: ((RangeP[2*(Watt/Meter^2), 36*(Watt/Meter^2)] | RangeP[2*(Lumen/Meter^2), 29000*(Lumen/Meter^2)]) | Automatic) | Null
TotalLightExposure
The total exposure of light that the incubated samples are exposed to during the course of the incubation. UVLight exposure is measured in Watt*Hour/Meter^2 and Visible Light exposure is measured in Lumen*Hour/Meter^2.
Programmatic Pattern: ((GreaterP[0*Watt*(Hour/Meter^2)] | GreaterP[0*Lumen*(Hour/Meter^2)]) | Automatic) | Null
LightExposureStandard
During light exposure experiments, a set of samples that are placed in an opaque box to receive identical incubation conditions without exposure to light. This option can only be set if incubating other samples in an environmental stability chamber with light exposure.
Pattern Description: List of one or more an object of type or subtype Object[Sample] or Object[Container] or a prepared sample entries or Null.
WorkCell
Preparation
Indicates if this unit operation is carried out primarily robotically or manually. Manual unit operations are executed by a laboratory operator and robotic unit operations are executed by a liquid handling work cell.
Protocol
Thaw
Indicates if any SamplesIn are incubated until visibly liquid, before they are mixed and/or incubated.
Default Calculation: Automatically set to True if any corresponding Thaw options are set. Otherwise, set to False.
ThawTime
Default Calculation: If Thaw is set to True, this option is automatically set to the ThawTime field in the Object[Sample], if specified. Otherwise, extra small volume samples (under 10mL) will be thawed for 5 Minutes, small volume samples (under 50mL) will be thawed for 15 Minutes, medium volume samples (under 100mL) will be 30 Minutes, and large volume samples (over 100mL) will be thawed for an hour.
MaxThawTime
ThawTemperature
Pattern Description: Greater than or equal to -20 degrees Celsius and less than or equal to 90 degrees Celsius or Null.
ThawInstrument
Default Calculation: Automatically set to the first instrument in the list of compatible instruments found by IncubateDevices with the given SamplesIn and ThawTemperature, if Thaw->True.
Pattern Description: An object of type or subtype Model[Instrument, HeatBlock] or Object[Instrument, HeatBlock] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, HeatBlock], Object[Instrument, HeatBlock]}] | Automatic) | Null
Mix
Default Calculation: Automatically set to True if any Mix related options are set. Otherwise, set to False.
MixType
Indicates the style of motion used to mix the sample. Options include Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, Nutate.
Default Calculation: Automatically sets based on the container of the sample and the Mix option. Specifically, if Mix is set to False, the option is set to Null. If MixInstrument is specified, the option is set based on the type of the Model[Instrument] or Object[Instrument] of the specified MixInstrument. If MixRate and Time are Null, when MixVolume is Null or larger than 50ml, the option is set to Invert, otherwise set to Pipette. If Amplitude, MaxTemperature, or DutyCycle is not Null, the option is set to Homogenizer. If MixRate is set, the option is set based on the type of the Model[Instrument] of the first instrument found by MixDevices that is compatible with the SamplesIn, Temperature, and MixRate.
Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.
MixUntilDissolved
Indicates if the mix should be continued up to the MaxTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute.
Instrument
Default Calculation: Automatically resolves based on the options Mix, Temperature, MixType and container of the sample.
Pattern Description: An object of type or subtype Model[Instrument, Roller], Model[Instrument, OverheadStirrer], Model[Instrument, Vortex], Model[Instrument, Shaker], Model[Instrument, BottleRoller], Model[Instrument, Roller], Model[Instrument, Sonicator], Model[Instrument, HeatBlock], Model[Instrument, Homogenizer], Model[Instrument, Disruptor], Model[Instrument, Nutator], Model[Instrument, Thermocycler], Model[Instrument, EnvironmentalChamber], Model[Instrument, Pipette], Object[Instrument, Roller], Object[Instrument, OverheadStirrer], Object[Instrument, Vortex], Object[Instrument, Shaker], Object[Instrument, BottleRoller], Object[Instrument, Roller], Object[Instrument, Sonicator], Object[Instrument, HeatBlock], Object[Instrument, Homogenizer], Object[Instrument, Disruptor], Object[Instrument, Nutator], Object[Instrument, Thermocycler], Object[Instrument, EnvironmentalChamber], or Object[Instrument, Pipette] or Null.
StirBar
Default Calculation: If MixRate is above 1000 RPM, or if no compatible impeller can be found for the given stirrer, StirBar is automatically set to the largest compatible stir bar found. Here, a compatible impeller means that it can fit in the aperture of the sample's container, can reach the bottom of the sample's container, and is compatible with the stir instrument given; a compatible stir bar means that its width can fit in the aperture of the sample's container and that its length is not greater than the InternalDiameter of the sample's container. Otherwise set to Null.
Pattern Description: An object of type or subtype Model[Part, StirBar] or Object[Part, StirBar] or Null.
Time
Default Calculation: Automatically set to 5 Minute for robotic preparation. For manual preparation, if Thaw is True, set to 0 Minute; else if MaxTime is specified, Time is automatically set to 1/3 of MaxTime; otherwise set to 15 Minute. As a special case in manual preparation, when LightExposure is not Null, Thaw is True, set to 0 Minute; else if TotalLightExposure is specified and LightExposureIntensity is not Null, Time is automatically set to TotalLightExposure/LightExposureIntensity; otherwise set to 1 Hour.
MaxTime
Maximum duration of time for which the samples are mixed, in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. Note this option only applies for mix type: Shake, Roll, Vortex or Sonicate.
Default Calculation: Automatically set to 5 Hour if MixUntilDissolved is True, when an applicable MixType is chosen, otherwise set to Null.
PreSonicationTime
Default Calculation: Automatically set to 15 Minute for sonication over 1 hour, 0 Minute for sonication less than 1 hour. For MixType other than Sonicate, set to Null.
DutyCycle
The style how the homogenizer mixes the given sample via pulsation of the sonication horn. This duty cycle is repeated indefinitely until the specified Time/MaxTime has elapsed. This option can only be set when mixing via homogenization.
Default Calculation: Automatically set to {10 Millisecond, 10 Millisecond} if mixing by homogenization.
MixRate
Default Calculation: Automatically set to 300 RPM for robotic preparation. For manual preparation, MixRate is set to 20% of the MaxRotationRate if MixType is Stir, or otherwise is set to the average of MinRotationRate and MaxRotationRate of the instrument.
Programmatic Pattern: ((RangeP[$MinMixRate, $MaxMixRate] | RangeP[0*GravitationalAcceleration, 100*GravitationalAcceleration]) | Automatic) | Null
MixRateProfile
The frequency of rotation of the mixing instrument used to mix the samples, over the course of time.
Programmatic Pattern: ({{RangeP[0*Minute, $MaxExperimentTime], RangeP[$MinMixRate, $MaxMixRate] | RangeP[0*GravitationalAcceleration, 100*GravitationalAcceleration]}..} | Automatic) | Null
NumberOfMixes
Figure 3.1: Operators will invert containers by hand based on the NumberOfMixes specified. One mix corresponds to inverting and re-inverting.
Default Calculation: If MaxNumberOfMixes is specified, automatically set to 1/3 of MaxNumberOfMixes (round to integer); else if MixUntilDissolved->True, automatically set to 25; otherwise set to 15.
Pattern Description: Greater than or equal to 1 and less than or equal to 50 in increments of 1 or Null.
MaxNumberOfMixes
The maximum number of times for which the samples are mixed, in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. Note this option only applies for mix type: Pipette or Invert.
Default Calculation: When MixUntilDissolved->True, automatically set to 2*NumberOfMixes if it is Numeric (specified or automatically set); if not, set to 50.
Pattern Description: Greater than or equal to 1 and less than or equal to 250 in increments of 1 or Null.
MixVolume
Default Calculation: For robotic preparation, automatically set to 970 Microliter or sample volume informed by the field Volume of the sample, whichever is smaller. For manual preparation, automatically set to 50 Milliliter or half of the sample volume informed by the field Volume of the sample, whichever is smaller.
Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 milliliters or Null.
Temperature
The temperature of the device that is used to mix/incubate the sample. If mixing via homogenization, the pulse duty cycle of the sonication horn is automatically adjusted if the measured temperature of the sample exceeds this set temperature.
Default Calculation: Automatically set to 40 Celsius if AnnealingTime is specified, if not, set to Ambient.
Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.
Programmatic Pattern: ((RangeP[$MinIncubationTemperature, $MaxIncubationTemperature] | Ambient) | Automatic) | Null
TemperatureProfile
Programmatic Pattern: ({{RangeP[0*Minute, $MaxExperimentTime], RangeP[$MinTemperatureProfileTemperature, $MaxTemperatureProfileTemperature]}..} | Automatic) | Null
MaxTemperature
The maximum temperature that the sample is allowed to reach during mixing via homogenization or sonication. If the measured temperature is above this MaxTemperature, the homogenizer/sonicator turns off until the measured temperature is 2C below the MaxTemperature, then it automatically resumes.
Pattern Description: Greater than or equal to 0 degrees Celsius and less than or equal to 100 degrees Celsius or Null.
OscillationAngle
Pattern Description: Greater than or equal to 0 degrees and less than or equal to 15 degrees or Null.
Amplitude
The amplitude of the sonication horn when mixing via homogenization. When using a microtip horn (ex. for 2mL and 15mL tubes), the maximum amplitude is 70 Percent, as specified by the manufacturer, in order not to damage the instrument.
Pattern Description: Greater than or equal to 10 percent and less than or equal to 100 percent or Null.
AnnealingTime
Minimum duration for which the SamplesIn should remain in the incubator allowing the system to settle to room temperature after the Time has passed.
Default Calculation: Automatically set to 0 Minute (or to Null in cases where the sample is not being incubated).
MixFlowRate
The speed at which liquid is aspirated and dispensed in a liquid before it is aspirated. This option can only be set if Preparation->Robotic.
Default Calculation: Automatically set to 100 Microliter/Second when mixing by pipetting if Preparation->Robotic.
Pattern Description: MixFlowRate speed at which liquid should be drawn up into the pipette tip or Null.
MixPosition
The location from which liquid should be mixed by pipetting. This option can only be set if Preparation->Robotic.
MixPositionOffset
The distance from the center of the well that liquid will aspirated/dispensed while mixing the sample. When specifying a Z Offset, the Z Offset is calculated either as the height below the top of the well, the height above the bottom of the well, or the height below the detected liquid level, depending on value of the AspirationPosition option (Top|Bottom|LiquidLevel). When an AspirationAngle is specified, the AspirationPositionOffset is measured in the frame of reference of the tilted labware (so that wells that are further away from the pivot point of the tilt are in the same frame of reference as wells that are close to the pivot point of the tilt). This option can only be set if Preparation->Robotic.
Default Calculation: Automatically set to 2 Millimeter if MixType->Pipette and Preparation->Robotic.
Programmatic Pattern: ((GreaterEqualP[0*Millimeter] | Coordinate[{DistanceP, DistanceP, GreaterEqualP[0*Millimeter]}]) | Automatic) | Null
MixTiltAngle
The angle that the sample's container is tilted during the mixing of the sample. The container is pivoted on its left edge when tilting occurs. This option can only be provided if Preparation->Robotic.
Pattern Description: Greater than or equal to 0 degrees and less than or equal to 10 degrees in increments of 1 degree or Null.
CorrectionCurve
The relationship between a target volume and the corrected volume that needs to be aspirated or dispensed to reach the target volume. This option can only be set if Preparation->Robotic.
Default Calculation: Automatically set to correction curve set in the PipettingMethod for the Object[Sample] if MixType->Pipette and Preparation->Robotic.
Programmatic Pattern: ({{RangeP[0*Microliter, 1000*Microliter], RangeP[0*Microliter, 1250*Microliter]}..} | Automatic) | Null
Tips
Default Calculation: If MixType->Pipette, automatically set to the preferred tips determined by TransferDevices with given MixVolume, as well as TipType and TipMaterial if specified, and it is also checked that the tips can reach the bottom of the container.
TipType
Default Calculation: If Tips is specified, automatically set to the field TipType of the Model[Item, Tips] or the Model of Object[Item,Tips]. Otherwise, set to Null.
TipMaterial
The material of the pipette tips used to aspirate and dispense the requested volume during the transfer.
Default Calculation: If Tips is specified, automatically set to the field Material of the Model[Item, Tips] or the Model of Object[Item,Tips]. Otherwise, set to Null.
Pattern Description: {ABS, PLA, Acrylic, AmorphousFluoropolymer, CPVC, CTFE, Cycloolefine, COC, Delrin, ECTFE, EPDM, ETFE, EVA, FEP, FFKM, HDPE, Hypalon, LDPE, NaturalRubber, NBR, Neoprene, Nitrile, Noryl, Nylon, PEEK, PEI, Perlast, PharmaPure, Polycarbonate, Polyester, Polyethylene, Polyisoprene, Polyolefin, Polyoxymethylene, Polypropylene, Polysulfone, Polystyrene, Polyurethane, PVC, PCTFE, PETG, PF, PFA, PPS, PTFE, PVDF, SEBS, Silicone, Styrofoam, SyntheticRubber, TFM, TPE, Tygon, UVPlastic, UVXPO, Viton}, {Aluminum, Alloy, AnodisedAluminum, Brass, Bronze, CarbonSteel, CastIron, Chrome, Copper, Elgiloy, Gold, Hastelloy, Lead, Magnesium, Molybdenum, MP35N, MP35NHPS, Nickel, Niobium, Platinum, Silver, Steel, StainlessSteel, Titanium, Tungsten, Zinc}, {Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, AnoporeAlumina}, {Silica, Alumina, ResinParticlesWithLatexMicroBeads, CrossLinkedDextranBeads, CrossLinkedPolystyrene, AerisCoreShell, KinetexCoreShell, CrossLinkedAgarose, Vydac218MS, JordiGel, Styrene, SilicaCompositeTWIN, BEH, CSH, HSS, CarboPacPA1, CarboPacPA10, BEH}, AluminiumOxide, ZirconiumOxide, Ceramic, Epoxy, EpoxyResin, GlassyCarbon, {BorosilicateGlass, Glass, OpticalGlass}, Graphite, Porcelain, Oxidizer, {Cardboard, Wood}, {Agate, Quartz, UVQuartz, ESQuartz, FusedQuartz, IRQuartz}, Ruby, Sapphire, Silicon, Viton, or {VacuumMeltedStainlessSteel} or Null.
MultichannelMix
Default Calculation: Automatically set to True if there are multiple samples that are mixed via pipette, if MixType->Pipette.
DeviceChannel
The channel of the work cell that should be used to perform the pipetting mixing. This option can only be set if Preparation->Robotic and MixType->Pipette.
Default Calculation: Automatically set to SingleProbe1 if MultichannelMix->False. Otherwise, set to the appropriate channel to perform the transfer, if Preparation->Robotic and MixType->Pipette.
Pattern Description: MultiProbeHead, SingleProbe1, SingleProbe2, SingleProbe3, SingleProbe4, SingleProbe5, SingleProbe6, SingleProbe7, or SingleProbe8 or Null.
ResidualIncubation
Indicates if the incubation and/or mixing should continue after Time/MaxTime has finished while waiting to progress to the next step in the protocol.
Default Calculation: Automatically set to True if Temperature is non-Ambient and the samples being incubated have non-ambient TransportTemperature.
ResidualTemperature
The temperature at which the sample(s) should remain incubating after Time has elapsed. This option can only be set if Preparation->Robotic.
Default Calculation: Automatically set to Temperature if ResidualIncubation is True and Preparation->Robotic.
Pattern Description: Ambient or Null or greater than or equal to 0 degrees Celsius and less than or equal to 105 degrees Celsius.
ResidualMix
Indicates that the sample(s) should remain shaking at the ResidualMixRate after Time has elapsed. This option can only be set if Preparation->Robotic.
ResidualMixRate
When mixing by shaking, this is the rate at which the sample(s) remains shaking after Time has elapsed. This option can only be set if Preparation->Robotic.
Pattern Description: Greater than or equal to 30 revolutions per minute and less than or equal to 2500 revolutions per minute or Null.
Preheat
Indicates if the incubation position is brought to Temperature before exposing the Sample to it. This option can only be set if Preparation->Robotic.
Cell Transformation
Transform
Indicates whether the incubation is intended to heat-shock cells in order to disrupt the cell membrane and allow a plasmid to be taken up and incorporated into the cell.
Figure 3.2: Procedural overview of an incubation to transform cells. Step 1: The cells are cooled. Step 2: The cells are heat shocked for no more than 120 seconds in order to disrupt the cell membrane and allow the plasmid to be taken up and incorporated into the cell. Step 3: The cells are again cooled.
Default Calculation: Automatically set to True if any Transform-related options are specified. Otherwise, automatically set to Null if there are no cells detected in the input samples.
TransformHeatShockTemperature
The temperature at which the cells should be heat-shocked in order to disrupt the cell membrane and allow the plasmid to be taken up and incorporated into the cell.
Pattern Description: Greater than or equal to 37 degrees Celsius and less than or equal to 47 degrees Celsius or Null.
TransformHeatShockTime
The length of time for which the cells should be heat-shocked in order to disrupt the cell membrane and allow the plasmid to be taken up and incorporated into the cell.
Pattern Description: Greater than or equal to 0 seconds and less than or equal to 120 seconds or Null.
TransformPreHeatCoolingTime
The length of time for which the cells should be cooled prior to heat shocking in order to disrupt the cell membrane and allow the plasmid to be taken up and incorporated into the cell.
Pattern Description: Greater than or equal to 0 minutes and less than or equal to 120 minutes or Null.
TransformPostHeatCoolingTime
The length of time for which the cells should be cooled after heat shocking in order to disrupt the cell membrane and allow the plasmid to be taken up and incorporated into the cell.
Pattern Description: Greater than or equal to 0 minutes and less than or equal to 60 minutes or Null.
Sample Preparation
CentrifugeAliquotContainer
The desired type of container that should be used to prepare and house the centrifuge samples which should be used in lieu of the SamplesIn for the experiment.
FilterAliquotContainer
The desired type of container that should be used to prepare and house the filter samples which should be used in lieu of the SamplesIn for the experiment.
Model Input
PreparedModelAmount
Indicates the amount of a Model[Sample] specified as input to the experiment function that will be prepared in the PreparedModelContainer. When set to All and the input model sample is not preparable, the entire amount of the input model sample that comes from one of the Products is prepared. The selected product must have both Amount and DefaultContainerModel populated, and it must not be a KitProduct. When set to All and the input model is preparable such as water, 1 Milliliter of the input model sample is prepared.
Programmatic Pattern: ((Null | (RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All)) | Automatic) | Null
PreparedModelContainer
Indicates the container in which a Model[Sample] specified as input to the experiment function will be prepared.
Default Calculation: If PreparedModelAmount is set to All and when the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise set to Model[Container, Vessel, "2mL Tube"].
Post Experiment
SamplesInStorageCondition
The non-default conditions under which the SamplesIn of this experiment should be stored after the protocol is completed. If left unset, SamplesIn will be stored according to their current StorageCondition.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Sample Prep Options
Preparatory Centrifugation
Centrifuge
Indicates if the SamplesIn should be centrifuged prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
Default Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.
CentrifugeInstrument
Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic) | Null
CentrifugeIntensity
The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.
Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.
Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
CentrifugeTime
CentrifugeTemperature
The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.
Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.
CentrifugeAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
CentrifugeAliquot
The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.
Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
Preparatory Filtering
Filtration
Indicates if the SamplesIn should be filter prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
Default Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.
FiltrationType
Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.
FilterInstrument
Default Calculation: Will automatically resolved to an instrument appropriate for the filtration type.
Pattern Description: An object of type or subtype Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], or Object[Instrument, SyringePump] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], Object[Instrument, SyringePump]}] | Automatic) | Null
Filter
The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
Default Calculation: Will automatically resolve to a filter appropriate for the filtration type and instrument.
Pattern Description: An object of type or subtype Model[Container, Plate, Filter], Model[Container, Vessel, Filter], or Model[Item, Filter] or Null.
Programmatic Pattern: (ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}] | Automatic) | Null
FilterMaterial
The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
Default Calculation: Resolves to an appropriate filter material for the given sample is Filtration is set to True.
Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.
PrefilterMaterial
The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.
Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.
FilterPoreSize
The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.
Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.
Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
PrefilterPoreSize
The pore size of the filter; all particles larger than this should be removed during the filtration.
Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
FilterSyringe
Default Calculation: Resolves to an syringe appropriate to the volume of sample being filtered, if Filtration is set to True.
Pattern Description: An object of type or subtype Model[Container, Syringe] or Object[Container, Syringe] or a prepared sample or Null.
Programmatic Pattern: ((ObjectP[{Model[Container, Syringe], Object[Container, Syringe]}] | _String) | Automatic) | Null
FilterHousing
The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.
Default Calculation: Resolve to an housing capable of holding the size of the membrane being used, if filter with Membrane FilterType is being used and Filtration is set to True.
Pattern Description: An object of type or subtype Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], or Object[Instrument, FilterBlock] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], Object[Instrument, FilterBlock]}] | Automatic) | Null
FilterIntensity
Default Calculation: Will automatically resolve to 2000 GravitationalAcceleration if FiltrationType is Centrifuge and Filtration is True.
Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.
Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
FilterTime
Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.
FilterTemperature
The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.
Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.
FilterContainerOut
The desired container filtered samples should be produced in or transferred into by the end of filtration, with indices indicating grouping of samples in the same plates, if desired.
Default Calculation: Automatically set as the PreferredContainer for the Volume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one.
Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.
Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1] | Automatic, (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
FilterAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
FilterAliquot
The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.
Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
FilterSterile
Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.
Aliquoting
AliquotAmount
Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container if a liquid, or the current Mass or Count if a solid or counted item, respectively.
Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
TargetConcentration
The desired final concentration of analyte in the AliquotSamples after dilution of aliquots of SamplesIn with the ConcentratedBuffer and BufferDiluent which should be used in lieu of the SamplesIn for the experiment.
TargetConcentrationAnalyte
Default Calculation: Automatically set to the first value in the Analytes field of the input sample, or, if not populated, to the first analyte in the Composition field of the input sample, or if none exist, the first identity model of any kind in the Composition field.
Pattern Description: An object of type or subtype Model[Molecule], Model[Molecule, cDNA], Model[Molecule, Oligomer], Model[Molecule, Transcript], Model[Molecule, Protein], Model[Molecule, Protein, Antibody], Model[Molecule, Carbohydrate], Model[Molecule, Polymer], Model[Resin], Model[Resin, SolidPhaseSupport], Model[Lysate], Model[ProprietaryFormulation], Model[Virus], Model[Cell], Model[Cell, Mammalian], Model[Cell, Bacteria], Model[Cell, Yeast], Model[Tissue], Model[Material], or Model[Species] or Null.
AssayVolume
Default Calculation: Automatically determined based on Volume and TargetConcentration option values.
Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
ConcentratedBuffer
The concentrated buffer which should be diluted by the BufferDilutionFactor in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
BufferDilutionFactor
The dilution factor by which the concentrated buffer should be diluted in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
Default Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.
BufferDiluent
The buffer used to dilute the aliquot sample such that ConcentratedBuffer is diluted by BufferDilutionFactor in the final solution. The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is specified; otherwise, resolves to Null.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
AssayBuffer
The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.
Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
AliquotSampleStorageCondition
The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
DestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.
Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null
AliquotPreparation
Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.
ConsolidateAliquots
AliquotContainer
The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired.
Default Calculation: Automatically set as the PreferredContainer for the AssayVolume of the sample. For plates, attempts to fill all wells of a single plate with the same model before aliquoting into the next.
Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null or {Index, Container} or list of one or more an object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null entries or list of one or more Automatic or Null or {Index, Container} entries.
Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null))..} | {({GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | (Automatic | Null))..}) | Automatic) | Null
Aliquot
Indicates if aliquots should be taken from the SamplesIn and transferred into new AliquotSamples used in lieu of the SamplesIn for the experiment.
Sample Preparation
PreparatoryUnitOperations
Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSamplePreparation.
Protocol Options
Organizational Information
Template
A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.
Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.
Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null
Name
A object name which should be used to refer to the output object in lieu of an automatically generated ID number.
Post Experiment
MeasureWeight
Indicates if any solid samples that are modified in the course of the experiment should have their weights measured and updated after running the experiment. Please note that public samples are weighed regardless of the value of this option.
MeasureVolume
Indicates if any liquid samples that are modified in the course of the experiment should have their volumes measured and updated after running the experiment. Please note that public samples are volume measured regardless of the value of this option.
ImageSample
Example Calls
Basic Examples
Mix the specified samples. ExperimentMix will automatically resolve the best suited instrument to mix the samples on:
Samples that have warm TransportTemperature in their Model and are being incubated with heat will be left in their instrument to continue heating and mixing after Time/MaxTime until the operator returns to continue the protocol:
Thaw the samples before mixing at 50 Celsius. The sample will be thawed for a minimum of 30 Minutes, then will continue being thawed for up to 2 Hours, until it is completely thawed. Samples always go through the thaw stage (if Thaw->True) before they are mixed/incubated:
Vortex the specified sample using a particular vortex for 1 Hour, then continue mixing the sample up to 5 Hours until it is completely dissolved:
Shake the given samples at a constant 50 Gs (only available when using the LabRAM II Acoustic Mixer):
Homogenizer Specific Options
Specify a duty cycle of 10 Milliseconds On, 20 Milliseconds Off when mixing the given sample by Homogenization:
Specify a sample to be mixed via homogenization aiming to maintain a temperature of 50C with a maximum temperature of 80C (where the instrument will turn off if the sample reaches this temperature and wait for it to cool down):
Pipette Specific Options
Specify that the samples should be mixed via pipette for 20 times, then if they are not fully dissolved, mix them again up to 25 more times:
Inversion Specific Options
Specify that the samples should be mixed via inversion for 20 times, then if they are not fully dissolved, mix them again up to 25 more times:
Environmental Chamber Specific Options
Specify that the samples should be kept in an environmental chamber for 24 Hours with UV light exposure:
Preferred Input Containers
Warnings and Errors
Messages (16)
ConflictingUnitOperationMethodRequirements (1)
CorrectionCurveIncomplete (1)
CorrectionCurveNotMonotonic (1)
InstrumentPrecision (5)
If a MaxTime with a greater precision that 1. Second is given, it is rounded:
If a MixRate with a greater precision that 1. RPM is given, it is rounded:
If a MixVolume with a greater precision that 1. Microliter is given, it is rounded:
If a Temperature with a greater precision that 1. Celsius is given, it is rounded:
If a Time with a greater precision that 1. Second is given, it is rounded:
InvalidCorrectionCurveZeroValue (1)
MixInstrumentTypeMismatch (1)
MixTypeIncorrectOptions (1)
MixTypeNumberOfMixesMismatch (1)
MixVolumeGreaterThanAvailable (1)
Possible Issues
Last modified on Fri 15 Aug 2025 17:48:52