ExperimentMedia
ExperimentMedia[MediaModel]⟹Protocol
generates a Protocol for preparation of liquid or solid cell growth media according to its formula and preparation parameters defined in the MediaModel.
ExperimentMedia[Components,Solvent,TotalVolume]⟹Protocol
creates a Protocol for combining the exact amounts of the given list of Components, including optional GellingAgents such as Agar for solid media, and using Solvent to fill to TotalVolume after initial component combination. If no existing MediaModel matches the specified list of Components, a new MediaModel will be created using UploadMedia with the provided components, Solvent, and total volume.
ExperimentMedia[UnitOperations]⟹Protocol
creates a Protocol for media that is prepared by following the specified UnitOperations.
Biological media are substances that support the growth and storage of cells and microorganisms. A medium for a particular organism contains nutrients and minerals that are essential for growth, plus any other substances that are necessary for the organism in the context of an experiment, such as isotopically-enriched metabolites or antibiotics for selection. The chemical components of a medium is specified by its formula, and additional gelling agents may be added to the formula of a liquid medium to create a solid-phase medium.
Experimental Principles
Figure 1.1: Default procedural overview of liquid media preparation. The process is analogous to that of ExperimentStockSolution. Step 1: The components of a medium are combined in quantities specified by the user or indicated in the formula of the provided media model. Step 2 (optional): The mixture is heated and/or mixed according to the incubation and mix parameters specified by the user or in the provided media model. Step 3 (optional): The mixture is adjusted to the desired pH by addition of acid or base titrants. Step 4 (optional): Additional solvent is added to the mixture to adjust its volume to the final volume specified by the user or indicated in the provided media model. The final volume of the mixture is assessed by ultrasonic methods, by graduation markings on the container, or by weight (ex. solvent is added until the mixture reaches a mass that corresponds to the mass of the desired final volume of this medium). Step 5 (optional): The mixture is filtered to remove particulates over critical size per the user's specifications, such as inorganic particulates and/or microorganisms. Step 6 (optional): The mixture is autoclaved to kill any remaining microorganisms. Step 7 (optional) The final solution is imaged.
Figure 1.2: Default procedural overview of solid media preparation. The process is analogous to that of ExperimentStockSolution, with the addition of gelling agents that convert liquid media into a solid matrix and optional plating of media from a preparatory bottle into incubation plates. Step 1: Steps from Figure 1.1 are followed to create a solution that contains all components of the medium minus the heat-sensitive components and gelling agents. Step 2: Gelling agents are added to the mixture from Step 1 in quantities specified by the user or indicated in the formula of the provided media model. Step 3 (optional): The mixture is mixed prior to autoclave and addition of any heat-sensitive reagents. Step 4: The mixture is autoclaved to dissolve the gelling agents and obtain a sterile heated solution. Step 5 (optional): At a reduced temperature, heat-sensitive components are added to the solution from Step 3 as sterile stock solutions whose solvents are identical to the solvent for the medium. Step 6 (optional): The mixture is heated and/or mixed according to the incubation and mix parameters specified by the user or indicated in the provided media model. Step 7 (optional): The mixture is transferred from its original bottle into incubation plates. Step 8 (optional): The incubation plates containing the medium are held at ambient temperature for the medium to solidify. Step 9 (optional): The incubation plates containing the solid medium are individually imaged.
Instrumentation
Drum Roller
Figure 2.1: 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 2.2: 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.
AHP-1200CPV
Figure 2.3: 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 2.4: 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.
SFX550 Sonifer with AHP-1200CPV
Figure 2.5: 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.
MINISTAR 40 with C-MAG HS 10 Hot Plate
Figure 2.6: 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.
Enviro-Genie
Figure 2.7: 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.
Genie Temp-Shaker 300
Figure 2.8: 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 2.9: 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.
Branson 1510
Figure 2.10: 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 2.11: 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.
20 mm Bottle Vortex Genie
Figure 2.12: 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 2.13: 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 2.15: 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
SevenExcellence (for pH)
Figure 2.17: Seven Excellence methods can be pre-programmed with Mothod Modules. pH probes are held with a holding arm for pH measurements of samples by submerging into samples or measuring on surface of samples.
Mettler Toledo InLab Micro
Figure 2.18: The probe is immersed in the test sample. pH is measured by measuring the generated voltage between two electrodes which directly proportional to the pH of the solution.
Mettler Toledo InLab Reach 225
Figure 2.19: The probe is immersed in the test sample. pH is measured by measuring the generated voltage between two electrodes which directly proportional to the pH of the solution.
Filter Membrane Housing, 142 mm
Figure 2.20: Instrument diagram for the Filter Membrane Housing, 142 mm: The housing is made up of a top plate that is attached to the inlet port, and a bottom plate that is attached to the outlet port. A semi-permeable filter membrane is immobilized between the top and bottom plates as they are brought together. Liquid is then pumped from the inlet port through the filter membrane and into the outlet port, where it is diverted via tubing into a collection vessel.
Filter Block
Figure 2.21: Instrument diagram for the Filter Block: A filter plate containing sample is positioned inside of a collar which fits over a collection plate within the vacuum manifold. A vacuum generates a pressure gradient that causes the sample to flow through the filter into the collection vessel.
Avanti J-15R
Figure 2.22: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional heating or cooling. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Avanti J-15R with JA-10.100 Fixed Angle Rotor
Figure 2.23: Samples to be centrifuged are counterbalanced in available centrifuge rotor slots. The centrifuge spins the rotors around the axis of the main rotor, while applying optional heating or cooling. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Microfuge 16
Figure 2.24: Samples to be centrifuged are counterbalanced in available centrifuge slots. The centrifuge spins the samples around the axis of the rotor. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Sterile Microfuge 16
Figure 2.25: Samples to be centrifuged are counterbalanced in available centrifuge slots. The centrifuge spins the samples around the axis of the rotor. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Beckman Coulter Microfuge 20R
Figure 2.26: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional heating or cooling. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Eppendorf 5920R
Figure 2.27: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional cooling to prevent a buildup of heat caused by the friction of spinning the rotor. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Unisteri 559-1ED
Figure 2.28: Items to be sterilized are placed into a low-walled, secondary containment bin. Bottles should be loosely capped and items should be spaced apart in the bin to ensure efficient flow of steam around the items. The selected Autoclave Program (Universal, Liquid, or Dry) runs the sterilization cycle through preset temperatures, sterilization times, and cooling times, depending on the nature of the items to be autoclaved. The sterilization temperature can range from 120-135°C and the chamber pressure is held at > 100 kPa during sterilization.
Experiment Options
General
Supplements
Additional substances that would traditionally appear in the name of the media, such as 2% Ampicillin in LB + 2% Ampicillin. These components will be added to the Formula field of the Model[Sample,Media] but are specially called out in the media name following the "+" symbol. For example, ExperimentMedia[Model[Sample,Media,"Liquid LB"], Supplements->{Model[Molecule,"Ampicillin"], 50*Microgram/Liter}] will create a new Model[Sample,Media,"Liquid LB + Ampicillin, 50*Microgam/Liter"] with Supplements->{Model[Molecule,"Ampicillin"], 50*Microgram/Liter} added to the Formula of the input media.
Programmatic Pattern: {{RangeP[0.1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | RangeP[10*(Milligram/Liter), 10*(Kilogram/Liter)] | GreaterP[0., 1.], ObjectP[{Model[Sample], Object[Sample]}] | _String}..} | None
DropOuts
Substances from the Formula of ModelMedia that are completely excluded in the preparation of media. When specified, a new Model[Sample,Media] will be created with Formula that excludes these components from the Formula of the input media model. For example, if the user calls ExperimentMedia[Model[Sample,Media,"Synthetic Complete Medium"], DropOuts->Model[Molecule,"Uracil"], a new Model[Sample,Media,"Synthetic Complete Medium - Uracil] will be created whose Formula corresponds to the Formula of Model[Sample,Media,"Synthetic Complete Medium"] lacking Uracil.
Pattern Description: List of one or more an object of type or subtype Model[Molecule] or Model[Sample] entries or None.
GellingAgents
The types and amount by weight volume percentages of substances added to solidify the prepared media.
Default Calculation: Automatically set to {Model[Sample, "Agar"], 20*Gram/Liter} if MediaPhase is set to Solid and there is no GellingAgent present in the Formula field. If any GellingAgent is detected in the Formula field of Model[Sample,Media] and the GellingAgents option has been specified, the former will be removed from the Formula and replaced with GellingAgents.
Pattern Description: List of one or more {Amount, GellingAgent} entries or None or Automatic or Null.
Programmatic Pattern: (({{RangeP[0.1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | RangeP[10*(Milligram/Liter), 10*(Kilogram/Liter)] | GreaterP[0., 1.], ObjectP[{Model[Sample], Object[Sample]}] | _String}..} | (None | Automatic)) | Automatic) | Null
MediaPhase
The physical state of the prepared media at ambient temperature and pressure. This may be Solid (for conventional plate media), liquid, or semisolid (with lower gelling agent concentration).
Preparation
OrderOfOperations
The order in which solution preparation steps will be carried out to create the media. By default, the order is {FixedReagentAddition, FillToVolume, pHTitration, Incubation, Filtration}. FixedReagentAddition must always be first, Incubation/Mixing must always occur after FillToVolume/pHTitration and Filtration must always occur last. The FillToVolume/pHTitration stages are allowed to be swapped.
Default Calculation: By default, the order is {FixedReagentAddition, FillToVolume, pHTitration, Incubation, Filtration}. FixedReagentAddition must always be first, Incubation/Mixing must always occur after FillToVolume/pHTitration and Filtration must always occur last. The FillToVolume/pHTitration stages are allowed to be swapped. When using a UnitOperations input, set to Null.
Pattern Description: List of one or more FixedReagentAddition, FillToVolume, pHTitration, Incubation, or Filtration entries or Null.
Programmatic Pattern: ({(FixedReagentAddition | FillToVolume | pHTitration | Incubation | Filtration)..} | Automatic) | Null
Volume
The volume of the media model that should be prepared. Formula component amounts will be scaled according to the TotalVolume specified in the media model if this Volume differs from the model's TotalVolume. This option is not be used with the direct formula definition.
Default Calculation: Automatically set to the TotalVolume field of the media, or to the sum of the volumes of any liquid formula components if the TotalVolume is unknown for a first-time preparation of a media.
Programmatic Pattern: RangeP[$MinStockSolutionComponentVolume, $MaxStockSolutionComponentVolume] | Automatic
FillToVolumeMethod
The method by which to add the Solvent specified in the media model to the bring the media up to the TotalVolume specified in the media model.
Default Calculation: Automatically set to Null if there is no Solvent/TotalVolume. Otherwise, will resolved based on the FillToVolumeMethod in the given Model[Sample,Media].
PrepareInResuspensionContainer
Indicate if the media should be prepared in the original container of the FixedAmount component in its formula. PrepareInResuspensionContainer cannot be True if there is no FixedAmount component in the formula, and it is not possible if the specified amount does not match the component's FixedAmount.
HeatSensitiveReagents
Indicates that the given component of the formula is heat-sensitive and therefore must be added after autoclave.
Pattern Description: List of one or more an object of type or subtype Model[Sample] or Object[Sample] or a prepared sample entries or Null.
GraduationFilling
Indicates if the Solvent specified in the stock solution model is added to bring the stock solution model up to the TotalVolume based on the horizontal markings on the container indicating discrete volume levels, not necessarily in a volumetric flask.
Incubation
Incubate
Indicates if the media should be treated at a specified temperature following component combination and filling to volume with solvent. May be used in conjunction with mixing.
Default Calculation: Automatically set to True if any other incubate options are specified, or, if a template model is provided, set based on whether that template has incubation parameters.
Incubator
The instrument that should be used to treat the media at a specified temperature following component combination and filling to volume with solvent.
Default Calculation: Automatically set to an appropriate instrument based on container model, or Null if Incubate is set to False.
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.
IncubationTemperature
Temperature at which the media should be treated for the duration of the IncubationTime following component combination and filling to volume with solvent.
Default Calculation: Automatically set to the maximum temperature allowed for the incubator and container, 37 Celsius if the sample is being incubated, or Null if Incubate is set to False.
Pattern Description: Greater than or equal to 22 degrees Celsius and less than or equal to 500 degrees Celsius or Null.
IncubationTime
Duration for which the media should be treated at the IncubationTemperature following component combination and filling to volume with solvent. Note that if you are mixing AND incubating and this option is specified, it must be the same as the specified value of the MixTime option.
Default Calculation: Automatically set to 0.5 Hour if Incubate is set to True and Mix is set to False, or Null otherwise.
AnnealingTime
Minimum duration for which the media should remain in the incubator allowing the solution and incubator to return to room temperature after the MixTime has passed if mixing while incubating.
Mixing
Mix
Indicates if the components of the media should be mechanically incorporated following component combination and filling to volume with solvent.
Default Calculation: Automatically set to True if a new media formula is provided, to True if an existing media model with mixing parameters is provided, and to False if the provided media model has no mixing parameters.
MixType
The style of motion used to mechanically incorporate the components of the media following component combination and filling to volume with solvent.
Default Calculation: Automatically set based on the Volume option and size of the container in which the media is prepared.
Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.
MixUntilDissolved
Indicates if the complete dissolution of any solid components should be verified following component combination, filling to volume with solvent, and any specified mixing steps.
Mixer
The instrument that should be used to mechanically incorporate the components of the media following component combination and filling to volume with solvent.
Default Calculation: Automatically set based on the MixType and the size of the container in which the media is prepared.
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.
MixTime
The duration for which the media should be mixed following component combination and filling to volume with solvent.
Default Calculation: Automatically set from the MixTime field of the media model. If the model has no preferred time, set to 3 minutes. If MixType is Pipette or Invert, set to Null. 0 minutes indicates no mixing. Note that if you are mixing AND incubating and this option is specified, it must be the same as the specified value of the IncubationTime option.
MaxMixTime
The maximum duration for which the liquid media should be mixed in an attempt to dissolve any solid components following component combination and filling to volume with solvent.
Default Calculation: Automatically set based on the MixType if MixUntilDissolved is set to True. If MixUntilDissolved is False, set to Null.
MixRate
The frequency of rotation the mixing instrument should use to mechanically incorporate the components of the media following component combination and filling to volume with solvent.
Default Calculation: Automatically set based on the MixType and the size of the container in which the solution is prepared.
Pattern Description: Greater than or equal to 0.2 revolutions per minute and less than or equal to 3200 revolutions per minute or Null.
NumberOfMixes
The number of times the media should be mixed by inversion or repeatedly aspirated and dispensed using a pipette following component combination and filling to volume with solvent.
Default Calculation: Automatically set to 10 when MixType is Pipette, 3 when MixType is Invert, or Null otherwise.
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 the media should be mixed in an attempt to dissolve any solid components following component combination and filling to volume with solvent.
Default Calculation: Automatically set based on the MixType if MixUntilDissolved is set to True, and to Null otherwise.
Pattern Description: Greater than or equal to 1 and less than or equal to 50 in increments of 1 or Null.
MixPipettingVolume
The volume of the media that should be aspirated and dispensed with a pipette to mix the solution following component combination and filling to volume with solvent.
Default Calculation: Automatically set to 50% of the total media volume if MixType is Pipette, and Null otherwise.
Pattern Description: Greater than or equal to 1 microliter and less than or equal to 5 milliliters or Null.
StirBar
Indicates which model stir bar to be inserted to mix the stock solution prior to autoclave when HeatSensitiveReagents is not Null.
Pattern Description: An object of type or subtype Model[Part, StirBar] or Object[Part, StirBar] or Null.
pH Titration
AdjustpH
Indicates if the pH (measure of acidity or basicity) of this media should be adjusted after component combination, filling to volume with solvent, and/or mixing.
Default Calculation: Automatically set to True if any other pHing options are specified, or if NominalpH is specified in the template model, or False otherwise.
pH
The pH to which this media should be adjusted following component combination, filling to volume with solvent, and/or mixing.
MinpH
The minimum allowable pH this media should have after pH adjustment, where pH adjustment occurs following component combination, filling to volume with solvent and/or mixing.
Default Calculation: Automatically set to the MinpH field of the media, to 0.1 below the resolved pH value if the media has no MinpH, or to Null if the pH option set to Null.
MaxpH
The maximum allowable pH this media should have after pH adjustment, where pH adjustment occurs following component combination, filling to volume with solvent, and/or mixing.
Default Calculation: Automatically set to the MaxpH field of the media, to 0.1 above the resolved pH value if the media has no MaxpH, or to Null if the pH option set to Null.
pHingAcid
The acid that should be used to lower the pH of the solution following component combination, filling to volume with solvent, and/or mixing.
Default Calculation: Automatically set based on the pHingAcid field in the media, to 6N HCl if the pH option is specified but the media has no pHingAcid, or to Null if the pH option is unspecified.
pHingBase
The base that should be used to raise the pH of the solution following component combination, filling to volume with solvent, and/or mixing.
Default Calculation: Automatically set based on the pHingBase field in the media, to 1.85M NaOH if the pH option is specified but the media has no pHingBase, or to Null if the pH option is unspecified.
Filtration
Filter
Indicates if the media should be passed through a porous medium to remove solids or impurities following component combination, filling to volume with solvent, mixing, and/or pH titration.
Default Calculation: Automatically set to False if a new media formula is provided, to True if an existing media model with filtration parameters is provided, and to False if the provided media model has no filtration parameters.
FilterType
The method that will be used to pass this media through a porous medium to remove solids or impurities following component combination, filling to volume with solvent, mixing, and/or pH titration.
Default Calculation: Automatically set to a method with the lowest dead volume given the volume of media being prepared.
FilterMaterial
The composition of the medium through which the media should be passed following component combination, filling to volume with solvent, mixing, and/or pH titration.
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.
FilterSize
The size of the membrane pores through which the media should be filtered following component combination, filling to volume with solvent, mixing, and/or pH titration.
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.
FilterInstrument
The instrument that should be used to filter the media following component combination, filling to volume with solvent, mixing, and/or pH titration.
Default Calculation: Automatically set to an instrument appropriate to the volume of sample being filtered.
Pattern Description: An object of type or subtype Model[Instrument, Centrifuge], Model[Instrument, SyringePump], Model[Instrument, PeristalticPump], or Model[Instrument, VacuumPump] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, Centrifuge], Model[Instrument, SyringePump], Model[Instrument, PeristalticPump], Model[Instrument, VacuumPump]}] | Automatic) | Null
FilterModel
The model of filter that should be used to filter the media following component combination, filling to volume with solvent, mixing, and/or pH titration.
Default Calculation: Automatically set to a model of filter compatible with the FilterInstrument/FilterSyringe being used for the filtration.
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
FilterSyringe
The syringe that should be used to force the media through a filter following component combination, filling to volume with solvent, mixing, and/or pH titration.
Default Calculation: Automatically set to a syringe appropriate to the volume of media being filtered.
FilterHousing
The instrument that should be used to hold the filter membrane through which the media is filtered following component combination, filling to volume with solvent, mixing, and/or pH titration.
Default Calculation: Automatically set to a housing capable of holding the size of the filter membrane being used.
Pattern Description: An object of type or subtype Model[Instrument, FilterHousing] or Model[Instrument, FilterBlock] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, FilterHousing], Model[Instrument, FilterBlock]}] | Automatic) | Null
PreFiltrationImage
If filtration is being done indicates if the stock solutions being prepared should be imaged before filtration, otherwise this option must be set to False.
Autoclaving
Autoclave
Indicates that this media should be treated at an elevated temperature and pressure (autoclaved) once all components are added.
AutoclaveProgram
Indicates the type of autoclave cycle to run. Liquid cycle is recommended for liquid samples, and Universal cycle is recommended for everything else.
Storage Information
ContainerOut
The container model in which the newly-made media sample will reside following all preparative steps.
Default Calculation: Automatically selected from ECL's stocked containers based on the volume of solution being prepared.
LightSensitive
Indicates if the media contains components that may be degraded or altered by prolonged exposure to light, and thus should be prepared in light-blocking containers when possible.
Default Calculation: Automatically set based on the light sensitivity of the formula components and solvent if generating a new media model from formula input, or to Null if preparing an existing media model.
Expires
Default Calculation: Automatically set to True if generating a new media model from formula input, or to Null if preparing an existing media model.
ShelfLife
The duration of time after preparation that media prepared according to the provided formula are recommended for use before they should be discarded.
Default Calculation: Automatically set to the shortest of any shelf lives of the formula components and solvent, or 5 years if none of the formula components expire. If Expires is set to False, set to Null. If preparing an existing media model, set to Null.
UnsealedShelfLife
The duration of time after first use that media prepared according to the provided formula are recommended for use before they should be discarded.
Default Calculation: Automatically set to the shortest of any unsealed shelf lives of the formula components and solvent, or Null if none of the formula components have recorded unsealed shelf lives. If Expires is set to False, set to Null. If preparing an existing media model, set to Null.
DiscardThreshold
Indicates when samples of this media are automatically discarded. Specifically, gives the percentage of the total initial volume below which samples of the media will automatically be marked as AwaitingDisposal. For instance, if DiscardThreshold is set to 5% and the initial volume of the media was set to 100 mL, that media sample is automatically marked as AwaitingDisposal once its volume is below 5mL. Set DiscardThreshold -> 0 Percent if you never wish to auto-discard this media.
Default Calculation: Automatically set to 5 Percent if generating a new media model from formula input, or to Null if preparing an existing media model.
Pattern Description: Greater than or equal to 0 percent and less than or equal to 100 percent or Null.
TransportTemperature
Indicates the temperature by which media prepared according to the provided formula should be heated or chilled during transport when used in experiments.
Programmatic Pattern: ((RangeP[-86*Celsius, 10*Celsius] | RangeP[27*Celsius, 105*Celsius]) | Automatic) | Null
PlatedMediaShelfLife
Organizational Information
MediaName
The name that should be given to the media model generated from the provided formula. Note that if no model will be created (i.e., if a sample without a model is used in the formula overload), this option will be ignored.
Synonyms
Default Calculation: Automatically set to contain the Name of the the new media model if generating a new media model from formula input with a provided MediaName, or Null otherwise. Note that if no model will be created (i.e., if a sample without a model is used in the formula overload), this option will be ignored.
New Formulation
DefaultStorageCondition
The condition in which media prepared according to the provided formula are stored when not in use by an experiment.
Default Calculation: Automatically set based on the default storage conditions of the formula components and any safety information provided for this new formula. If preparing an existing media model, set to Null.
Pattern Description: AmbientStorage, Refrigerator, Freezer, or DeepFreezer or an object of type or subtype Model[StorageCondition] or Null.
Programmatic Pattern: (((AmbientStorage | Refrigerator | Freezer | DeepFreezer) | ObjectP[Model[StorageCondition]]) | Automatic) | Null
Physical Properties
Density
ExtinctionCoefficients
Health & Safety
Ventilated
Indicates if media prepared according to the provided formula must be handled in a ventilated enclosure.
Default Calculation: Automatically set to False if generating a new media model from formula input, or to Null if preparing an existing media model.
Flammable
Indicates if media prepared according to the provided formula are easily set aflame under standard conditions.
Default Calculation: Automatically set to False if generating a new media model from formula input, or to Null if preparing an existing media model.
Acid
Indicates if media prepared according to the provided formula are strong acids (pH <= 2) and require dedicated secondary containment during storage.
Default Calculation: Automatically set to False if generating a new media model from formula input, or to Null if preparing an existing media model.
Base
Indicates if media prepared according to the provided formula are strong bases (pH >= 12) and require dedicated secondary containment during storage.
Default Calculation: Automatically set to False if generating a new media model from formula input, or to Null if preparing an existing media model.
Fuming
Indicates if media prepared according to the provided formula emit fumes spontaneously when exposed to air.
Default Calculation: Automatically set to False if generating a new media model from formula input, or to Null if preparing an existing media model.
Compatibility
IncompatibleMaterials
Default Calculation: Automatically set to None if generating a new media model from formula input, or to Null if preparing an existing media model.
Pattern Description: A selection of one or more of 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 {None} or Null.
Programmatic Pattern: ((DuplicateFreeListableP[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 | VacuumMeltedStainlessSteel] | {None}) | Automatic) | Null
CentrifugeIncompatible
SafetyOverride
Indicates if the automatic safety checks should be overridden when making sure that the order of component additions does not present a laboratory hazard (e.g. adding acids to water vs water to acids). If this option is set to True, you are certifying that you are sure the order of component addition specified will not cause a safety hazard in the lab.
Plating
PlateMedia
Indicates if the prepared media is subsequently transferred to plates for future use for cell incubation and growth.
Default Calculation: Automatically set to True if MediaPhase is set to Solid or SemiSolid and/or if GellingAgents is specified.
PlateOut
Programmatic Pattern: ObjectP[Model[Container, Plate]] | {GreaterEqualP[1, 1], ObjectP[Model[Container, Plate]]} | (ObjectP[Object[Container, Plate]] | _String)
NumberOfPlates
PrePlatingIncubationTime
The duration of time for which the media will be heated/cooled with optional stirring to the target PlatingTemperature.
Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or None or Automatic or Null.
MaxPrePlatingIncubationTime
The maximum duration of time for which the media will be heated/cooled with optional stirring to the target PlatingTemperature. If the media is not liquid after the PrePlatingIncubationTime, it will be allowed to incubate further and checked in cycles of PrePlatingIncubationTime up to the MaxIncubationTime to see if it has become liquid and can thus be poured. If the media is not liquid after MaxPrePlatingIncubationTime, the plates will not be poured, and this will be indicated in the PouringFailed field in the protocol object.
Default Calculation: Automatically set to three times the duration of the PrePlatingIncubationTime setting.
Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or None or Automatic or Null.
PrePlatingMixRate
The rate at which the stir bar within the liquid media is rotated prior to pumping the media into incubation plates.
Pattern Description: Greater than or equal to 0.2 revolutions per minute and less than or equal to 3200 revolutions per minute or None or Automatic or Null.
PlatingTemperature
The temperature at which the autoclaved media with gelling agents is incubated prior to and during the media plating process.
Pattern Description: Greater than or equal to 25 degrees Celsius and less than or equal to 110 degrees Celsius or Null.
PlatingVolume
Pattern Description: Greater than or equal to 1 milliliter and less than or equal to 20 liters or None or Automatic or Null.
SolidificationTime
The duration of time after transferring the liquid media into incubation plates that they are held at ambient temperature for the media containing gelling agents to solidify before allowing them to be used for experiments.
Pattern Description: Greater than or equal to 0 minutes and less than or equal to 1 day or None or Null.
Protocol
NumberOfReplicates
Post Experiment
SamplesOutStorageCondition
The non-default conditions under which any new samples generated by this experiment should be stored after the protocol is completed. If left unset, the new samples will be stored according to their Models' DefaultStorageCondition.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
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
Warnings and Errors
Messages (12)
ConflictingMediaPhaseGellingAgentsOptions (1)
GellingAgentPresentInMediaFormula (1)
MissingDropOutTarget (1)
ObjectDoesNotExist (8)
Throw a message if we have a media model that does not exist (ID form):
Throw a message if we have a media model that does not exist (name form):
Throw a message if we have a model in our formula that does not exist (ID form):
Throw a message if we have a model in our formula that does not exist (name form):
Throw a message if we have a sample in our formula that does not exist (ID form):
Throw a message if we have a sample in our formula that does not exist (name form):
Throw a message if we have a solvent model that does not exist (ID form):
Throw a message if we have a solvent model that does not exist (name form):
Last modified on Fri 26 Sep 2025 23:46:12