ExperimentPlateMedia

ExperimentPlateMedia[Media]⟹Protocol

generates a Protocol for transferring the Media that consists of sterile liquid or heated solid media containing gelling agents to plates for cell culture incubation and growth.

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. Typically, cell cultures are grown on plated biological media. 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 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 in the HelpFile for ExperimentMedia 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: 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: The mixture is transferred from its original bottle into incubation plates. Step 8: 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

pipetus

Figure 2.1.1: The above diagram lists the compatible serological tip sizes that are available at the ECL.

Serial Filler

Experiment Options

Plating

Instrument

The instrument used to transfer the heated media from the bottle in which it was prepared to the incubation plates.

Default Value: Automatic

Default Calculation: Automatically set to Model[Instrument,PlatePourer,"Serial Filler"] if PlatingMethod is set to Pump and/or if PumpFlowRate is specified, or to Model[Instrument,Pipette,"pipetus"] if PlatingMethod is set to Pour.

Pattern Description: An object of type or subtype Model[Instrument, PlatePourer], Object[Instrument, PlatePourer], Model[Instrument, Pipette], or Object[Instrument, Pipette] or Null.

Programmatic Pattern: ((Alternatives[ObjectP[{Model[Instrument, PlatePourer], Object[Instrument, PlatePourer], Model[Instrument, Pipette], Object[Instrument, Pipette]}]]) | Automatic) | Null

Index Matches to: media

PlatingVolume

The volume of media transferred from its source container into each incubation plate.

Default Value: Automatic

Default Calculation: Automatically set to 50% of the MaxVolume of each PlateOut model.

Pattern Description: Automatic or greater than or equal to 1 milliliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((RangeP[1*Milliliter, $MaxTransferVolume] | Automatic) | Automatic) | Null

Index Matches to: media

PlatingMethod

Indicates how the liquid media will be transferred from its source container to the incubation plates.

Default Value: Pour

Default Calculation: Automatically set to Pump if PlateMedia is set to True and PlatePourer and/or PumpFlowRate are specified, or Null if PlateMedia is set to False.

Pattern Description: None or Automatic or Pump or Pour or Null.

Programmatic Pattern: (MediaPlatingMethodP | (None | Automatic)) | Null

Index Matches to: media

PrePlatingIncubationTime

The duration of time for which the media will be heated/cooled with optional stirring to the target PlatingTemperature.

Default Value: 2 hours

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or None or Automatic or Null.

Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | (None | Automatic)) | Null

Index Matches to: media

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 Value: Automatic

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.

Programmatic Pattern: ((RangeP[0*Minute, $MaxExperimentTime] | (None | Automatic)) | Automatic) | Null

Index Matches to: media

PlatingTemperature

The temperature at which the autoclaved media with gelling agents is incubated prior to and during the media plating process.

Default Value: Automatic

Default Calculation: Automatically set to 1.025 times the melting temperature (in Kelvin) of the GellingAgents if MediaPhase is set to Solid/SemiSolid and/or if GellingAgents is specified.

Pattern Description: Greater than or equal to 25 degrees Celsius and less than or equal to 110 degrees Celsius.

Programmatic Pattern: RangeP[$AmbientTemperature, $MaxTemperatureProfileTemperature] | Automatic

Index Matches to: media

PumpFlowRate

The volume of liquid media pumped per unit time from its source container into incubation plates by the serial filler instrument.

Default Value: Automatic

Default Calculation: Automatically set to TBD if PlatePourer is specified or PlatingMethod is set to Pump, otherwise set to Null.

Pattern Description: Greater than or equal to 1 milliliter per second and less than or equal to 8 milliliters per second or None or Automatic or Null.

Programmatic Pattern: ((RangeP[1*(Milliliter/Second), 8*(Milliliter/Second)] | (None | Automatic)) | Automatic) | Null

Index Matches to: media

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.

Default Value: 1 hour

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 1 day or None or Automatic or Null.

Programmatic Pattern: (RangeP[0*Minute, 1*Day] | (None | Automatic)) | Null

Index Matches to: media

General

PlateOut

The models of plates into which the prepared media will be transferred.

Default Value: Model[Container, Plate, Omni Tray Sterile Media Plate]

Pattern Description: Existing Plate or New Plate or New Plate with Index.

Programmatic Pattern: ObjectP[Model[Container, Plate]] | {GreaterEqualP[1, 1], ObjectP[Model[Container, Plate]]} | (ObjectP[Object[Container, Plate]] | _String)

Index Matches to: media

NumberOfPlates

The number of plates to which the prepared media should be transferred.

Default Value: 1

Pattern Description: Greater than or equal to 0 or Null.

Programmatic Pattern: (Alternatives[GreaterEqualP[0]]) | Null

Index Matches to: media

DestinationWell

The position in the destination container in which the source media sample will be placed.

Default Value: All

Default Calculation: Automatically set to all wells of the PlateOut.

Pattern Description: All or list of one or more any well from A1 to H12 entries.

Programmatic Pattern: {WellPositionP..} | All

Index Matches to: media

Storage Information

PlatedMediaShelfLife

The duration of time after which the prepared plates are considered to be expired.

Default Value: 1 week

Pattern Description: Greater than 0 days.

Programmatic Pattern: Alternatives[GreaterP[0*Day]]

Index Matches to: media

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.

Default Value: Null

Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

Index Matches to: experiment samples

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.

Default Value: Null

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.

Default Value: Null

Pattern Description: A string or Null.

Programmatic Pattern: _String | Null

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.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

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.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Indicates if any samples that are modified in the course of the experiment should be freshly imaged after running the experiment. Please note that public samples are imaged regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Example Calls

Basics

Create a protocol for preparation of plates of solid media:

Warnings and Errors

Messages (3)

InsufficientMediaForPlating (1)

Throw an error if there is not enough volume of the input media sample to prepare the user-specified NumberOfPlates of media plates in the given PlateOut: