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Home | Getting Started | Generic Tools | EchoProto | EchoProto Templates | OTProto | OTProto Templates

BiomationScripter - EchoProto Templates

Overview

BiomationScripter Templates can be used to help quickly and easily generate automation protocols for common experiments or procedures. Protocols generated using the same Template will all follow the same basic instructions, but will differ depending on user inputs. For example, the PCR Template accepts user inputs for aspects such as the type of polyemrase and buffer, the final volume of the reactions, and the DNA templates and primers to use in each reaction.

If you can't find a Template for a specific protocol, you can try raising an issue on the GitHub to see if anyone can help, or create your own Template following the walkthrough found here.

Below you can find documentation for Echo Templates included with BiomationScripter.

Echo Templates

Any Template can be imported using the statement below:

from BiomationScripter.EchoProto.Templates import <TEMPLATE_NAME>

Replace <TEMPLATE_NAME> in the code above with one of the template names below:

Loop_Assembly | PCR

Template: Loop_Assembly

Overview

This Template is used to generate an Echo protocol for preparing Loop assembly reactions. The protocol is based on the methods described by Pollak et al. 2018.

Generic Protocol Steps

The basic protocol is described below. Volumes stated below are for 5 uL final reaction volumes. These amounts will be scaled based on the user-defined final volume. DNA parts are assumed to be at 10 fmol/uL.

  1. Add 0.5 uL of buffer
    • The buffer type is determined by the user
    • A list of buffers can be supplied - in this case each buffer is added in equal amounts such that the total buffer volume is 0.5 uL
  2. Add 0.125 uL of enzyme
    • The enzyme type is determined by the user, although the protocol is intended for use with SapI (even level assemblies) or BsaI (odd level assemblies)
  3. Add 0.125 uL of T4 ligase
    • The ligase type can be modified by the user, but T4 Ligase is the intended reagent
  4. Add DNA backbone as supplied by the user
    • The volume is 0.25 uL adjusted by the backbone to part ratio supplied by the user
  5. Add the DNA part(s) supplied by the user
    • The volume is 0.25 uL per part, adjusted by the backbone to part ratio supplied by the user
  6. Add nuclease free water so that the final volume is 5 uL

Following set up by the Echo, the destination plate(s) should be vortexed and briefly span down to ensure all liquid is at the bottom of the wells.

Usage

!!! example

See an example protocol using this template [here](protocol_examples/EchoProto/Templates/EchoProto-Templates-Loop_Assembly.ipynb).

The Template object is created using the following code:

from BiomationScripter.EchoProto.Templates import Loop_Assembly

Protocol_Template = Loop_Assembly.Template(
  Enzyme: str,
  Buffer: str | List[str],
  Volume: float, # uL
  Assemblies: List[BiomationScripter.Assembly],
  Backbone_to_Part: List[str] = ["1:1"],
  Repeats: int = 1,
  DNA_Concentration: float = 10, # uM
  Name: str,
  Source_Plates: List[BiomationScripter.Labware_Layout],
  Destination_Plate_Layout: BiomationScripter.Labware_Layout,
  Picklist_Save_Directory: str = ".",
  Metadata: dict[str, str],
  Merge: bool = False
)

Full Documentation

Attributes:

Methods:

  • __init__(self, Enzyme: str, Buffer: Union[str, List[str]], Volume: float, Assemblies: List[_BMS.Assembly], Backbone_to_Part: List[str] = ["1:1"], Repeats: int = 1, DNA_Concentration: float = 10, # fmol **kwargs) returns BMS.EchoProto.Templates.Loop_Assembly.Template object * Creates a BMS.EchoProto.Templates.Loop_Assembly.Template object * Initiates the default reaction volumes (see above)
  • run(self) returns None * Creates the Echo picklists for the protocol

Template: PCR

Overview

This Template is used to generate an Echo protocol for preparing PCR reactions. It is based upon the protocol described here for no mastermix, and here for with mastermix.

Generic Protocol Steps

The basic protocol is described below. Volumes stated below are for 5 uL final reaction volumes. These amounts will be scaled based on the user-defined final volume. Primer stocks are assumed to be at 10 μM. dNTPs are assumed to be pre-mixed in equimolar amounts to a final stock of 10mM.

If Master_Mix is None:

  1. Add template DNA according as specified by the user (DNA_Amounts)
    • If a list of volumes (in uL) is specified, multiple reactions will be prepared, one for each volume
    • If no volumes are given, then 1 uL of DNA is added
  2. Add 0.25 uL of forward primer, and 0.25 uL of reverse primer
    • Primers are added to the DNA templates as specified by Reactions
  3. Add 0.1 uL of dNTP solution
  4. Add the buffer specified by Polymerase_Buffer
    • The volume of buffer to add is determined by Polymerase_Buffer_Stock_Conc
  5. Add 0.05 uL of the polymerase specified by Polymerase
  6. Add nuclease free water so that the final volume is 5 uL

Following set up by the Echo, the destination plate(s) should be vortexed and briefly span down to ensure all liquid is at the bottom of the wells.

If Master_Mix is not None:

  1. Add template DNA according as specified by the user (DNA_Amounts)
    • If a list of volumes (in uL) is specified, multiple reactions will be prepared, one for each volume
    • If no volumes are given, then 1 uL of DNA is added
  2. Add 0.25 uL of forward primer, and 0.25 uL of reverse primer
    • Primers are added to the DNA templates as specified by Reactions
  3. Add the mastermix specified by Master_Mix
    • The volume of mastermix to add is determined by Master_Mix_Stock_Conc
  4. Add nuclease free water so that the final volume is 5 uL

Following set up by the Echo, the destination plate(s) should be vortexed and briefly span down to ensure all liquid is at the bottom of the wells.

Usage

!!! example

See an example protocol using this template [here](protocol_examples/EchoProto/Templates/EchoProto-Templates-PCR.ipynb).

The Template object is created using the following code:

from BiomationScripter.EchoProto.Templates import PCR

Protocol_Template = PCR.Template(
  Volume: float,
  Reactions: Tuple[str, str, str],
  Polymerase: str = None,
  Polymerase_Buffer: str = None,
  Polymerase_Buffer_Stock_Conc: float = None,
  Master_Mix: str = None,
  Master_Mix_Stock_Conc = None,
  Repeats: int = 1,
  DNA_Amounts = None,
  Name: str,
  Source_Plates: List[BiomationScripter.Labware_Layout],
  Destination_Plate_Layout: BiomationScripter.Labware_Layout,
  Picklist_Save_Directory: str = ".",
  Metadata: dict[str, str],
  Merge: bool = False
)

Full Documentation

Attributes:

  • name | str: A name for the protocol (from BMS.EchoProto.EchoProto_Template superclass)
  • metadata | dict[str]: A dictionary describing the metadata for the protocol (from BMS.EchoProto.EchoProto_Template superclass)
  • save_dir | str: The directory where the picklist files should be saved (from BMS.EchoProto.EchoProto_Template superclass)
  • _protocol | BiomationScripter.EchoProto.Protocol: A BiomationScripter.EchoProto.Protocol object (from BMS.EchoProto.EchoProto_Template superclass)
  • merge | bool: Defines whether source plates of the same type should be merged into one picklist (True) or if each source plate should have a different picklist (False) (from BMS.EchoProto.EchoProto_Template superclass)
  • source_plate_layouts | list[BiomationScripter.Labware_Layout]: A list of BiomationScripter.Labware_Layout objects describing the source plates available for use (from BMS.EchoProto.EchoProto_Template superclass)
  • destination_plate_layouts | list[BiomationScripter.Labware_Layout]: A list of BiomationScripter.Labware_Layout objects which define the destination plates, including their intended content once the transfer has completed (from BMS.EchoProto.EchoProto_Template superclass)
  • volume | float: Final volume of each reaction in microlitres
  • repeats | int: The number of repeats for each unique assembly reaction
  • polymerase | str: The name of the polymerase to be used
  • buffer | str OR List[str] OR None: The name of the buffer (or list of buffers) to be used
  • buffer_stock_conc | float OR None: The stock concentration of the specified buffer - ignored if buffer is None - must not be None if buffer is defined
  • master_mix | str OR None: The name of the mastermix to be used - no mastermix is used if None
  • master_mix_stock_conc | float OR None: The stock concentration of the specified mastermix - ignored if master_mix is None - must not be None if master_mix is defined
  • dna_amounts | float OR List[float] OR None: The amount of DNA template to be added (in uL) to each reaction - if a list is given a new reaction will be created with each different volume - if None then 1/5 of the total volume is used
  • dNTPs | str: The name of the dNTPs to be used
  • water | str: The name of the water to be used

Methods:

  • __init__(self, Volume: float, Reactions: Tuple[str, str, str], Polymerase: str = None, Polymerase_Buffer: str = None, Polymerase_Buffer_Stock_Conc: float = None, Master_Mix: str = None, Master_Mix_Stock_Conc = None, Repeats: int = 1, DNA_Amounts = None, **kwargs) returns BMS.EchoProto.Templates.PCR.Template object * Creates a BMS.EchoProto.Templates.PCR.Template object * Initiates the default reaction volumes (see above)
  • run(self) returns None * Creates the Echo picklists for the protocol

Superclass: EchoProto_Template

Usage:

This class should ONLY be used as an extension of an Echo Template class, e.g.:

class My_New_Template(BMS.EchoProto.EchoProto_Template):
  def __init__(self, My_Arg1, My_Arg2, **kwargs):

    super().__init__(**kwargs)

    self.my_arg1 = My_Arg1
    self.my_arg2 = My_Arg2

  def run(self):
    pass

See the walkthrough here.

Attributes:

  • name | str: A name for the protocol
  • metadata | dict[str]: A dictionary describing the metadata for the protocol
  • save_dir | str: The directory where the picklist files should be saved
  • _protocol | BiomationScripter.EchoProto.Protocol: A BiomationScripter.EchoProto.Protocol object
  • merge | bool: Defines whether source plates of the same type should be merged into one picklist (True) or if each source plate should have a different picklist (False)
  • source_plate_layouts | list[BiomationScripter.Labware_Layout]: A list of BiomationScripter.Labware_Layout objects describing the source plates available for use
  • destination_plate_layouts | list[BiomationScripter.Labware_Layout]: A list of BiomationScripter.Labware_Layout objects which define the destination plates, including their intended content once the transfer has completed

Methods:

  • __init__(self, Name: str, Source_Plates: List[BiomationScripter.Labware_Layout], Destination_Plate_Layout: BiomationScripter.Labware_Layout, Picklist_Save_Directory: str = ".", Metadata: dict[str, str], Merge: bool = False) returns BMS.EchoProto.EchoProto_Template superclass * This method is inherently called when an Echo Template class extends the BMS.EchoProto.EchoProto_Template superclass * The BiomationScripter.Labware_Layout objects used for Source_Plates must contain content representing the source material available * The BiomationScripter.Labware_Layout object used for Destination_Plate_Layout should have no content specified; this is generated by the Template class * The Destination_Plate_Layout will be assumed to have all wells available if its available_wells attribute has not been specified
  • add_source_layout(self, Layout: BiomationScripter.Labware_Layout) returns None * This method is used to add a source plate layout * This is called within the __init__ function when a Template object is generated, and so users should not need to call it manually * If source plate layouts are added after object creation, they should only be added using this method; if they are added by simply appending to self.source_plate_layouts unexpected behaviour will occur
  • add_destination_layout(self, Layout: BiomationScripter.Labware_Layout) returns None * This method is used to add a destination plate layout * The first destination layout is added when __init__ is called * Users may need to call this during the run method of their template if additional destination plates are required * If destination plate layouts are added after object creation, they should only be added using this method; if they are added by simply appending to self.destination_plate_layouts unexpected behaviour will occur
  • create_picklists(self) returns None * This method should be called at the end of a Template run method to generate the Echo picklists