Steps¶

Steps represent each step of a protocol for assembling the Design. These steps are necessary when using pre-made protocols like Gibson and GoldenGate.

class synbio.protocol.Step¶: A single Step of a Protocol.

Steps: lab processes to assemble a design.

class synbio.steps.Add(add: Union[Bio.SeqRecord.SeqRecord, Bio.Restriction.Restriction.RestrictionType, synbio.primers.Primers, synbio.reagents.Reagent, synbio.species.Species], volume: float, name: str = '', instructions: List[str] = None)¶

Add contents to the existing containers.

add¶: the src container or content to add

volume¶: the volume of the new content to add

name¶: the name of this step in the protocol

instructions¶: extra instructions to add to this step

synbio.steps.HeatShock = [<synbio.steps.Move object>, <synbio.steps.Add object>, <synbio.steps.ThermoCycle object>, <synbio.steps.Add object>, <synbio.steps.Incubate object>]¶

A composite HeatShock step for getting DNA into E coli.

>>> [
...    Move(volume=3.0),
...    Add(add=Species("E coli"), volume=10.0),
...    ThermoCycle(name="Heat shock", temps=[Temperature(temp=42, time=30)]),
...    Add(add=Reagent("SOC"), volume=150.0),
...    Incubate(temp=Temperature(temp=37, time=3600)),
... ]

class synbio.steps.Incubate(temp: synbio.instructions.Temperature, name: str = 'Incubate', mutate: Optional[Callable[[synbio.containers.Container], synbio.containers.Container]] = None)¶

Incubate contents for some time at a set temperature.

Incubate the contents of containers and in a fridge or some other incubator.

name¶: the name of this step in the protocol

temp¶: the target the container should be in (default: {None})

mutate¶: a function to mutate the contents of a container after thermo cycling. Used to anneal digested/ligated fragments or amplify DNA with primers

class synbio.steps.Move(volume: float, dest: synbio.containers.Container = None, name: str = '')¶

Move a fixed volume from each container to another container of same or new type

volume¶: the amount in millileters to move to the new container

type¶: the type of new container to move the contents to

class synbio.steps.Pipette(target: Sequence[synbio.containers.Container], name: str = '', instructions: List[str] = None)¶

Pipette the input containers to match a ‘target’ list of containers

Create transfers to map the input containers to a new list of output containers (target)

target¶: target container list/ordering (default: {None})

name¶: the name of this step in the protocol

instructions¶: extra instructions to add to this step

class synbio.steps.Setup(target: Sequence[synbio.containers.Container], dest: synbio.containers.Container = None, name: str = '', instructions: List[str] = None)¶

Create a list of transfers to make a list of setup containers

All transfers for a Setup step come from the magical and bottomless ‘Fridge’

target¶: target container list/ordering (default: {None})

dest¶: the type of target container (default: {first target container})

name¶: the name of this step in the protocol

instructions¶: extra instructions to add to this step,

class synbio.steps.ThermoCycle(temps: List[synbio.instructions.Temperature], name: str = '', cycles: int = 1, mutate: Optional[Callable[[synbio.containers.Container], synbio.containers.Container]] = None, extension: synbio.instructions.Temperature = None, instructions: List[str] = None)¶

Thermo cycle for PCR, digestion/ligation, etc.

Make a list of temperature instructions with the temperature to set it at, the length of time and the number of cycles.

Example

An example of a ThermoCycle for PCR: >>> ThermoCycle(cycles=30, temps=[ … Temperature(temp=97, time=5 * 60), # denature … Temperature(temp=55, time=30), # annealing … Temperature(temp=72, time=60), # extension … ])

temps¶: list of temperatures in a gradient

name¶: the name of this step in the protocol

cycles¶: the number of thermo cycles (default: {1})

mutate¶: a function to mutate the contents of a container after thermo cycling. Used to anneal digested/ligated fragments or amplify DNA with primers

instructions¶: list of additional instructions to add

extension¶: last extension after other thermocycle steps. Example is a final 5 minute extension at the end of PCR that’s common