Separation and Fractionation

Culsma separates material with sep(...), selects source-local separation portions inside transfer statements, and creates ordered fractions with frac(...).

Both forms take a sample and a program.

sep(...)

sep(...) splits one container into a fixed two-slot group.

let g = sep(sample = lysate, program = centrifuge_program(drive = 12000g));

The result is a sep_container_group. Access its slots with group[0] and group[1].

output << [g[0]:40uL];

When a separated portion is used only as the source of one transfer, write the selection directly on the source container:

waste << [sample.partition(magnetic_program(duration = 5min))[1]:120uL];

source.partition(program)[i] uses the same two-slot separation semantics as sep(...), but it is not a group-producing operation. It is valid only inside the right-hand source list of <<. Use sep(...) when the separated slots need names, later reuse, or multiple downstream operations.

Separation Programs

sep(...) and source.partition(program)[i] accept mechanism-specific binary separation programs.

Program	Required fields	Optional fields	Meaning
centrifuge_program(...)	drive	keep_source	Centrifuge separation.
magnetic_program(...)	none	duration, device	Magnetic separation.
disrupt_program(...)	none	duration	Disruption or lysis-oriented separation.
field_program(...)	field	duration	Field-driven separation.
filtration_program(...)	membrane, drive	none	Filtration separation.
phase_partition_program(...)	solvent	none	Phase partition.
precipitation_program(...)	reagent	duration	Precipitation.

centrifuge_program(...) does not take duration. To express "centrifuge for 5 min at 4C", put the sep(...) inside an environment block:

with env(thermal = 4C, duration = 5min) {
    let g = sep(sample = lysate, program = centrifuge_program(drive = 12000g));
}

Slot Meaning

The two slots have stable meanings determined by the program.

Program	group[0]	group[1]
centrifuge_program	supernatant	pellet
magnetic_program	bound	flowthrough
disrupt_program	lysate	debris_or_residue
field_program	target_band_fraction	non_target_fraction
filtration_program	filtrate	retentate
phase_partition_program	target_phase	other_phase
precipitation_program	precipitate	supernatant

For source-local selection, the index has the same meaning: sample.partition(program)[0] selects the slot described in the group[0] column, and sample.partition(program)[1] selects the slot described in the group[1] column.

Material Partition Estimates

Runtime material compute estimates how much tracked content moves into each slot. This estimate is bookkeeping for protocol execution, not a scientific prediction.

Supported content classes use one of three ratio shapes:

Ratio	Meaning
0.99 / 0.01	Near-complete separation into one slot.
0.95 / 0.05	Strong enrichment with a small carryover.
0.50 / 0.50	Conservative fallback when Culsma cannot infer a better partition.

Unsupported, unknown, compatibility-normalized, or composite content can still run. In those cases the runtime uses the conservative 0.50 / 0.50 fallback and emits MAT_CONTENT_PARTITION_FALLBACK.

keep_source

keep_source is only for centrifuge_program(...).

let g = sep(
    sample = lysate,
    program = centrifuge_program(drive = 12000g, keep_source = pellet)
);

keep_source = supernatant reuses the input container for group[0]. keep_source = pellet reuses the input container for group[1].

If keep_source is omitted, both slots are new containers.

frac(...)

frac(...) creates an ordered fraction group.

let fg = frac(
    sample = tube,
    program = density_gradient_program(axis = "density", order = "top_to_bottom", bins = 8)
);

The result is a fraction_group. Access slots with fg[0], fg[1], and so on.

Fractionation Programs

Program	Required fields	Meaning
density_gradient_program(...)	axis, order, bins	Density or layer-based fractionation.
chromatography_program(...)	axis, order, bins	Retention-order fractionation.

Index Rules

Group indexes are zero-based.

• sep_container_group supports only group[0] and group[1].
• source.partition(program)[i] supports only static indexes 0 and 1.
• fraction_group[i] must be within 0 <= i < bins when bins is known.
• Slices, multidimensional indexes, and dynamic index semantics are not part of this authoring surface.