Input Mapping File¶

The input mapping .csv lists 86 essential parameters in columns and (indepdendent) selection experiments in rows. Here is an example of mapping file with two independent experiments.

selected_function

protocol

seed

exp_id

overwrite_plate

passage_overwrite_plate

output_dir

save_function

save_composition

save_plate

function_lograte

composition_lograte

scale

n_inoc

rich_medium

monoculture

dilution

n_wells

n_propagation

n_transfer

n_transfer_selection

metacommunity_sampling

power_alpha

lognormal_mean

lognormal_sd

phi_distribution

phi_mean

phi_sd

phi_lower

phi_upper

ruggedness

function_ratio

binary_threshold

g0

cost_distribution

cost_mean

cost_sd

cost_lower

cost_upper

invader_index

invader_sampling

invader_strength

target_resource

directed_selection

knock_out

knock_in

knock_in_threshold

bottleneck

bottleneck_size

migration

n_migration

s_migration

coalescence

frac_coalescence

resource_shift

r_type

r_percent

sampling

sn

sf

Sgen

rn

rf

R0_food

food

supply

muc

sigc

c0

c1

q

sparsity

fs

fw

g

w

l

m

n

response

sigma_max

regulation

nreg

tau

r

S

f1_additive

simple_screening

1

f1_additive-simple_screening-1

NA

False

/home/cc2553/project/community-selection/data/independent_f1_additive/

True

False

1

20

1000000

1e+06

TRUE

False

0.001

96

1

40

20

Power

0.01

8

Norm

0

1

0

1

NA

1

Norm

0

1

2

Gamma

10

NA

False

NA

False

NA

False

1000000

NA

False

NA

False

NA

Binary_Gamma

2100

1

0

90

1

1000

NA

0

NA

type III

1

NA

f1_additive

simple_screening

1

f1_additive-monoculture-1

NA

False

/home/cc2553/project/community-selection/data/independent_f1_additive/

True

False

1

20

1000000

1e+06

TRUE

True

0.001

96

1

40

20

Power

0.01

8

Norm

0

1

0

1

NA

1

Norm

0

1

2

Gamma

10

NA

False

NA

False

NA

False

1000000

NA

False

NA

False

NA

Binary_Gamma

2100

1

0

90

1

1000

NA

0

NA

type III

1

NA

The mapping file has five categories of parameters:

File operation
Protocol-specific parameters
Species contribution to function
Directed evolution
Community-simulator parameters

File operation ¶

selected_function¶

Type:	string
Default:	`f1_additive`

Function under selection. Available options are f1_additive and f2_interaction, f2a_interaction, f3_additive_binary, f4_interaction_binary, f5_invader_growth, and resource_distance_community_function.

protocol¶

Type:	string
Default:	`simple_screening`

Protocol to implement. Only the protocols listed in E_protocols.py can be used.

seed¶

Type:	integer
Default:	`1`

Random seed to initiate pseudorandom number generator.

exp_id¶

Type:	string
Default:	`f1_additive-simple_screening-1`

Experiment-specific ID, which will also determine the naming convention of output files. For example, the community function is saved in f1_additive-simple_screening-1_function.txt if save_function=True, whereas community compostition is saved in f1_additive-simple_screening-1_compostition.txt if save_composition=True.

overwrite_plate¶

Type:	string
Default:	`NA`

To replace the initial plate composition with an arbitrary plate, specify a text file of the community composition that containes four columns: Type, ID, Well, and Abundance. If an output text file (e.g., f1_additive-simple_screening-1_compostition.txt) is specified and it contains composition for more than two transfers, by default only the metacommunity compostition of the latter tranfer is read.

passage_overwrite_plate¶

Type:	boolean
Default:	`False`

If overwrite_plate != NA, set TRUE if the community from overwrite_plate is at equilibrium and need an addititonal transfer.

output_dir¶

Type:	string
Default:	`data/`

Directory where the output files will be stored.

save_function¶

Type:	boolean
Default:	`True`

Set True to save function data.

save_composition¶

Type:	boolean
Default:	`True`

Set True to save composition data.

save_plate¶

Type:	boolean
Default:	`False`

Set True to save initial Metacommunity in a pickle file.

function_lograte¶

Type:	integer
Default:	`1`

How often you save the function in transfers. Default is saving functional data from every transfer.

composition_lograte¶

Type:	integer
Default:	`20`

How often do you save the composition in transfers.

Protocol-specific parameters ¶

scale¶

Type:	integer
Default:	`1000000`

Number of cells equivalent to \(N_i = 1\).

n_inoc¶

Type:	integer
Default:	`1000000`

Number of cells in the initial inoculum.

rich_medium¶

Type:	boolean
Default:	`True`

Set True to generate a rich medium sampled from an uniform distribution. Set False to generate a minimal medium with only the first resource is supplied.

monoculture¶

Type:	boolean
Default:	`False`

Set True to run simple screening with all monocultures from the regional species pool. The number of wells is equal to the number of species in the regional pool.

dilution¶

Type:	float
Default:	`0.001`

Dilution factor in the batch culture.

n_wells¶

Type:	integer
Default:	`96`

Number of wells (communities) in a plate (metacommunity).

n_propagation¶

Type:	float
Default:	`1`

Incubation time of a transfer.

n_transfer¶

Type:	integer
Default:	`40`

Number of total transfers (generations) to be run in the protocol.

n_transfer_selection¶

Type:	interger
Default:	`20`

Number of transfers (generations) that consecutively executes selection matrices from the start of an experiment. The number of stabilizaiton transfer equals to the difference between n_transfer_total and n_transfer_selection.

metacommunity_sampling¶

Type:	string
Default:	`Power`

Sampling method for initial metacommunity. Available options are Power, Lognormal, Default.

power_alpha¶

Type:	float
Default:	`0.01`

lognormal_mean¶

Type:	float
Default:	`8`

lognormal_sd¶

Type:	float
Default:	`8`

Species contribution to function ¶

phi_distribution¶

Type:	string
Default:	`Norm`

{“Norm”, “Uniform”}

phi_mean¶

Type:	float
Default:	`0`

Mean of normal distribution when phi_distribution is set to Norm

phi_sd¶

Type:	float
Default:	`1`

Standard deviation of normal distribution when phi_distribution is set to Norm

phi_lower¶

Type:	float
Default:	`0`

Lower boundary of normal distribution when phi_distribution is set to Unif

phi_upper¶

Type:	float
Default:	`1`

Upper boundary of normal distribution when phi_distribution is set to Unif

ruggedness¶

Type:	fload
Default:	`0.8`

(1-ruggedness) of the additive and non-additive per-capita functino will contribute to community function, whereas the rest will be set to 0.

binary_threshold¶

Type:	float
Default:	`1`

Threshold for binary functions.

g0¶

Type:	float
Default:	`1`

The baseline conversion factor of biomass per energy.

cost_distribution¶

Type:	string
Default:	`Norm`

{“Gamma”, “Unif”}

cost_mean¶

Type:	float
Default:	`0`

Mean fraction of cost feeded normal distribution. Suggested maximum to 0.05.

cost_sd¶

Type:	float
Default:	`0`

Standard deviation of fraction of cost feeded into a gamma distribution. cost_sd = 0 if cost_mean = 0, cost_sd = 0.01 if cost_mean > 0.

cost_lower¶

Type:	float
Default:	`0`

Lower bound for cost if cost_distribution is set to Uniform

cost_upper¶

Type:	float
Default:	`1`

Upper bound for cost if cost_distribution is set to Uniform

invader_index¶

Type:	integer
Default:	`2`

Index of an invader. Only one index is choosen. Currently a invasive community is not allowed.

invader_sampling¶

Type:	string
Default:	`Gamma`

Sampling algorithm to generate the invader uptake rate vector. Options are Gaussian, Binary, Gamma, Binary_Gamma.

invader_strength¶

Type:	positive float
Default:	`10`

Mean utiliration vector for the invader versus the average of the species in the pool

target_resource¶

Type:	integer
Default:	`NA`

Target resource production when selected_function is set to f6_target_resourece

Directed evolution ¶

directed_selection¶

Type:	boolean
Default:	`False`

Set True to run directed selection, one of flags below in directed evolution has to be also set True.

knock_out¶

Type:	boolean
Default:	`False`

Set True to perform knock out pertubation.

knock_in¶

Type:	boolean
Default:	`F`

Set True performs knock in pertubation.

knock_in_threshold¶

Type:	float
Default:	`0.95`

If knock_in = True, use the default knock_in_threshold=0.95, which means that top 5% species in the pool is prepared to be knocked in a community, whereas the rest 95% of are not used.

bottleneck¶

Type:	boolean
Default:	`False`

Set True to perform bottleneck pertubations.

bottleneck_size¶

Type:	float
Default:	`0.00001`

If bottleneck=T, perform an bottleneck shock to the specified communities by a dilution factor default to bottleneck_size=0.00001. This bottleneck dilutoon is in addition to the regular dilution factor in the batch culture dilution=0.001.

migration¶

Type:	boolean
Default:	`False`

Set True to perform migration pertubations.

n_migration¶

Type:	integer
Default:	`1000000`

Number of cells in the migrant community.

s_migration¶

Type:	integer
Default:	`NA`

Number of species in the migrant community. If NA (as default), the migrant community is sampled from a regional pool where the species abundance follows power-law distribution. If set into an integer, n_migration cells will be equally allocated to s_migrations species from the pool to build the migrant community.

coalescence¶

Type:	boolean
Default:	`False`

Set True to perform coalescence pertubation.

f_coalescence¶

Type:	float
Default:	`0.5`

Between 0 and 1. Fraction of migrant community during coalescence. The fraction of a perturbed community is 1-f_coalescence.

resource_shift¶

Type:	boolean
Default:	`False`

Set True performs resource pertubations.

r_type¶

Type:	string
Default:	`add`

Type of resource pertubation. Available options are rescale_add, rescale_remove, add, remove, old. A fraction r_percent of resource A is removed, and that amount of resource is added to another resource B.

r_percent¶

Type:	float
Default:	`1`

Fraction of specified resource that is removed. r_percent=1 means all resource A is removed.

Community-simulator parameters ¶

The parameters in this section are inherited and some with differnt values from community-simulator.

sampling¶

Type:	string
Default:	`Binary_Gamma`

Specify choice of sampling algorithm to generate the consumer uptake rate vector. Options are Gaussian, Binary, Gamma, Binary_Gamma.

sn¶

Type:	integer
Default:	`2100`

Number of microbial species in the global pool.

sf¶

Type:	integer
Default:	`1`

Number of specialist family.

s_gen¶

Type:	integer
Default:	`0`

Number/Richness of generalist taxa.

rn¶

Type:	integer
Default:	`90`

Number of resource types.

rf¶

Type:	integer
Default:	`1`

Number of resource classes.

R0_food¶

Type:	float
Default:	`1000`

Total resource abundance.

food¶

Type:	float
Default:	`1000`

Index of food source being supplied in the minimal medium. Only works when rich_medium=False.

supply¶

Type:	string
Default:	`off`

Choice of intrinsic resoruce dynamics. Set off for batch culture where resource is not renewing within a transfer.

muc¶

Type:	float
Default:	`10`

Mean sum over a row of the preference matrix ciα.

sigc¶

Type:	float
Default:	`3`

Standard deviation of sum over a row of the preference matrix ciα.

c0¶

Type:	float
Default:	`0`

Low consumption level for binary ciα.

c1¶

Type:	integer
Default:	`1`:

High consumption level for binary ciα.

q¶

Type:	float
Default:	`0`

Fraction of consumption capacity allocated to preferred resource class.

sparsity¶

Type:	float
Default:	`0.2`

Sparsity of metabolic matrix.

fs¶

Type:	float
Default:	`0.45`

Fraction of secreted byproducts allocated to the same resource class.

fw¶

Type:	float
Default:	`0.45`

Fraction of secreted byproducts allocated to waste resource class.

g¶

Type:	float
Default:	`1`

Conversion factor from energy uptake to growth rate (1/energy).

w¶

Type:	float
Default:	`1`

Energy content of resource α (energy/mass).

l¶

Type:	float
Default:	`0`

Leakage fraction.

m¶

Type:	float
Default:	`0`

Minimal energy uptake for maintenance of species i (energy/time). Mortality.

n¶

Type:	integer
Default:	`2`

Hill coefficient for functional response (unitless).

response¶

Type:	string
Default:	`type III`

Functional response of uptaking rates.

sigma_max¶

Type:	float
Default:	`1`

Maximum input flux (mass/time) for type III functional response.

regulation¶

Type:	string
Default:	`independent`

Metabolic regulation.

nreg¶

Type:	integer
Default:	`10`

Hill coefficient that tunes steepness of metabolic regulation.

tau¶

Type:	float
Default:	`1`

External resource supply rate when supply="external" for chemostat setting.

r¶

Type:	string
Default:	`independent`

Renewal rate for self renewing resources when supply="self-renewing" for chemostat setting.

Input Mapping File¶

File operation¶

Protocol-specific parameters¶

Species contribution to function¶

Directed evolution¶

Community-simulator parameters¶

File operation ¶

Protocol-specific parameters ¶

Species contribution to function ¶

Directed evolution ¶

Community-simulator parameters ¶