configuration_file_template.csv

########################################################################
# Setup file of C-STABILITY.
#
# File description:
# 	template
# 
# File editing rules:
# 	- empty lines and lines starting with "#" are skipped by the program. 
# 	- simple values are defined with "=" and a blank separator.
# 	- complex lines starts with a specific flag and all fields are 
#	separated by a tabulation noted \t in documentation.
########################################################################

########################################################################
# Simulation timeline:
#
# 	This section should contain:
#		timeUnit = (string)
#		initialDate = (integer)
#		finalDate = (integer) 
#
#	Example: 
#		timeUnit = day
#		initialDate = 0
#		finalDate = 300
########################################################################

timeUnit = day
initialDate = 0
finalDate = 200

########################################################################
# Numerical scheme and methods:
#
#	This section should contain:
#		userTimeStep = (double) in ]0,1[
#		userPolymerizationStep = (double)
#		integrationMethod = (string) available options: 
#			- INTEGRATION_TRAPEZE, 
#			- INTEGRATION_RECTANGLE_LEFT
#			- INTEGRATION_RECTANGLE_RIGHT 
#
#	Example:
#		userTimeStep = 0.1
#		userPolymerizationStep = 0.01
#		integrationMethod = INTEGRATION_TRAPEZE
########################################################################

userTimeStep = 0.01
userPolymerizationStep = 0.01
integrationMethod = INTEGRATION_TRAPEZE

########################################################################
# Biochemical classes:
#
#	This section should contain at least two biochemical classes.
#
#	Line format: 
#		BIOCHEMICAL_CLASS \t bcName \t polymerization 
#		- bcName (String) is the name of the biochemical class
#		- polymerization (Interval) is the interval used to describe 
# 		  the polymerization of the biochemical class
#
#	Example: 
#		BIOCHEMICAL_CLASS \t cellulose \t [0,2]
########################################################################

BIOCHEMICAL_CLASS	lipid	[0,2]
BIOCHEMICAL_CLASS	protein	[0,2]
BIOCHEMICAL_CLASS	cellulose	[0,2]
BIOCHEMICAL_CLASS	lignin	[0,2]

########################################################################
# Substrate pools:
#
#	This section should contain at least an accessible pool per 
#	biochemical class.
#
#	Line format:
#		POOL_ACCESSIBILITY \t bcName \t accessibility
#		- bcName (String) has to be defined previously
#		- accessibility (String) is a list of accessibility status 
# 		  available for the biochemical class. Status are: 
#			* ACCESSIBLE
#			* INACCESSIBLE_AGGREGATION
#		 	* INACCESSIBLE_MINERAL_ASSOCIATION
#		 	* INACCESSIBLE_MINERAL_ASSOCIATION 
#
#	Example: 
#		POOL_ACCESSIBILITY \t cellulose
#							...\t [ACCESSIBLE,INACCESSIBLE_AGGREGATION]
########################################################################

POOL_ACCESSIBILITY	lipid	[ACCESSIBLE,INACCESSIBLE_MINERAL_ASSOCIATION]
POOL_ACCESSIBILITY	protein	[ACCESSIBLE,INACCESSIBLE_MINERAL_ASSOCIATION]
POOL_ACCESSIBILITY	cellulose	[ACCESSIBLE,INACCESSIBLE_EMBEDMENT]
POOL_ACCESSIBILITY	lignin	[ACCESSIBLE,INACCESSIBLE_AGGREGATION]

########################################################################
# Environment variable (not available):
#
#	This section contains environmental variables required for the 
#	simulation.
#
#	Line format:
#		ENVIRONMENT_VARIABLE \t ....
#		- ... 
#
#	Example: 
########################################################################

# ENVIRONMENT_VARIABLE

########################################################################
# Enzyme traits:
#
#	This section permits to define the simulation enzymes traits.
#
#	Line format:
#		ENZYME_TRAITS \t enzName \t bcName
#			... \t depolymerizationRateFunction \t kernelFunction
#		- enzName (String) is the name of the enzyme
#		- bcName (String) is the biochemical class associated to the
#		  enzyme
#		- depolymerizationDomain (Interval) is the polymerization 
#		  interval of the biochemical class targeted by the enzyme
#		- depolymerizationRateFunction (String) is the function 
# 		  defining the depolymerization rate of the enzyme
#		- kernelFunction (String) is the function defining the 
#		  transformation kernel of the enzyme
# 		- kernelIntegrationMethod (String): STANDARD_KERNEL_INTEGRATION
#										 or INTEGRAL_KERNEL_INTEGRATION 
#
#	Example:
#		ENZYME_TRAITS \t cellulolysis \t cellulose \t [0,2] 
#				...\t uniformLinear([0,2];1.8) \t kernelAlpha([0,2];5) 
#					...\t INTEGRAL_KERNEL_INTEGRATION
########################################################################

ENZYME_TRAITS	lipidase	lipid	[0,2]	uniformLinear([0,2];1)	kernelAlpha([0,2];2.1)	INTEGRAL_KERNEL_INTEGRATION
ENZYME_TRAITS	ligninase	lipid	[0,2]	uniformLinear([0,2];1)	kernelAlpha([0,2];2.1)	INTEGRAL_KERNEL_INTEGRATION
ENZYME_TRAITS	cellulase	cellulose	[0,2]	uniformLinear([0,2];1)	kernelAlpha([0,2];3.2)	INTEGRAL_KERNEL_INTEGRATION

########################################################################
# Microbe signature:
#
#	This section describes the microbes involved in the simulation and 
# 	their biochemical and polymerization composition.
#
#	Line format:
# 		SIGNATURE \t micName \t bcName \t proportion 
#									...\t polymerizationFunction
# 		- micName (String) is the name of the microbial community
# 		- bcName (String) is the name of the biochemical class 
# 		  composing the microbes
# 		- proportion (double in [0,1]) is the proportion of the 
# 		  components of the considered biochemical class composing the 
# 		  microbes
# 		- polymerizationFunction (String) is the function describing 
#		  the polymerization of biochemical elements considered
#
#	Example: 
#		SIGNATURE \t cellulose_degrader \t microbe_sugar \t 1
#		  ...\t gaussianTruncatedNormalized(microbe_sugar;1.5;0.1;[0,2])
########################################################################

SIGNATURE	brown_rot_fungi	lipid	0.12	gaussianTruncatedNormalized(lipid;1;0.4;[0,2])
SIGNATURE	brown_rot_fungi	protein	0.88	gaussianTruncatedNormalized(protein;1.1;0.2;[0.5,2])
SIGNATURE	white_rot_fungi	lipid	0.12	gaussianTruncatedNormalized(lipid;1;0.4;[0,2])
SIGNATURE	white_rot_fungi	protein	0.88	gaussianTruncatedNormalized(protein;1.1;0.2;[0.5,2])

########################################################################
# Microbe enzyme production (secretome):
#
#	This section describes how enzymes are produced by the microbes.
#
#	Line format:
# 		ENZYME_PRODUCTION \t micName \t producedEnzyme 
# 									...\t productionRateFunction
#		- micName (String) is the name of the microbial community
#		- producedEnzyme (String) is the name of the enzymes produces by
# 		  the microbes
#		- productionRateFunction (String) is the function describing the 
# 		  production rate of the enzyme
#
#	Example: 
#		ENZYME_PRODUCTION \t cellulose_degrader 
#										...\t cellulase \t linear(1.)
########################################################################

ENZYME_PRODUCTION	brown_rot_fungi	lipidase	linear(0.1)
ENZYME_PRODUCTION	brown_rot_fungi	cellulase	linear(2.1)
ENZYME_PRODUCTION	white_rot_fungi	ligninase	linear(2.1)

########################################################################
# Microbe assimilation:
#
#	This section describes how microbes assimilate C from the accessible
#	substrate pools. Assimilation of each microbe has to be defined.
#
#	Line format:
#		ASSIMILATION \t micName \t bcName \t 
#			uptakeFluxFunction \t carbonUseEfficiencyFunction
#		- micName (String) is the name of the microbial community
#		- bcName (String) is the biochemical class where carbon is taken 
# 		  up by microbes, 
#		- uptakeFluxFunction (String) is the function describing the 
# 		rate of uptake of carbon
#		- carbonUseEfficiencyFunction (String) is the function 
# 		  describing the carbon use efficiency of the taken up carbon
#
#	Example: 
# 		ASSIMILATION \t cellulose_degrader \t cellulose
#						...\t uniformLinear([0,0.4];5.) \t constant(0.4)
########################################################################

ASSIMILATION	brown_rot_fungi	cellulose	uniformLinear([0,0.4];1)	constant(0.3)
ASSIMILATION	brown_rot_fungi	lignin	uniformLinear([0,0.4];1)	constant(0.3)
ASSIMILATION	white_rot_fungi	cellulose	uniformLinear([0,0.4];1)	constant(0.3)
ASSIMILATION	white_rot_fungi	lignin	uniformLinear([0,0.4];1)	constant(0.3)

########################################################################
# Microbe mortality:
#
#	This section describes the mortality rate of the microbes. The 
#	mortality of each microbe has to be defined.
#
#	Line format:
#		MORTALITY \t micName \t mortalityFunction
#		- micName (String) is the name of the microbial community
#		- mortalityFunction (String) is the function describing the 
# 		  mortality rate of microbes
#
#	Example: 
#		MORTALITY \t cellulose_degrader \t linear(0.02)
########################################################################

MORTALITY	brown_rot_fungi	linear(0.1)
MORTALITY	white_rot_fungi	linear(0.1)

########################################################################
# Substrate pool transfers (optional):
#
#	This section is optional if the simulations contains only ACCESSIBLE
#	pools. For a same biochemical class, exchange between accessible and
#	inaccessible pool can occur.
#
#	Line format:
#		POOL_TRANSFER \t bcName \t origin \t arrival \t transferFunction
# 		- bcName (String) is the biochemical class
# 		- origin (String) is the accessibility of the origin pool
# 		- arrival (String) is the accessibility of the arrival pool
# 		- transferFunction (String) is the function describing the 
# 		  transfer rate between the pools
#
#	Example:
#		POOL_TRANSFER \t cellulose \t INACCESSIBLE_EMBEDMENT
#			...\t ACCESSIBLE \t enzymaticLinearTransfer(lignolase;1)
########################################################################

POOL_TRANSFER	cellulose	INACCESSIBLE_EMBEDMENT	ACCESSIBLE	enzymaticLinearTransfer(ligninase;13)

########################################################################
# Substrate pools initialization:
#
#	This section contain...
#
#	Line format:
#		POOL_INITIALIZATION \t bcName 
# 							...\t accessibility \t carbonPolymerization
#		- bcName
#		- accessibility
#		- carbonPolymerization
#	Example: 
#		POOL_INITIALIZATION \t lipîd \t ACCESSIBLE
# 	...\t gaussianTruncatedProportionalized(lipid;0.95;1.5;0.1;[0,2])
########################################################################

POOL_INITIALIZATION	cellulose	INACCESSIBLE_EMBEDMENT	gaussianTruncatedProportionalized(cellulose;95.;1.5;0.1;[0,2])
POOL_INITIALIZATION	lignin	ACCESSIBLE	gaussianTruncatedProportionalized(cellulose;95.;1.5;0.1;[0,2])

########################################################################
# Substrate pools temporal inputs:
#
#	This section should contains the C composition of specified pools.
#
#	Line format:
#		POOL_INPUT \t bcName \t accessibility \t carbonInputFunction
#		- bcName (String) is the biochemical class
#		- accessibility (String) is the accessibility of the pool
# 		- carbonInputFunction (String) is the function describing the 
# 		amount and polymerization of the carbon input
#
#	Example: 
#		POOL_INPUT \t cellulose \t ACCESSIBLE \t 
#		...\t constantInput(0.1:
#			... gaussianTruncatedNormalized(cellulose;1.5;0.1;[0,2]))
########################################################################

POOL_INPUT	cellulose	ACCESSIBLE	constantInput(0.1:gaussianTruncatedNormalized(cellulose;1.5;0.1;[0,2]))

########################################################################
# Microbe initial state:
#
#	This section contains the initial biomass of each microbe
#
#	Line format:
# 		MICROBE_INITIALIZATION \t micName \t mass
#		- micName the name of the microbial community considered
#		- mass (double>0) is the initial amount of carbon composing 
# 		  microbial community in g 
#
#	Example: 
#		MICROBE_INITIALIZATION \t cellulose_degrader \t 0.05
########################################################################

MICROBE_INITIALIZATION	brown_rot_fungi	1.0
MICROBE_INITIALIZATION	white_rot_fungi	1.0

########################################################################
# Observations:
# 	 
#	This section contains the observations needed by the user at the end
#	of the simulation. If no observations are specified, all observers 
#	are generated.
# 
#	Line formats available:
#		STATE_OBSERVER \t observableVariable \t datesToObserve
# 		  - observableVariable is the observed variable (chosen among:
# 		   "respiration")
# 		  - datesToObserve can be formated as follow:
#			* [0,2,5] to observe date 0, 2 and 5
#			* [1:2:11] to observe date between 1 and 11 with a step 2
#			* [1:2:14,25,33] which is a combination of the two previous 
#			  formats	
#		POOL_OBSERVER \t [bcName, accessibility] 
# 						...\t observableVariable \t datesToObserve 
#		  - bcName (String) is the biochemical class considered
# 		  - accessibility (String) is the accessibility of the pool 
#			considered, observableVariable is the observed variable 
#			(chosen among "mass","mass_distribution")
# 		  - datesToObserve can be formated as above
#		POOL_TRANSFER_OBSERVER \t [bcName,originPool,arrivalPool] 
# 		  					...\t observableVariable \t datesToObserve
# 		  - bcName (String) is the biochemical class considered
# 		  - originPool (String) is the accessibility of the origin 
#			pool
# 		  - arrivalPool (String) is the accessibility of the arrival 
#			pool
# 		  - observableVariable is the observed variable (chosen among 
#			"flux_distribution")
# 		  - datesToObserve can be formated as above
#		MICROBE_OBSERVER \t micName 
#							...\t observableVariable \t datesToObserve
#		  - micName (String) is the name of the considered microbes
#		  - observableVariable is the observed variable (chosen among
#			"mass", "uptake_flux_distribution_map",  "respiration",
#			"carbon_use_efficiency_distribution_map", "mortality_flux")
# 		  - datesToObserve can be formated as above
#		ENZYME_OBSERVER \t enzName 
#							...\t observableVariable \t datesToObserve
#		  - enzName is the name of the considered enzymes
#		  - observableVariable is the observed variable (chosen among 
#			"depolymerization_rate_distribution, 
#			"activity_distribution")
# 		  - datesToObserve can be formated as above 
#
#	Examples: 
#		STATE_OBSERVER \t respiration \t [0,1]
#		POOL_OBSERVER \t [cellulose,ACCESSIBLE] \t 	mass \t [0,1]
#		POOL_TRANSFER_OBSERVER 
#				...\t [cellulose,INACCESSIBLE_EMBEDMENT,ACCESSIBLE]
#					...\t flux_distribution \t [0,1]
#		MICROBE_OBSERVER \t cellulose_degrader 
#				...\t uptake_flux_distribution \t [0,1]
#		ENZYME_OBSERVER \t cellulolysis
#				...\t depolymerization_rate_distribution \t [0,1]
########################################################################

POOL_OBSERVER	[lipid,ACCESSIBLE]	mass	[0,1]
ENZYME_OBSERVER	lipidase	depolymerization_rate_distribution	[0,1]
MICROBE_OBSERVER	brown_rot_fungi	uptake_flux_distribution_map	[0,1]