diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 4eda8b4..52dd497 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-03T18:53:04","documenter_version":"1.5.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-03T22:53:38","documenter_version":"1.5.0"}} \ No newline at end of file diff --git a/dev/API/index.html b/dev/API/index.html index 281863e..b655d5b 100644 --- a/dev/API/index.html +++ b/dev/API/index.html @@ -8,11 +8,11 @@ forward_model_selection::Bool; save_train_results::Bool = false, enzyme_name::String = "Enzyme", -)

This function is used to perform data-driven rate equation selection using a general rate equation and data. The function will select the best rate equation by iteratively removing parameters from the general rate equation and finding an equation that yield best test scores on data not used for fitting.

Arguments

Keyword Arguments

Returns trainresults, testresults and list of practicallyunidentifiableparams and optionally saves a csv file for each num_params with the results of the training for each combination of parameters tested and a csv file with test results for top 10% of the best results with each number of parameters tested.

source
DataDrivenEnzymeRateEqs.display_rate_equation — Method
display_rate_equation(
+)

This function is used to perform data-driven rate equation selection using a general rate equation and data. The function will select the best rate equation by iteratively removing parameters from the general rate equation and finding an equation that yield best test scores on data not used for fitting.

Arguments

  • general_rate_equation::Function: Function that takes a NamedTuple of metabolite concentrations (with metab_names keys) and parameters (with param_names keys) and returns an enzyme rate.
  • data::DataFrame: DataFrame containing the data with column Rate and columns for each metab_names where each row is one measurement. It also needs to have a column source that contains a string that identifies the source of the data. This is used to calculate the weights for each figure in the publication.
  • metab_names::Tuple: Tuple of metabolite names that correspond to the metabolites of rate_equation and column names in data.
  • param_names::Tuple: Tuple of parameter names that correspond to the parameters of rate_equation.
  • range_number_params::Tuple{Int,Int}: A tuple of integers representing the range of the number of parameters of generalrateequation to search over.
  • forward_model_selection::Bool: A boolean indicating whether to use forward model selection (true) or reverse model selection (false).

Keyword Arguments

  • save_train_results::Bool: A boolean indicating whether to save the results of the training for each number of parameters as a csv file.
  • enzyme_name::String: A string for enzyme name that is used to name the csv files that are saved.

Returns trainresults, testresults and list of practicallyunidentifiableparams and optionally saves a csv file for each num_params with the results of the training for each combination of parameters tested and a csv file with test results for top 10% of the best results with each number of parameters tested.

source
DataDrivenEnzymeRateEqs.display_rate_equation — Method
display_rate_equation(
 rate_equation::Function,
 metab_names::Tuple{Symbol,Vararg{Symbol}},
 param_names::Tuple{Symbol,Vararg{Symbol}};
-nt_param_removal_code = nothing

)

Return the symbolic rate equation for the given rate_equation function.

Arguments

  • rate_equation::Function: The rate equation function.
  • metab_names::Tuple{Symbol,Vararg{Symbol}}: The names of the metabolites.
  • param_names::Tuple{Symbol,Vararg{Symbol}}: The names of the parameters.
  • nt_param_removal_code::NamedTuple: The named tuple of the parameters to remove from the rate equation.
source
DataDrivenEnzymeRateEqs.fit_rate_equation — Method
fit_rate_equation(
+nt_param_removal_code = nothing

)

Return the symbolic rate equation for the given rate_equation function.

Arguments

  • rate_equation::Function: The rate equation function.
  • metab_names::Tuple{Symbol,Vararg{Symbol}}: The names of the metabolites.
  • param_names::Tuple{Symbol,Vararg{Symbol}}: The names of the parameters.
  • nt_param_removal_code::NamedTuple: The named tuple of the parameters to remove from the rate equation.
source
DataDrivenEnzymeRateEqs.fit_rate_equation — Method
fit_rate_equation(
     rate_equation::Function,
     data::DataFrame,
     metab_names::Tuple{Symbol, Vararg{Symbol}},
@@ -24,4 +24,4 @@
     source = ["Figure 1", "Figure 1", "Figure 2"]
 )
 rate_equation(metabs, params) = params.Vmax * metabs.S / (1 + metabs.S / params.K_S)
-fit_rate_equation(rate_equation, data, (:A,), (:Vmax, :K_S))
source
DataDrivenEnzymeRateEqs.@derive_general_mwc_rate_eq — Macro
derive_general_mwc_rate_eq(metabs_and_regulators_kwargs...)

Derive a function that calculates the rate of a reaction using the general MWC rate equation given the list of substrates, products, and regulators that bind to specific cat or reg sites.

The general MWC rate equation is given by:

\[Rate = \frac{{V_{max}^a \prod_{i=1}^{n} \left(\frac{S_i}{K_{a, i}}\right) - V_{max, rev}^a \prod_{i=1}^{n} \left(\frac{P_i}{K_{a, i}}\right) \cdot Z_{a, cat}^{n-1} \cdot Z_{a, reg}^n + L \left(V_{max}^i \prod_{i=1}^{n} \left(\frac{S_i}{K_{i, i}}\right) - V_{max, rev}^i \prod_{i=1}^{n} \left(\frac{P_i}{K_{i, i}}\right)\right) \cdot Z_{i, cat}^{n-1} \cdot Z_{i, reg}^n}}{Z_{a, cat}^n \cdot Z_{a, reg}^n + L \cdot Z_{i, cat}^n \cdot Z_{i, reg}^n}\]

where:

  • $V_{max}^a$ is the maximum rate of the forward reaction
  • $V_{max, rev}^a$ is the maximum rate of the reverse reaction
  • $V_{max}^i$ is the maximum rate of the forward reaction
  • $V_{max, rev}^i$ is the maximum rate of the reverse reaction
  • $S_i$ is the concentration of the $i^{th}$ substrate
  • $P_i$ is the concentration of the $i^{th}$ product
  • $K_{a, i}$ is the Michaelis constant for the $i^{th}$ substrate
  • $K_{i, i}$ is the Michaelis constant for the $i^{th}$ product
  • $Z_{a, cat}$ is the allosteric factor for the catalytic site
  • $Z_{i, cat}$ is the allosteric factor for the catalytic site
  • $Z_{a, reg}$ is the allosteric factor for the regulatory site
  • $Z_{i, reg}$ is the allosteric factor for the regulatory site
  • $L$ is the ratio of inactive to active enzyme conformations in the absence of ligands
  • $n$ is the oligomeric state of the enzyme

Arguments

  • metabs_and_regulators_kwargs...: keyword arguments that specify the substrates, products, catalytic sites, regulatory sites, and other parameters of the reaction.

Returns

  • A function that calculates the rate of the reaction using the general MWC rate equation
  • A tuple of the names of the metabolites and parameters used in the rate equation
source
DataDrivenEnzymeRateEqs.@derive_general_qssa_rate_eq — Macro
derive_general_qssa_rate_eq(metabs_and_regulators_kwargs...)

Derive a function that calculates the rate of a reaction using the Quasi Steady State Approximation (QSSA) given the list of substrates, products, and regulators.

The general QSSA rate equation is given by:

\[Rate = \frac{V_{max} \left(\frac{\prod_{i=1}^{n}S_i}{(K_{S1...Sn})^n}\right) - V_{max, rev} \left(\frac{\prod_{i=1}^{n}P_i}{(K_{P1...Pn})^n}\right)}{Z}\]

where:

  • $V_{max}$ is the maximum rate of the forward reaction
  • $V_{max, rev}$ is the maximum rate of the reverse reaction
  • $S_i$, $P_i$, $R_i$ is the concentration of the $i^{th}$ substrate (S), product (P), or regulator (R)
  • $K_{X_1...X_n}$ is the kinetic constant
  • $Z$ is a combination of all terms containing products of [S], [P], and [R] divided by KSP_R

Arguments

  • metabs_and_regulators_kwargs...: keyword arguments that specify the substrates, products, catalytic sites, regulatory sites, and other parameters of the reaction.

Returns

  • A function that calculates the rate of the reaction using the general qssa rate equation
  • A tuple of the names of the metabolites and parameters used in the rate equation
source
+fit_rate_equation(rate_equation, data, (:A,), (:Vmax, :K_S))source
DataDrivenEnzymeRateEqs.@derive_general_mwc_rate_eq — Macro
derive_general_mwc_rate_eq(metabs_and_regulators_kwargs...)

Derive a function that calculates the rate of a reaction using the general MWC rate equation given the list of substrates, products, and regulators that bind to specific cat or reg sites.

The general MWC rate equation is given by:

\[Rate = \frac{{V_{max}^a \prod_{i=1}^{n} \left(\frac{S_i}{K_{a, i}}\right) - V_{max, rev}^a \prod_{i=1}^{n} \left(\frac{P_i}{K_{a, i}}\right) \cdot Z_{a, cat}^{n-1} \cdot Z_{a, reg}^n + L \left(V_{max}^i \prod_{i=1}^{n} \left(\frac{S_i}{K_{i, i}}\right) - V_{max, rev}^i \prod_{i=1}^{n} \left(\frac{P_i}{K_{i, i}}\right)\right) \cdot Z_{i, cat}^{n-1} \cdot Z_{i, reg}^n}}{Z_{a, cat}^n \cdot Z_{a, reg}^n + L \cdot Z_{i, cat}^n \cdot Z_{i, reg}^n}\]

where:

  • $V_{max}^a$ is the maximum rate of the forward reaction
  • $V_{max, rev}^a$ is the maximum rate of the reverse reaction
  • $V_{max}^i$ is the maximum rate of the forward reaction
  • $V_{max, rev}^i$ is the maximum rate of the reverse reaction
  • $S_i$ is the concentration of the $i^{th}$ substrate
  • $P_i$ is the concentration of the $i^{th}$ product
  • $K_{a, i}$ is the Michaelis constant for the $i^{th}$ substrate
  • $K_{i, i}$ is the Michaelis constant for the $i^{th}$ product
  • $Z_{a, cat}$ is the allosteric factor for the catalytic site
  • $Z_{i, cat}$ is the allosteric factor for the catalytic site
  • $Z_{a, reg}$ is the allosteric factor for the regulatory site
  • $Z_{i, reg}$ is the allosteric factor for the regulatory site
  • $L$ is the ratio of inactive to active enzyme conformations in the absence of ligands
  • $n$ is the oligomeric state of the enzyme

Arguments

  • metabs_and_regulators_kwargs...: keyword arguments that specify the substrates, products, catalytic sites, regulatory sites, and other parameters of the reaction.

Returns

  • A function that calculates the rate of the reaction using the general MWC rate equation
  • A tuple of the names of the metabolites and parameters used in the rate equation
source
DataDrivenEnzymeRateEqs.@derive_general_qssa_rate_eq — Macro
derive_general_qssa_rate_eq(metabs_and_regulators_kwargs...)

Derive a function that calculates the rate of a reaction using the Quasi Steady State Approximation (QSSA) given the list of substrates, products, and regulators.

The general QSSA rate equation is given by:

\[Rate = \frac{V_{max} \left(\frac{\prod_{i=1}^{n}S_i}{(K_{S1...Sn})^n}\right) - V_{max, rev} \left(\frac{\prod_{i=1}^{n}P_i}{(K_{P1...Pn})^n}\right)}{Z}\]

where:

  • $V_{max}$ is the maximum rate of the forward reaction
  • $V_{max, rev}$ is the maximum rate of the reverse reaction
  • $S_i$, $P_i$, $R_i$ is the concentration of the $i^{th}$ substrate (S), product (P), or regulator (R)
  • $K_{X_1...X_n}$ is the kinetic constant
  • $Z$ is a combination of all terms containing products of [S], [P], and [R] divided by KSP_R

Arguments

  • metabs_and_regulators_kwargs...: keyword arguments that specify the substrates, products, catalytic sites, regulatory sites, and other parameters of the reaction.

Returns

  • A function that calculates the rate of the reaction using the general qssa rate equation
  • A tuple of the names of the metabolites and parameters used in the rate equation
source
diff --git a/dev/Tutorial/index.html b/dev/Tutorial/index.html index 28a8f24..43f40ee 100644 --- a/dev/Tutorial/index.html +++ b/dev/Tutorial/index.html @@ -1,2 +1,2 @@ -Tutorial · DataDrivenEnzymeRateEqs.jl
GitHub
+Tutorial · DataDrivenEnzymeRateEqs.jl
GitHub
diff --git a/dev/index.html b/dev/index.html index f35c3a8..b13ea24 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -Home · DataDrivenEnzymeRateEqs.jl
GitHub
+Home · DataDrivenEnzymeRateEqs.jl
GitHub