File Formats

BSTModelKit.jl supports several file formats for defining BST models. The build function automatically detects the format based on the file extension.

TOML Format (recommended)

The TOML format (.toml) is the recommended way to define models. A TOML model file has two sections: [metadata] and [model].

Example: Linear pathway with feedback inhibition

[metadata]
author = "jdv27@cornell.edu"
date = "12/17/22"
version = "0.1"
description = "Linear pathway with feedback inhibition"

[model]
list_of_static_species = ["E1", "E2", "E3"]
list_of_dynamic_species = ["X1", "X2", "X3", "X4", "X5"]

list_of_connection_records = [
    # name::{reactants} --> {products}
    "r1::{X1} --> X2",
    "r2::{X2} --> X3",
    "r3::X3 --> X4",
    "r5::X3 --> X5",

    # source and sink reactions use empty braces {}
    "r0::{} --> X1",
    "r4::X4 --> {}"
]

list_of_kinetics_records = [
    # name::{factor_1,factor_2,...}
    "r0::{}",
    "r1::{X1,X4,E1}",
    "r2::{X2,E2}",
    "r3::{X3,E3}",
    "r4::{X4}",
    "r5::{X3}"
]

list_of_stoichiometry_records = [
    # name,species,coefficient
    "r1,X1,2.0"
]

Section descriptions

[metadata] — optional metadata about the model:

author: Author of the model
date: Date the model was created
version: Model version
description: A short description of the model

[model] — the model definition:

list_of_static_species: Species with constant (externally set) concentrations, e.g., enzymes
list_of_dynamic_species: Species governed by ODEs
list_of_connection_records: Reaction connectivity in the format name::{reactants} --> {products}. Use empty braces {} for source or sink reactions
list_of_kinetics_records: Kinetic dependencies in the format name::{factor_1,factor_2,...}. Lists which species appear in the rate law for each reaction
list_of_stoichiometry_records: Override default stoichiometric coefficients (default is $\pm 1$). Format: name,species,coefficient

BST Format

The BST format (.bst) is a custom text format using section markers. Comments are prefixed with //.

Example

// Linear pathway with feedback inhibition

#static::start
    E1,E2,E3
#static::end

#dynamic::start
    X1, X2, X3, X4, X5
#dynamic::end

#structure::start
    r1::{X1} --> X2
    r2::{X2} --> X3
    r3::X3 --> X4
    r5::X3 --> X5
    r0::{} --> X1
    r4::X4 --> {}
#structure::end

#rate::start
    r0::{}
    r1::{X1,X4,E1}
    r2::{X2,E2}
    r3::{X3,E3}
    r4::{X4}
    r5::{X3}
#rate::end

#stoichiometry::start
    r1,X1,2.0
#stoichiometry::end

Sections

#static — comma-separated list of static species
#dynamic — comma-separated list of dynamic species
#structure — reaction connectivity (same syntax as TOML list_of_connection_records)
#rate — kinetic dependencies (same syntax as TOML list_of_kinetics_records)
#stoichiometry — stoichiometric coefficient overrides

Models can be saved to and loaded from JLD2 binary files (.jld2) using the savemodel and loadmodel functions. This is useful for serializing a fully configured model (with parameters, initial conditions, etc.) for later use.

# save a configured model
savemodel("my_model.jld2", model)

# load it back
model = loadmodel("my_model.jld2")

# or equivalently
model = build("my_model.jld2")