mxlmodels 1.0.0__py3-none-any.whl

mxlmodels/__init__.py

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+"""MxlModels is a Python package of reference mechanistic models.
+
+It contains the same models as in the [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks) repo,
+but written as single, flat files to make inspection easier.
+
+"""
+
+from .dyn_entro import create_model as get_dynamic_enterobactin
+from .ebeling2026 import create_model as get_ebeling_2026
+from .lotka_volterra_v1 import create_model as get_lotka_volterra_v1
+from .lotka_volterra_v2 import create_model as get_lotka_volterra_v2
+from .matuszynska2016_npq import create_model as get_matuszynska2016_npq
+from .matuszynska2016_phd import create_model as get_matuszynska2016_phd
+from .matuszynska2019 import create_model as get_matuszynska2019
+from .poolman2000 import create_model as get_poolman2000
+from .pop_dyn import create_model as get_population_dynamics
+from .saadat2021 import create_model as get_saadat2021
+from .trip_dyn import create_model as get_tripartite_dynamics
+from .yokota1985 import create_model as get_yokota1985
+
+__all__ = [
+    "get_dynamic_enterobactin",
+    "get_ebeling_2026",
+    "get_lotka_volterra_v1",
+    "get_lotka_volterra_v2",
+    "get_matuszynska2016_npq",
+    "get_matuszynska2016_phd",
+    "get_matuszynska2019",
+    "get_poolman2000",
+    "get_population_dynamics",
+    "get_saadat2021",
+    "get_tripartite_dynamics",
+    "get_yokota1985",
+]

mxlmodels/dyn_entro.py

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+"""Dynamic enterobactin competition model: E. coli vs C. glutamicum siderophore cross-feeding."""
+
+from mxlpy import Model
+
+
+def _a_c(
+    a_e: float,
+) -> float:
+    """Affinity of C. glutamicum for enterobactin: conservation with E. coli affinity."""
+    return 10.0 - a_e
+
+
+def _uptake_e_growth(
+    a_e: float,
+    enterobactin: float,
+    k_e: float,
+) -> float:
+    """Michaelis-Menten uptake of enterobactin by E. coli, scaled by E. coli affinity."""
+    return a_e * enterobactin / (k_e + enterobactin)
+
+
+def _uptake_c_growth(
+    enterobactin: float,
+    _a_c: float,
+    k_c: float,
+) -> float:
+    """Michaelis-Menten uptake of enterobactin by C. glutamicum, scaled by its affinity."""
+    return _a_c * enterobactin / (k_c + enterobactin)
+
+
+def _cons_term_e(
+    a_e: float,
+    e_coli: float,
+    k_e: float,
+    mu_e: float,
+) -> float:
+    """Enterobactin consumption term for E. coli: affinity * population * growth rate."""
+    return a_e * e_coli * mu_e / (k_e + a_e)
+
+
+def _cons_term_c(
+    mu_c: float,
+    _a_c: float,
+    k_c: float,
+    c_gluta: float,
+) -> float:
+    """Enterobactin consumption term for C. glutamicum: affinity * population * growth rate."""
+    return _a_c * c_gluta * mu_c / (k_c + _a_c)
+
+
+def _d_edt(
+    mu_e: float,
+    e_coli: float,
+    _uptake_e_growth: float,
+) -> float:
+    """Net growth rate of E. coli population."""
+    return e_coli * mu_e * _uptake_e_growth
+
+
+def _d_cdt(
+    mu_c: float,
+    c_gluta: float,
+    _uptake_c_growth: float,
+    theta: float,
+) -> float:
+    """Net growth rate of C. glutamicum minus density-dependent death."""
+    return c_gluta * mu_c * _uptake_c_growth - c_gluta**2.0 * theta
+
+
+def _d_bdt(
+    enterobactin: float,
+    r_cons_e: float,
+    _cons_term_e: float,
+    r_prod: float,
+    _cons_term_c: float,
+    r_cons_c: float,
+) -> float:
+    """Net rate of change of enterobactin: production by E. coli minus consumption by both species."""
+    return -_cons_term_c * r_cons_c - _cons_term_e * r_cons_e + enterobactin * r_prod
+
+
+def create_model() -> Model:
+    """Build the dynamic enterobactin cross-feeding model (E. coli / C. glutamicum)."""
+    return (
+        Model()
+        .add_variable(
+            "e_coli",
+            initial_value=5.0,
+        )
+        .add_variable(
+            "c_gluta",
+            initial_value=5.0,
+        )
+        .add_variable(
+            "enterobactin",
+            initial_value=1.0,
+        )
+        .add_parameter(
+            "mu_e",
+            value=0.4,
+        )
+        .add_parameter(
+            "mu_c",
+            value=0.3,
+        )
+        .add_parameter(
+            "a_e",
+            value=6.0,
+        )
+        .add_parameter(
+            "K_e",
+            value=0.5,
+        )
+        .add_parameter(
+            "K_c",
+            value=0.5,
+        )
+        .add_parameter(
+            "theta",
+            value=0.001,
+        )
+        .add_parameter(
+            "r_prod",
+            value=0.2,
+        )
+        .add_parameter(
+            "r_cons_e",
+            value=1.0,
+        )
+        .add_parameter(
+            "r_cons_c",
+            value=1.0,
+        )
+        .add_derived(
+            "a_c",
+            fn=_a_c,
+            args=["a_e"],
+        )
+        .add_derived(
+            "uptake_E_growth",
+            fn=_uptake_e_growth,
+            args=["a_e", "enterobactin", "K_e"],
+        )
+        .add_derived(
+            "uptake_C_growth",
+            fn=_uptake_c_growth,
+            args=["enterobactin", "a_c", "K_c"],
+        )
+        .add_derived(
+            "cons_term_E",
+            fn=_cons_term_e,
+            args=["a_e", "e_coli", "K_e", "mu_e"],
+        )
+        .add_derived(
+            "cons_term_C",
+            fn=_cons_term_c,
+            args=["mu_c", "a_c", "K_c", "c_gluta"],
+        )
+        .add_reaction(
+            "dEdt",
+            fn=_d_edt,
+            args=["mu_e", "e_coli", "uptake_E_growth"],
+            stoichiometry={"e_coli": 1.0},
+        )
+        .add_reaction(
+            "dCdt",
+            fn=_d_cdt,
+            args=["mu_c", "c_gluta", "uptake_C_growth", "theta"],
+            stoichiometry={"c_gluta": 1.0},
+        )
+        .add_reaction(
+            "dBdt",
+            fn=_d_bdt,
+            args=[
+                "enterobactin",
+                "r_cons_e",
+                "cons_term_E",
+                "r_prod",
+                "cons_term_C",
+                "r_cons_c",
+            ],
+            stoichiometry={"enterobactin": 1.0},
+        )
+    )