in-silico-cancer-cell 0.2.4__cp311-cp311-win_amd64.whl

in_silico_cancer_cell/__init__.py

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+# Welcome!
+from in_silico_cancer_cell import _in_rusty_silico  # type: ignore reportAttributeAccessIssue
+from ._in_rusty_silico import (
+    A549CancerCell,
+    CellPhase,
+    ChannelCountsProblem,
+    InSilicoMethod,
+    PatchClampProtocol,
+    PatchClampData,
+    find_best_fit_for,
+    setup_logging,
+)
+
+
+def useless_python_function():
+    print("hello")
+
+
+__doc__ = _in_rusty_silico.__doc__
+__all__ = [
+    "A549CancerCell",
+    "CellPhase",
+    "ChannelCountsProblem",
+    "InSilicoMethod",
+    "PatchClampProtocol",
+    "PatchClampData",
+    "find_best_fit_for",
+    "setup_logging",
+    "useless_python_function",
+]

in_silico_cancer_cell/_in_rusty_silico.pyi

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+import enum
+
+class A549CancerCell:
+    @staticmethod
+    def new() -> A549CancerCell:
+        pass
+
+    def evaluate(self, protocol: PatchClampProtocol, phase: CellPhase) -> float:
+        pass
+
+class PatchClampProtocol(enum.Enum):
+    Activation = enum.auto()
+    Deactivation = enum.auto()
+    Ramp = enum.auto()
+
+class CellPhase(enum.Enum):
+    G0 = enum.auto()
+    G1 = enum.auto()
+
+class ChannelCountsProblem:
+    @staticmethod
+    def new(data: PatchClampData) -> ChannelCountsProblem:
+        pass
+    def precompute_single_channel_currents(self):
+        pass
+    def get_current_basis(self) -> list[list[float]]:
+        pass
+
+class InSilicoMethod(enum.Enum):
+    Projection = enum.auto()
+    ParticleSwarm = enum.auto()
+    SteepestDescent = enum.auto()
+    LBFGS = enum.auto()
+
+class PatchClampData:
+    @staticmethod
+    def pyload(protocol: PatchClampProtocol, phase: CellPhase) -> PatchClampData:
+        pass
+    def to_list(self) -> list[float]:
+        pass
+
+def find_best_fit_for(data: PatchClampData, using: InSilicoMethod) -> list[float]:
+    pass
+
+def setup_logging():
+    pass

in_silico_cancer_cell/fit.py

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+import clarabel
+import numpy as np
+from scipy import sparse
+import scipy
+
+from . import CellPhase, ChannelCountsProblem, PatchClampData, PatchClampProtocol
+from .utils import moving_average
+
+
+def load_problem(n):
+    measurements = PatchClampData.pyload(PatchClampProtocol.Activation, CellPhase.G0)
+    data = moving_average(np.array(measurements.to_list()), n)
+    # data = np.array(measurements.to_list())[::12]
+    problem = ChannelCountsProblem.new(measurements)
+    problem.precompute_single_channel_currents()
+    single_channels = moving_average(np.array(problem.get_current_basis()), n)
+    # single_channels = np.array(problem.get_current_basis())[:, (3,)]
+    # single_channels = np.concatenate([single_channels, np.ones((single_channels.shape[0], 1))], axis=1)
+    return single_channels[: data.shape[0]], data
+
+
+def solve_as_quadratic_problem(single_channels, data):
+    # LSQ formulation min 1/2 ||Rx - d||^2
+    R = single_channels
+    d = data
+
+    # converted into QP formulation
+    P = sparse.csc_matrix(R.T @ R)
+    q = -R.T @ d
+    A = -sparse.identity(11).tocsc()
+    b = np.zeros(11)
+    cones = [clarabel.NonnegativeConeT(11)]
+
+    # solve
+    settings = clarabel.DefaultSettings()
+    solver = clarabel.DefaultSolver(P, q, A, b, cones, settings)
+    solution = solver.solve()
+    return np.array(solution.x)
+
+
+def solve_with(single_channels, data, method):
+    if method == "lstsq":
+        channel_counts, res, rank, s = np.linalg.lstsq(single_channels[: len(data), :], data, rcond=None)
+    elif method == "nnls":
+        channel_counts, rnorm = scipy.optimize.nnls(single_channels[: len(data), :], data)
+    elif method == "qp":
+        channel_counts = solve_as_quadratic_problem(single_channels, data)
+    elif method == "langthaler":
+        channel_counts = np.array([22, 78, 5, 1350, 40, 77, 19, 200, 17, 12, 13])
+    channel_counts = channel_counts.round().astype(int)
+    print(f"Best fit: {channel_counts}")
+    return channel_counts

in_silico_cancer_cell/plot.py

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+import pathlib
+
+import matplotlib.axes
+import matplotlib.pyplot as plt
+import numpy as np
+
+from . import setup_logging
+from .fit import load_problem, solve_with
+
+RESULTS = pathlib.Path.cwd()
+setup_logging()
+
+
+def plot_measurement():
+    fig = plt.figure()
+    axes: matplotlib.axes.Axes = fig.add_subplot(1, 1, 1)
+    axes.plot()
+    axes.set_xlabel("")
+    axes.set_ylabel("")
+    axes.legend()
+    fig.savefig(str(RESULTS / "plot.pdf"))
+
+
+def plot_full_comparison(method="nnls", n=800):
+    single_channels, data = load_problem(n)
+    channel_counts = solve_with(single_channels, data, method)
+    diff = (single_channels * channel_counts).sum(axis=1) - data
+    print(f"Error: {np.sqrt((diff ** 2).sum() / len(diff)):.2f}")
+    time = np.linspace(0, 9.901, single_channels.shape[0])
+    fig = plt.figure(figsize=(8, 4))
+    axes: matplotlib.axes.Axes = fig.add_subplot(1, 1, 1)
+    axes.plot(time[: len(data)], data, label="Measurements")
+    axes.plot(time, (single_channels * channel_counts).sum(axis=1), label="Simulation")
+    axes.set_xlabel("Time $t$ / s")
+    axes.set_ylabel("Current $I$ / pA")
+    axes.legend()
+    fig.savefig(str(RESULTS / "data-vs-simulation.pdf"))
+
+
+def set_results_folder(path: pathlib.Path):
+    global RESULTS
+    RESULTS = path

in_silico_cancer_cell/utils.py

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+import numpy as np
+
+
+def moving_average(a: np.ndarray, n=3) -> np.ndarray:
+    """Generate a moving average
+
+    Args:
+        a (np.array): original datum
+        n (int, optional): Average stencil order. Defaults to 3.
+
+    Returns:
+        np.ndarray: averaged array
+    """
+    ret = np.cumsum(a, dtype=float, axis=0)
+    ret[n:] = ret[n:] - ret[:-n]
+    return ret[n - 1 :] / n

in_silico_cancer_cell-0.2.4.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: in_silico_cancer_cell
+Version: 0.2.4
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Dist: matplotlib>=3.10.8
+Requires-Dist: numpy>=2.4.2
+Requires-Dist: clarabel>=0.11.1
+Summary: Simulation of an electrophysiological A549 cancer cell model using individual ion channels across the membrane
+Author-email: MrP01 <peter@waldert.at>
+License-Expression: MIT
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: homepage, https://in-silico-cancer-cell.waldert.at/
+Project-URL: repository, https://github.com/MrP01/InSilicoCancerCell
+
+# Electrophysiological Cancer Cell Model
+
+![PyPI - Version](https://img.shields.io/pypi/v/in-silico-cancer-cell)
+
+Attempt to model an A549 cancer cell's ion channels using an HMM (Hidden Markov Model) and simulation of voltage + current development accross the membrane of the cell.
+
+This software comes in three flavours:
+
+- to run the `main.rs` simulation, do `cargo run`,
+- to compile the Python module, do `maturin develop --features pyo3`,
+- to precompile for the Astro dashboard, do `bun run wasm-pack build frontend`.
+
+## A visual to capture your interest:
+
+![Ion Channels](https://journals.plos.org/ploscompbiol/article/figure/image?size=large&download=&id=10.1371/journal.pcbi.1009091.g002)
+(Image source: [here](https://doi.org/10.1371/journal.pcbi.1009091.g002)).
+
+This computational model is based on [Langthaler et al., 2021](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009091): **A549 in-silico 1.0: A first computational model to simulate cell cycle dependent ion current modulation in the human lung adenocarcinoma**.
+
+## The Simulation Dashboard
+
+![Screenshot of the User Interface](./figures/full-length-screenshot.png)
+

in_silico_cancer_cell-0.2.4.dist-info/RECORD

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+in_silico_cancer_cell\_in_rusty_silico.pyi,sha256=FkZk0u5D_4o_fMAA5j7pKou7KAReXhWsyOtBMw1cH6Q,1145
+in_silico_cancer_cell\fit.py,sha256=I1mXIBxkUbS8kmwgEmhHGDC-fvH2kPuuvinb-CcLJWU,2021
+in_silico_cancer_cell\plot.py,sha256=zy11eGa_OBBqr8SXFsLLdgUt2HJIa9rQOIa-vmlzNfI,1307
+in_silico_cancer_cell\py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+in_silico_cancer_cell\utils.py,sha256=HE2irwwNnF0LoSOSCcOk1bT5a1VfJ8JL6oM6CugnyP0,399
+in_silico_cancer_cell-0.2.4.dist-info\METADATA,sha256=DfOLCmnaeW_eKxUI9o1I5sroyHDf9B2kzfJiMh_-uFA,1940
+in_silico_cancer_cell-0.2.4.dist-info\WHEEL,sha256=X79LywvMB9iCuFHu88xBAFTJDhRqJi6Yh9hhoCI9jao,97
+in_silico_cancer_cell-0.2.4.dist-info\RECORD,,

in_silico_cancer_cell-0.2.4.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: maturin (1.11.5)
+Root-Is-Purelib: false
+Tag: cp311-cp311-win_amd64