in-silico-cancer-cell 0.1.0__tar.gz → 0.2.0__tar.gz

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: Build Main and Frontend
+name: Build Main, Frontend and Deploy
 on:
   push:
 env:
@@ -28,3 +28,14 @@ jobs:
       - run: yarn run wasm-pack build frontend --release
       - run: cargo run --release --target=${{ matrix.target }} save-patch-clamp-data 225
       - run: yarn run build
+
+      # deploy
+      - uses: jsmrcaga/action-netlify-deploy@master
+        with:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+          NETLIFY_DEPLOY_MESSAGE: "Production deploy v${{ github.ref }}"
+          NETLIFY_DEPLOY_TO_PROD: true
+          install_command: "echo Skipping..."
+          build_command: "echo Skipping..."
+          build_directory: dist/

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/Cargo.lock

@@ -302,7 +302,7 @@ dependencies = [
 
 [[package]]
 name = "frontend"
-version = "0.1.0"
+version = "0.2.0"
 dependencies = [
  "console_error_panic_hook",
  "futures",
@@ -443,7 +443,7 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
 [[package]]
 name = "in_silico_cancer_cell"
-version = "0.1.0"
+version = "0.2.0"
 dependencies = [
  "argmin",
  "argmin-math",

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "in_silico_cancer_cell"
-version = "0.1.0"
+version = "0.2.0"
 edition = "2021"
 
 [lib]

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: in_silico_cancer_cell
-Version: 0.1.0
+Version: 0.2.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -9,6 +9,8 @@ Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 
 # 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:

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/README.md

@@ -1,5 +1,7 @@
 # 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:

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/main.py

@@ -1,10 +1,13 @@
+#!/usr/bin/env python
 import pathlib
 
 import in_silico_cancer_cell.plot as insilico_plot
+import matplotlib.pyplot as plt
 
 RESULTS = pathlib.Path(__file__).resolve().parent / "figures" / "results"
 
 
 if __name__ == "__main__":
     insilico_plot.set_results_folder(RESULTS)
-    insilico_plot.plot_measurement()
+    insilico_plot.plot_full_comparison()
+    plt.show()

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/poetry.lock

@@ -744,6 +744,48 @@ files = [
 [package.dependencies]
 six = ">=1.5"
 
+[[package]]
+name = "scipy"
+version = "1.13.1"
+description = "Fundamental algorithms for scientific computing in Python"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "scipy-1.13.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:20335853b85e9a49ff7572ab453794298bcf0354d8068c5f6775a0eabf350aca"},
+    {file = "scipy-1.13.1-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:d605e9c23906d1994f55ace80e0125c587f96c020037ea6aa98d01b4bd2e222f"},
+    {file = "scipy-1.13.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:cfa31f1def5c819b19ecc3a8b52d28ffdcc7ed52bb20c9a7589669dd3c250989"},
+    {file = "scipy-1.13.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f26264b282b9da0952a024ae34710c2aff7d27480ee91a2e82b7b7073c24722f"},
+    {file = "scipy-1.13.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:eccfa1906eacc02de42d70ef4aecea45415f5be17e72b61bafcfd329bdc52e94"},
+    {file = "scipy-1.13.1-cp310-cp310-win_amd64.whl", hash = "sha256:2831f0dc9c5ea9edd6e51e6e769b655f08ec6db6e2e10f86ef39bd32eb11da54"},
+    {file = "scipy-1.13.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:27e52b09c0d3a1d5b63e1105f24177e544a222b43611aaf5bc44d4a0979e32f9"},
+    {file = "scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:54f430b00f0133e2224c3ba42b805bfd0086fe488835effa33fa291561932326"},
+    {file = "scipy-1.13.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e89369d27f9e7b0884ae559a3a956e77c02114cc60a6058b4e5011572eea9299"},
+    {file = "scipy-1.13.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a78b4b3345f1b6f68a763c6e25c0c9a23a9fd0f39f5f3d200efe8feda560a5fa"},
+    {file = "scipy-1.13.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:45484bee6d65633752c490404513b9ef02475b4284c4cfab0ef946def50b3f59"},
+    {file = "scipy-1.13.1-cp311-cp311-win_amd64.whl", hash = "sha256:5713f62f781eebd8d597eb3f88b8bf9274e79eeabf63afb4a737abc6c84ad37b"},
+    {file = "scipy-1.13.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:5d72782f39716b2b3509cd7c33cdc08c96f2f4d2b06d51e52fb45a19ca0c86a1"},
+    {file = "scipy-1.13.1-cp312-cp312-macosx_12_0_arm64.whl", hash = "sha256:017367484ce5498445aade74b1d5ab377acdc65e27095155e448c88497755a5d"},
+    {file = "scipy-1.13.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:949ae67db5fa78a86e8fa644b9a6b07252f449dcf74247108c50e1d20d2b4627"},
+    {file = "scipy-1.13.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:de3ade0e53bc1f21358aa74ff4830235d716211d7d077e340c7349bc3542e884"},
+    {file = "scipy-1.13.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:2ac65fb503dad64218c228e2dc2d0a0193f7904747db43014645ae139c8fad16"},
+    {file = "scipy-1.13.1-cp312-cp312-win_amd64.whl", hash = "sha256:cdd7dacfb95fea358916410ec61bbc20440f7860333aee6d882bb8046264e949"},
+    {file = "scipy-1.13.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:436bbb42a94a8aeef855d755ce5a465479c721e9d684de76bf61a62e7c2b81d5"},
+    {file = "scipy-1.13.1-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:8335549ebbca860c52bf3d02f80784e91a004b71b059e3eea9678ba994796a24"},
+    {file = "scipy-1.13.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d533654b7d221a6a97304ab63c41c96473ff04459e404b83275b60aa8f4b7004"},
+    {file = "scipy-1.13.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:637e98dcf185ba7f8e663e122ebf908c4702420477ae52a04f9908707456ba4d"},
+    {file = "scipy-1.13.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:a014c2b3697bde71724244f63de2476925596c24285c7a637364761f8710891c"},
+    {file = "scipy-1.13.1-cp39-cp39-win_amd64.whl", hash = "sha256:392e4ec766654852c25ebad4f64e4e584cf19820b980bc04960bca0b0cd6eaa2"},
+    {file = "scipy-1.13.1.tar.gz", hash = "sha256:095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c"},
+]
+
+[package.dependencies]
+numpy = ">=1.22.4,<2.3"
+
+[package.extras]
+dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"]
+doc = ["jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.12.0)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0)", "sphinx-design (>=0.4.0)"]
+test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -825,4 +867,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "fac77b09117ba9cbfde590a664a4a3f90c57adf9f1c74427c572b04b4146aa74"
+content-hash = "9fe98bea4425784508fb9457af032039a3b0c241311d7a20dc44b4cb06014293"

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/pyproject.toml

@@ -19,7 +19,7 @@ features = ["pyo3/extension-module"]
 
 [tool.poetry]
 name = "in_silico_cancer_cell"
-version = "0.1.0"
+version = "0.2.0"
 description = "Electrophysiological model of an A549 cancer cell"
 authors = ["MrP01 <peter@waldert.at>"]
 license = "MIT"
@@ -33,6 +33,7 @@ numpy = "^1.26.4"
 [tool.poetry.group.dev.dependencies]
 ipython = "^8.23.0"
 pytest = "^8.1.1"
+scipy = "^1.13.1"
 
 [tool.ruff]
 line-length = 120

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/python/in_silico_cancer_cell/_in_rusty_silico.pyi

@@ -21,10 +21,8 @@ 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
 
@@ -38,6 +36,8 @@ 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

in_silico_cancer_cell-0.2.0/python/in_silico_cancer_cell/plot.py

@@ -0,0 +1,53 @@
+import pathlib
+
+import matplotlib.axes
+import matplotlib.pyplot as plt
+import numpy as np
+import scipy.optimize
+
+from in_silico_cancer_cell import CellPhase, ChannelCountsProblem, PatchClampData, PatchClampProtocol, setup_logging
+
+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="langthaler"):
+    measurements = PatchClampData.pyload(PatchClampProtocol.Activation, CellPhase.G0)
+    data = np.array(measurements.to_list()) + 22
+    problem = ChannelCountsProblem.new(measurements)
+    problem.precompute_single_channel_currents()
+    single_channels = np.array(problem.get_current_basis())
+    # single_channels = np.array(problem.get_current_basis())[:, (3,)]
+    # single_channels = np.concatenate([single_channels, np.ones((single_channels.shape[0], 1))], axis=1)
+    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 == "langthaler":
+        channel_counts = np.array([22, 78, 5, 1350, 40, 77, 19, 200, 17, 12, 13])
+    channel_counts = channel_counts.astype(int)
+    time = np.linspace(0, 9.901, single_channels.shape[0])
+    print(f"Best fit: {channel_counts}")
+
+    fig = plt.figure()
+    axes: matplotlib.axes.Axes = fig.add_subplot(1, 1, 1)
+    axes.plot(time[: len(data)], data)
+    axes.plot(time, (single_channels * channel_counts).sum(axis=1))
+    axes.set_xlabel("Time $t$ / s")
+    axes.set_ylabel("Current $I$ / nA")
+    fig.savefig(str(RESULTS / "data-vs-simulation.pdf"))
+
+
+def set_results_folder(path: pathlib.Path):
+    global RESULTS
+    RESULTS = path

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/cell.rs

@@ -43,48 +43,48 @@ pub type ChannelCounts = [u32; N_CHANNEL_TYPES];
 
 #[cfg_attr(feature = "pyo3", pyo3::pyclass)]
 pub struct A549CancerCell {
-  crac1_channel: channels::crac1::CRAC1IonChannelCat,
-  trpc6_channel: channels::trpc6::TRPC6IonChannelCat,
-  trpv3_channel: channels::trpv3::TRPV3IonChannelCat,
   kv13_channel: channels::kv13::KV13IonChannelCat,
   kv31_channel: channels::kv31::KV31IonChannelCat,
   kv34_channel: channels::kv34::KV34IonChannelCat,
   kv71_channel: channels::kv71::KV71IonChannelCat,
   kca11_channel: channels::kca11::KCa11IonChannelCat,
   kca31_channel: channels::kca31::KCa31IonChannelCat,
-  clc2_channel: channels::clc2::CLC2IonChannelCat,
   task1_channel: channels::task1::Task1IonChannelCat,
+  crac1_channel: channels::crac1::CRAC1IonChannelCat,
+  trpc6_channel: channels::trpc6::TRPC6IonChannelCat,
+  trpv3_channel: channels::trpv3::TRPV3IonChannelCat,
+  clc2_channel: channels::clc2::CLC2IonChannelCat,
 }
 
 impl A549CancerCell {
   pub fn channels(&self) -> Vec<&dyn IsChannel> {
     vec![
-      &self.crac1_channel,
-      &self.trpc6_channel,
-      &self.trpv3_channel,
       &self.kv13_channel,
       &self.kv31_channel,
       &self.kv34_channel,
       &self.kv71_channel,
       &self.kca11_channel,
       &self.kca31_channel,
-      &self.clc2_channel,
       &self.task1_channel,
+      &self.crac1_channel,
+      &self.trpc6_channel,
+      &self.trpv3_channel,
+      &self.clc2_channel,
     ]
   }
   pub fn channels_mut(&mut self) -> Vec<&mut dyn IsChannel> {
     vec![
-      &mut self.crac1_channel,
-      &mut self.trpc6_channel,
-      &mut self.trpv3_channel,
       &mut self.kv13_channel,
       &mut self.kv31_channel,
       &mut self.kv34_channel,
       &mut self.kv71_channel,
       &mut self.kca11_channel,
       &mut self.kca31_channel,
-      &mut self.clc2_channel,
       &mut self.task1_channel,
+      &mut self.crac1_channel,
+      &mut self.trpc6_channel,
+      &mut self.trpv3_channel,
+      &mut self.clc2_channel,
     ]
   }
 
@@ -190,32 +190,24 @@ impl A549CancerCell {
   #[cfg_attr(feature = "pyo3", staticmethod)]
   pub fn new() -> A549CancerCell {
     A549CancerCell {
-      crac1_channel: channels::crac1::CRAC1IonChannelCat::new(),
-      trpc6_channel: channels::trpc6::TRPC6IonChannelCat::new(),
-      trpv3_channel: channels::trpv3::TRPV3IonChannelCat::new(),
       kv13_channel: channels::kv13::KV13IonChannelCat::new(),
       kv31_channel: channels::kv31::KV31IonChannelCat::new(),
       kv34_channel: channels::kv34::KV34IonChannelCat::new(),
       kv71_channel: channels::kv71::KV71IonChannelCat::new(),
       kca11_channel: channels::kca11::KCa11IonChannelCat::new(),
       kca31_channel: channels::kca31::KCa31IonChannelCat::new(),
-      clc2_channel: channels::clc2::CLC2IonChannelCat::new(),
       task1_channel: channels::task1::Task1IonChannelCat::new(),
+      crac1_channel: channels::crac1::CRAC1IonChannelCat::new(),
+      trpc6_channel: channels::trpc6::TRPC6IonChannelCat::new(),
+      trpv3_channel: channels::trpv3::TRPV3IonChannelCat::new(),
+      clc2_channel: channels::clc2::CLC2IonChannelCat::new(),
     }
   }
 
   pub fn set_channel_counts(&mut self, counts: ChannelCounts) {
-    self.kv13_channel.n_channels = counts[0];
-    self.kv31_channel.n_channels = counts[1];
-    self.kv34_channel.n_channels = counts[2];
-    self.kv71_channel.n_channels = counts[3];
-    self.kca11_channel.n_channels = counts[4];
-    self.kca31_channel.n_channels = counts[5];
-    self.task1_channel.n_channels = counts[6];
-    self.crac1_channel.n_channels = counts[7];
-    self.trpc6_channel.n_channels = counts[8];
-    self.trpv3_channel.n_channels = counts[9];
-    self.clc2_channel.n_channels = counts[10];
+    for (channel, count) in self.channels_mut().iter_mut().zip(counts) {
+      channel.set_n_channels(count);
+    }
   }
 
   pub fn set_langthaler_et_al_channel_counts(&mut self, phase: CellPhase) {

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/base.rs

@@ -21,6 +21,7 @@ pub trait IsChannel {
   fn display_name(&self) -> String;
   fn display_me(&self) -> String;
   fn metadata(&self) -> ChannelMetadata;
+  fn set_n_channels(&mut self, n_channels: u32);
 }
 
 #[macro_export]
@@ -71,10 +72,13 @@ macro_rules! define_ion_channel {
       fn reset_state(&mut self) {
         self.state = Self::initial_state();
       }
+      fn set_n_channels(&mut self, n_channels: u32) {
+        self.n_channels = n_channels;
+      }
       fn single_channel_current(&self, voltage: f64) -> f64 {
         let mut open = 0.0;
         $(open += self.state[$states_responsible_for_current];)+
-        Self::conductance * open * (self.n_channels as f64) * (voltage - $crate::constants::reversal_potential($iontype))
+        Self::conductance * open * (voltage - $crate::constants::reversal_potential($iontype))
       }
       fn current(&self, voltage: f64) -> f64 {
         (self.n_channels as f64) * self.single_channel_current(voltage)

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/clc2.rs

@@ -10,7 +10,7 @@ define_ion_channel!(
   "CLC2",
   12,                // number of states
   IonType::Chlorine, // ion type
-  2.8e-3,            // conductance
+  2.8,               // conductance (pS)
   (3, 6, 7, 9, 11)   // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/crac1.rs

@@ -8,7 +8,7 @@ define_ion_channel!(
   "CRACM1",
   2,                // number of states
   IonType::Calcium, // ion type
-  24e-6,            // conductance
+  24e-3,            // conductance (pS)
   (1)               // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/kca11.rs

@@ -6,12 +6,13 @@ use crate::{
 
 pub type Matrix10<T> = nalgebra::Matrix<T, nalgebra::U10, nalgebra::U10, nalgebra::ArrayStorage<T, 10, 10>>;
 
+// TODO: channel current does not match paper
 define_ion_channel!(
   KCa11IonChannelCat,
   "KCa11",
   10,              // number of states
   IonType::Kalium, // ion type
-  250e-3,          // conductance
+  250.0,           // conductance (pS)
   (5, 6, 7, 8, 9)  // states which count towards the current
 );
 
@@ -67,7 +68,7 @@ impl HasTransitionMatrix<10> for KCa11IonChannelCat {
 
     #[rustfmt::skip]
     return Matrix10::from_row_slice(&[
-      1.0-4.0 * ca_i_dt - b, kc, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, a,
+      1.0 - 4.0 * ca_i_dt - b, kc, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, a,
       4.0 * ca_i_dt, 1.0- kc -3.0 * ca_i_dt - d, 2.0 * kc, 0.0, 0.0, 0.0, 0.0, 0.0, c, 0.0,
       0.0, 3.0 * ca_i_dt, 1.0-2.0 * kc -2.0 * ca_i_dt - f, 3.0 * kc, 0.0, 0.0, 0.0, e, 0.0, 0.0,
       0.0, 0.0, 2.0 * ca_i_dt, 1.0-3.0 * kc - ca_i_dt - h, 4.0 * kc, 0.0, g, 0.0, 0.0, 0.0,

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/kca31.rs

@@ -6,12 +6,13 @@ use crate::{
   define_ion_channel,
 };
 
+// TODO: channel current does not match paper
 define_ion_channel!(
   KCa31IonChannelCat,
   "KCa31",
   4,               // number of states
   IonType::Kalium, // ion type
-  11e-3,           // conductance
+  11.0,            // conductance (pS)
   (3)              // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/kv13.rs

@@ -7,7 +7,7 @@ define_ion_channel!(
   "Kv13",
   7,               // number of states
   IonType::Kalium, // ion type
-  15e-3,           // conductance
+  15.0,            // conductance (pS)
   (5)              // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/kv31.rs

@@ -8,7 +8,7 @@ define_ion_channel!(
   "Kv31",
   6,               // number of states
   IonType::Kalium, // ion type
-  40e-3,           // conductance
+  40.0,            // conductance (pS)
   (5)              // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/kv34.rs

@@ -10,7 +10,7 @@ define_ion_channel!(
   "Kv34",
   7,               // number of states
   IonType::Kalium, // ion type
-  14e-3,           // conductance
+  14.0,           // conductance (pS)
   (5)              // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/kv71.rs

@@ -11,7 +11,7 @@ define_ion_channel!(
   "Kv71",
   5,               // number of states
   IonType::Kalium, // ion type
-  3.2e-3,          // conductance
+  3.2,          // conductance (pS)
   (2, 3)           // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/task1.rs

@@ -11,7 +11,7 @@ define_ion_channel!(
   "Task1",
   3,               // number of states
   IonType::Kalium, // ion type
-  16e-3,           // conductance
+  16.0,           // conductance (pS)
   (2)              // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/trpc6.rs

@@ -8,7 +8,7 @@ define_ion_channel!(
   "TRPC6",
   1,                // number of states
   IonType::Calcium, // ion type
-  35e-3,            // conductance
+  35.0,            // conductance (pS)
   (0)               // states which count towards the current
 );
 

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/channels/trpv3.rs

@@ -6,10 +6,10 @@ use crate::{constants::IonType, define_ion_channel};
 define_ion_channel!(
   TRPV3IonChannelCat,
   "TRPV3",
-  1,                           // number of states
+  1,                // number of states
   IonType::Calcium, // ion type
-  48e-3,                       // conductance
-  (0)                          // states which count towards the current
+  48.0,             // conductance (pS)
+  (0)               // states which count towards the current
 );
 
 impl HasTransitionMatrix<1> for TRPV3IonChannelCat {

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/constants.rs

@@ -3,14 +3,15 @@
 pub const slowest_dt: f64 = 5e-7; // initial timestep
 pub const delta_tolerance: f64 = 1e-6; // how much of a change in \Delta state the system is aiming for (squared)
 pub const Ca_i: f64 = 0.0647e-6; // initial calcium concentration
-pub const F: f64 = 96485.3329; // As/mol
-pub const R: f64 = 8.3144598; // kgm^2/s^2molK
-pub const T: f64 = 293.0; // K, TODO: 20°C good?
+pub const F: f64 = 96485.3329; // Faraday-Constant [F] = As/mol
+pub const R: f64 = 8.3144598; // Gas-Constant [R] = kgm^2/s^2molK
+pub const T: f64 = 293.0; // Temperature [T] = K, TODO: 20°C good?
 
 pub enum IonType {
   Kalium,
   Calcium,
   Chlorine,
+  Sodium,
 }
 
 pub fn reversal_potential(ion: IonType) -> f64 {
@@ -18,5 +19,6 @@ pub fn reversal_potential(ion: IonType) -> f64 {
     IonType::Kalium => -77.4e-3,  // reversal potential K,
     IonType::Calcium => 95.6e-3,  // reversal potential Ca,
     IonType::Chlorine => -7.9e-3, // reversal potential Cl,
+    IonType::Sodium => -5000.0,   // TODO: reversal potential Na,
   }
 }

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/main.rs

@@ -57,7 +57,7 @@ fn save_to_json(measurements: PatchClampData, subsampling: Option<usize>) {
 #[command(
   about = "In-Silico Cancer Cell Model Simulator",
   author = "Peter Waldert <peter@waldert.at>",
-  version = "0.1.0"
+  version = "0.2.0"
 )]
 struct Cli {
   /// Turn debugging information on

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/optimisation.rs

@@ -96,9 +96,8 @@ impl ChannelCountsProblem {
   }
 
   #[cfg(feature = "pyo3")]
-  fn get_current_basis(slf: pyo3::PyRef<'_, Self>) -> pyo3::PyObject {
-    use pyo3::IntoPy;
-    let matrix = slf.current_basis.clone().unwrap();
+  fn get_current_basis(&self) -> Vec<Vec<f64>> {
+    let matrix = self.current_basis.clone().unwrap();
     let mut list_of_lists = Vec::new();
     for row in matrix.row_iter() {
       let mut row_vector = Vec::new();
@@ -107,7 +106,7 @@ impl ChannelCountsProblem {
       }
       list_of_lists.push(row_vector);
     }
-    list_of_lists.into_py(slf.py())
+    list_of_lists
   }
 
   fn solve_through_projection(&self) -> ChannelCounts {

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/patchclampdata.rs

@@ -84,9 +84,9 @@ impl PatchClampData {
     current = Some(current.unwrap() / (raw_data.len() as f64));
     match (&phase, &protocol) {
       (CellPhase::G0, PatchClampProtocol::Activation) => {
-        let scaled = current.unwrap() * 1e11;
+        let scaled = current.unwrap() * 1e12; // in pico-Ampere
         current = Some(DVector::from_vec(
-          scaled.iter().cloned().map(|x| x.max(-24.0)).collect::<Vec<f64>>(),
+          scaled.iter().cloned().map(|x| x.max(-240.0)).collect::<Vec<f64>>(),
         ));
       }
       _ => {}
@@ -114,6 +114,10 @@ impl PatchClampData {
     }
   }
 
+  pub fn to_list(&self) -> Vec<f64> {
+    self.current.iter().cloned().collect::<Vec<f64>>()
+  }
+
   #[cfg_attr(feature = "pyo3", staticmethod)]
   pub fn demo() -> PatchClampData {
     let mut c = DVector::zeros(100);

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.0}/src/utils.rs

@@ -17,10 +17,13 @@ fn get_log_level() -> log::LevelFilter {
 #[cfg_attr(feature = "pyo3", pyo3::pyfunction)]
 pub fn setup_logging() {
   let log_level = get_log_level();
+  let mut config_builder = simplelog::ConfigBuilder::new();
+  #[cfg(target_arch = "wasm32")]
+  config_builder.set_time_level(simplelog::LevelFilter::Off);
   simplelog::CombinedLogger::init(vec![
     simplelog::TermLogger::new(
       log_level,
-      simplelog::Config::default(),
+      config_builder.build(),
       simplelog::TerminalMode::Mixed,
       simplelog::ColorChoice::Auto,
     ),

in_silico_cancer_cell-0.1.0/python/in_silico_cancer_cell/plot.py

@@ -1,20 +0,0 @@
-import matplotlib.axes
-import matplotlib.pyplot as plt
-import pathlib
-
-RESULTS = pathlib.Path.cwd()
-
-
-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 set_results_folder(path: pathlib.Path):
-    global RESULTS
-    RESULTS = path