Tom/Gene-Regulatory-Networks-Seminar
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

fixed some bugs, added dockerfile for running on windows. output files must be extracted manually.

Browse Source
This commit is contained in:
Tom Zuidberg
2026-06-22 17:27:42 +02:00
parent b96e5f7e38
commit 8e0d2842af
4 changed files with 119 additions and 78 deletions
Download Patch File Download Diff File Expand all files Collapse all files

11
code/Dockerfile Normal file
View File

@@ -0,0 +1,11 @@
FROM python:3.14-slim
WORKDIR /app
COPY ./main.py /app
COPY ./simulator.py /app
COPY ./requirements.txt /app
RUN pip install -r requirements.txt
CMD ["python", "main.py"]

109
code/main.py
View File

@@ -2,8 +2,10 @@ from functools import partial
from types import FunctionType
from typing import Callable, Optional
import numpy as np
from simple_term_menu import TerminalMenu
from simulator import BooleanNetwork
from typing_extensions import Concatenate
def ShowMenu(options: list[str], title: str = "", highlight_entry: int = 0) -> int:
@@ -22,8 +24,9 @@ def ShowMenu(options: list[str], title: str = "", highlight_entry: int = 0) -> i
return selectedIndex # pyright: ignore[reportReturnType]
def Continue() -> None:
ShowMenu(options=[None, "Continue"])
def Continue(title="") -> None:
ShowMenu(title=title, options=[None, "Continue"], highlight_entry=1)
print()
# def MainMenu() -> None:
@@ -47,70 +50,56 @@ def MainMenu() -> None:
def SelectExampleMenu() -> None:
def bn4nodeSync() -> None:
bn = (
BooleanNetwork(4)
.UseSynchronousScheme()
.SetFunctions(
[
functions = [
lambda x1, x2, x3, x4: not x2,
lambda x1, x2, x3, x4: x1,
lambda x1, x2, x3, x4: x1 ^ x4,
lambda x1, x2, x3, x4: x3,
]
)
)
bn = BooleanNetwork(4).UseSynchronousScheme().SetFunctions(functions)
global currentFunction
funcStrings = ["not x2", "x1", "x1 ^ x4", "x3"]
currentFunction = partial(BooleanNetworkMenu, bn, funcStrings)
currentFunction = partial(BooleanNetworkMenu, bn, functions, funcStrings)
def bn4nodeSeq() -> None:
functions = [
lambda x1, x2, x3, x4: not x2,
lambda x1, x2, x3, x4: x1,
lambda x1, x2, x3, x4: x1 ^ x4,
lambda x1, x2, x3, x4: x3,
]
bn = (
BooleanNetwork(4)
.UseSequentialScheme([1, 2, 3, 4])
.SetFunctions(
[
lambda x1, x2, x3, x4: not x2,
lambda x1, x2, x3, x4: x1,
lambda x1, x2, x3, x4: x1 ^ x4,
lambda x1, x2, x3, x4: x3,
]
)
.SetFunctions(functions)
)
global currentFunction
funcStrings = ["not x2", "x1", "x1 ^ x4", "x3"]
currentFunction = partial(BooleanNetworkMenu, bn, funcStrings)
currentFunction = partial(BooleanNetworkMenu, bn, functions, funcStrings)
def bn3nodeSync() -> None:
bn = (
BooleanNetwork(3)
.UseSynchronousScheme()
.SetFunctions(
[
functions = [
lambda x1, x2, x3: not x3,
lambda x1, x2, x3: not x1,
lambda x1, x2, x3: not x2,
]
)
)
bn = BooleanNetwork(3).UseSynchronousScheme().SetFunctions(functions)
global currentFunction
funcStrings = ["not x3", "not x1", "not x2"]
currentFunction = partial(BooleanNetworkMenu, bn, funcStrings)
currentFunction = partial(BooleanNetworkMenu, bn, functions, funcStrings)
def bn3nodeSeq() -> None:
bn = (
BooleanNetwork(3)
.UseSequentialScheme([1, 2, 3])
.SetFunctions(
[
functions = [
lambda x1, x2, x3: not x3,
lambda x1, x2, x3: not x1,
lambda x1, x2, x3: not x2,
]
)
bn = (
BooleanNetwork(3).UseSequentialScheme([1, 2, 3]).SetFunctions(functions)
)
global currentFunction
funcStrings = ["not x3", "not x1", "not x2"]
currentFunction = partial(BooleanNetworkMenu, bn, funcStrings)
currentFunction = partial(BooleanNetworkMenu, bn, functions, funcStrings)
def ReturnHelper() -> None:
global currentFunction
@@ -148,22 +137,23 @@ def MainMenu() -> None:
def BooleanNetworkMenu(
bn: Optional[BooleanNetwork] = None, funcStrings: Optional[list[str]] = None
bn: Optional[BooleanNetwork] = None,
funcs: Optional[list[Callable[Concatenate[bool, ...], bool]]] = None,
funcStrings: Optional[list[str]] = None,
) -> None:
global currentFunction
boolNetwork: BooleanNetwork = BooleanNetwork(3)
verbose: bool = False
writeToFile: bool = False
done: bool = False
functions: list = [None for _ in range(3)]
functionStrings: list = [None for _ in range(3)]
functionsDirtyFlag = False
current_highlight = 0
if bn is not None and funcStrings is not None:
if bn is not None and funcStrings is not None and funcs is not None:
boolNetwork = bn
verbose = False
functions = [None for _ in range(3)]
functions = funcs
functionStrings = funcStrings
def Menu() -> None:
@@ -178,10 +168,11 @@ def BooleanNetworkMenu(
for i in range(1, boolNetwork.size + 1)
],
None,
f"Toggle verbose update: (current: {verbose})",
"Update once",
"Update once (hold ENTER for continuous updates)",
"Update multiple times",
"Get stationairy distribution",
f"Write to file (works only with multi-update) (current: {writeToFile})",
"Get Markov-Chain matrix (resets timeStep and state)",
"Get stationairy distribution (resets timeStep and state)",
None,
"Return to main menu",
]
@@ -192,14 +183,19 @@ def BooleanNetworkMenu(
SetUpdateSchemeHelper,
*[partial(SetFunctionHelper, i) for i in range(boolNetwork.size)],
None,
ToggleVerboseHelper,
UpdateHelper,
MultiUpdateHelper,
ToggleWriteToFileHelper,
GetMarkovChainHelper,
GetStableDistrHelper,
None,
ReturnHelper,
]
if boolNetwork.updateScheme in ("synchronous", "sequential", None):
options.pop(-3)
actions.pop(-3)
selectedIndex = ShowMenu(
options=options, title=title, highlight_entry=current_highlight
)
@@ -235,7 +231,6 @@ def BooleanNetworkMenu(
return
try:
boolNetwork.SetState(state)
return
except AssertionError as e:
print("Invalid input:", e)
@@ -310,7 +305,7 @@ def BooleanNetworkMenu(
print("Error while simulating once:", e)
def MultiUpdateHelper() -> None:
nonlocal boolNetwork, verbose, functions, functionsDirtyFlag
nonlocal boolNetwork, writeToFile, functions, functionsDirtyFlag
if functionsDirtyFlag:
try:
boolNetwork.SetFunctions(functions)
@@ -335,17 +330,23 @@ def BooleanNetworkMenu(
except ValueError:
print("Invalid input")
try:
boolNetwork.Update(n, verbose=verbose)
if verbose:
Continue()
print("\n")
boolNetwork.Update(
n, verbose=not writeToFile or n < 1000, writeToFile=writeToFile
)
Continue("Writing to file completed") if writeToFile else Continue()
except Exception as e:
print("Error while simulating:", e)
def GetMarkovChainHelper() -> None:
nonlocal boolNetwork
print(boolNetwork.GetTransitionMatrix())
Continue()
boolNetwork.SetState([False for _ in range(boolNetwork.size)])
def GetStableDistrHelper() -> None:
print(boolNetwork.GetStableProbabilityDistribution())
Continue()
print("\n")
boolNetwork.SetState([False for _ in range(boolNetwork.size)])
def SetFunctionHelper(index: int) -> None:
nonlocal boolNetwork, functions, functionStrings, functionsDirtyFlag
@@ -374,9 +375,9 @@ def BooleanNetworkMenu(
except Exception as e:
print("Error while parsing function:", e)
def ToggleVerboseHelper():
nonlocal verbose
verbose = not verbose
def ToggleWriteToFileHelper():
nonlocal writeToFile
writeToFile = not writeToFile
def ReturnHelper():
nonlocal done
@@ -391,7 +392,7 @@ def BooleanNetworkMenu(
def main() -> None:
global currentFunction
currentFunction = MainMenu
np.set_printoptions(precision=4, linewidth=300, sign=" ")
while True:
currentFunction()

1
code/requirements.txt
View File

@@ -1,3 +1,4 @@
scipy
numpy
simple-term-menu
typing_extensions

44
code/simulator.py
View File

@@ -171,6 +171,7 @@ class BooleanNetwork:
if type(state) is str:
for i in range(self.size):
self.nodes[i] = bool(int(state[i]))
self.time_step = 0
return self
if isinstance(state, (list, tuple)):
@@ -178,19 +179,23 @@ class BooleanNetwork:
f"SetState error: given state list contains elements of type different from bool. All elements must be bools. got {state}"
)
self.nodes = list(state).copy()
self.time_step = 0
return self
raise Exception(
"SetState error: end of function reached. given state is not of type string nor list[bool]."
)
def Update(self, n: int = 1, /, verbose=False) -> None:
def Update(
self, n: int = 1, /, verbose: bool = False, writeToFile: bool = False
) -> None:
assert type(n) is int and n >= 0, (
f"Update error: amount of updates must be an integer and positive. got {n=}"
)
assert self.__has_update_functions, "Update error: no update functions defined"
assert self.__has_update_scheme, "Update error: no update scheme defined"
assert type(verbose) is bool, "Update error: verbose must be a bool"
assert type(writeToFile) is bool, "Update error: writeToFile must be a bool"
selected_update: Callable
@@ -208,10 +213,28 @@ class BooleanNetwork:
case _:
raise Exception("Update error: update scheme selection went wrong")
match (verbose, writeToFile):
case (False, False):
for _ in range(n):
selected_update()
self.time_step += 1
if verbose:
case (False, True):
with open("output.txt", "w") as f:
for _ in range(n):
selected_update()
self.time_step += 1
f.writelines([self.state, "\n"])
case (True, False):
for _ in range(n):
selected_update()
self.time_step += 1
print(self)
case (True, True):
with open("output.txt", "w") as f:
for _ in range(n):
selected_update()
self.time_step += 1
f.writelines([self.state, "\n"])
print(self)
def __str__(self) -> str:
@@ -222,13 +245,18 @@ class BooleanNetwork:
return "".join(str(int(node)) for node in self.nodes)
def GetStableProbabilityDistribution(self) -> np.ndarray:
matrix: np.ndarray = self.__get_transition_matrix()
eigenvalues, eigenvectors = scipy.linalg.eig(matrix.T)
stationary_vector = np.real(eigenvectors[:, np.isclose(eigenvalues, 1)])
stationary_distribution = stationary_vector / np.sum(stationary_vector)
return stationary_distribution.flatten()
matrix: np.ndarray = self.GetTransitionMatrix()
def __get_transition_matrix(self) -> np.ndarray:
eigenvalues, eigenvectors = scipy.linalg.eig(matrix.T)
idx = np.argmin(np.abs(eigenvalues - 1.0))
pi = eigenvectors[:, idx].real
pi = pi / pi.sum()
return pi
def GetTransitionMatrix(self) -> np.ndarray:
dimension = 2**self.size
matrix: np.ndarray = np.zeros((dimension, dimension))