Upload New File

Ex_3_1.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue May  2 22:26:53 2023
+
+@author: delvigne
+"""
+
+'''
+Exercice 3.1
+Analysis the adjacency martrix for three different systems
+'''
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pandas as pd
+
+'''
+System 1: 30 RPAs in series to model a plug-flow reactor
+'''
+n= 30 # number of CSTRs or RPAs in series
+a = np.ones(n)
+d1 = np.diag(a)
+
+b = np.ones(n-1)
+d2 = np.diag(b,-1)
+
+M2 = d1+d2
+
+plt.spy(M2)
+plt.show()
+
+'''
+System 2: 100 thermodynamic stages for modelling a S-L extractor
+'''
+n= 100 # number of extraction stages/thermodynamic equilibrium
+a = np.ones(n)
+d1 = np.diag(a)
+
+b = np.ones(n-1)
+d2 = np.diag(b,-1)
+
+c = np.ones(n-1)
+d3 = np.diag(c,1)
+
+M3 = d1+d2+d3
+
+plt.spy(M3)
+plt.show()
+
+'''
+System 3: 100 proteins for modelling the rpoS response in E. coli
+You need the file string_interactions_short_rpoS.xlsx
+'''
+
+df = pd.read_excel("string_interactions_short_rpoS.xlsx")
+node1 = df['#node1']
+node2 = df['node2']        
+
+adj_mat = pd.crosstab(df["#node1"], df["node2"], dropna=False)
+A = adj_mat.transpose() + adj_mat > 0
+
+plt.spy(A)
+plt.show()