Add files via upload

Chemostat

Chemostat.py

@@ -0,0 +1,123 @@
+#!/usr/bin/python
+import sys
+import matplotlib.pyplot as plt
+
+
+
+class Chemostat(object):
+    def __init__(self, strain1_vmax, strain1_km, strain1_yield, strain1_starting, strain2_vmax,
+              strain2_km, strain2_yield, strain2_starting):
+        # strain 1
+        self.strain1_vmax = strain1_vmax
+        self.strain1_km = strain1_km
+        self.strain1_yield = strain1_yield
+        self.strain1_starting = strain1_starting
+
+        # strain 2
+        self.strain2_vmax = strain2_vmax
+        self.strain2_km = strain2_km
+        self.strain2_yield = strain2_yield
+        self.strain2_starting = strain2_starting
+
+        self.plot_minutes = []
+        self.plot_prop = []
+
+    def set_start_conditions(self, flow_rate, volume, endtime, substrate_media, substrate_init):
+        """
+        :param flow_rate:
+        :param volume:
+        :param endtime:
+        :param substrate_media:
+        :param substrate_init:
+        :return:
+        """
+        self.flow_rate = flow_rate
+        self.volume = volume
+        self.endtime = endtime
+        self.substrate_media = substrate_media
+        self.substrate_init = substrate_init
+        self.dilution = flow_rate/volume
+
+    def set_parameter(self):
+        """
+        Set initial parameters
+        :return:
+        """
+        self.parameters = list()
+        self.parameters = map(float, self.parameters)
+        return self.parameters
+
+
+
+###creating file for output
+
+    """def write_output(self):
+        
+        writes the results to output file
+        :return: output file
+        
+        prop_out = open("simulation_results.tsv","w")
+        prop_out.write("Time\tNutr\tStrain1\tStrain2\tProp")"""
+
+#substrate = self.substrate_init
+#strain1 = self.strain1_starting
+#strain2 = self.strain2_starting
+    def simulation(self):
+        """
+        Looping through the simulation
+        :return:
+        """
+        for minutes in range(0, self.endtime):
+            if minutes < 10000:
+                #calculating the change in nutrients
+                nutr_flux = self.dilution*(self.substrate_media-self.substrate_init) - (self.strain1_starting/self.strain1_yield)*\
+                            ((self.strain1_vmax*self.substrate_init)/(self.strain1_km+self.substrate_init))
+                strain1_flux = ((self.strain1_vmax*self.substrate_init)/(self.strain1_km+self.substrate_init)-self.dilution)*self.strain1_yield
+
+                #recalculating substrate and strain1 count
+                substrate = self.substrate_init+nutr_flux
+                strain1 = self.strain1_yield+strain1_flux
+
+                if str(int(minutes)/int(250)).isdigit() == True:
+
+                    self.plot_minutes.append(minutes)
+                    #print(plot_minutes)
+                    self.plot_prop.append(0)
+
+                    print(str(minutes) + "\t" + str(substrate) + "\t" + str(strain1) + "\t" + "0" + "\t0\n")
+            if minutes >= 10000:
+                #calculating the change in nutrients after 2 strains
+                nutr_flux = self.dilution*(self.substrate_media-self.substrate_init) - \
+                            (self.strain1_starting/self.strain1_yield)*\
+                            ((self.strain1_vmax*self.substrate_init)/(self.strain1_km+self.substrate_init)) - \
+                            (self.strain2_starting/self.strain2_yield)*\
+                            ((self.strain2_vmax*self.substrate_init)/(self.strain2_km+self.substrate_init))
+                strain1_flux = ((self.strain1_vmax*self.substrate_init)/(self.strain1_km+self.substrate_init)-self.dilution)*self.strain1_starting
+                strain2_flux = ((self.strain2_vmax*self.substrate_init)/(self.strain2_km+self.substrate_init)-self.dilution)*self.strain2_starting
+
+            #recalculating substrate and strain1 count
+                substrate = self.substrate_init+nutr_flux
+                strain1 = self.strain1_starting+strain1_flux
+                strain2 = self.strain2_starting+strain2_flux
+                if str(minutes/250).isdigit() == True:
+                    proportion = strain2/(strain1+strain2)
+                    print((str(minutes) + "\t" + str(substrate) + "\t" + str(strain1) + "\t" + str(strain2) + "\t" + str(proportion) + "\n"))
+                    self.plot_minutes.append(minutes)
+                    self.plot_prop.append(proportion)
+            print(self.plot_minutes, self.plot_prop)
+            #self.write_output.close()
+            #plt.plot(plot_minutes, plot_prop, color='black')
+            #plt.show()
+
+    def plot_min_vs_proportion(self, filename = 'minutes_vs_proportion.png', plot_capacity=False):
+        """
+        Plot minutes vs proportion
+        """
+        '''Plot minutes vs proportion'''
+        fig1 = plt.figure()
+        ax1 = fig1.add_subplot(111)
+        ax1.set_xlabel("Minutes", fontsize=22)
+        ax1.set_ylabel("Proportion", fontsize=22)
+        ax1.plot(self.plot_minutes,self.plot_prop, color='black')
+        plt.show()
+        fig1.savefig(filename,dpi=300)

Chemostat_test.py

@@ -0,0 +1,20 @@
+from Chemostat import Chemostat
+strain1_vmax = 0.0030
+strain1_km = 481.26
+strain1_yield = 0.396345
+strain1_starting = 0.14
+strain2_vmax = 0.0024
+strain2_km = 751.19
+strain2_yield = 0.3963745
+strain2_starting = 0.001
+flow_rate = 0.00000347
+volume = 0.010
+endtime = 100000
+substrate_media = 2200
+substrate_init = 1100
+
+chemo = Chemostat(strain1_vmax, strain1_km, strain1_yield, strain1_starting, strain2_vmax, strain2_km, strain2_yield, strain2_starting)
+chemo.set_start_conditions(flow_rate, volume, endtime, substrate_media, substrate_init)
+chemo.simulation()
+chemo.plot_min_vs_proportion()
+