Smulation of Biol 3415/Chem 3515 Experiment 4, part B

Biol 3515-Chem 3515 Exp 4, part B

Gist Title

code_dict_exp4b.py

code_dict = {'0GXY02':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.0780933743000794e-05,'kcat':12.479059780623182,'km':8.563436439963315e-05,'ki':1.2818504047186639e-05,'i_type':'n','k2aebsf':2.770090118806899},
'DD0371':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.943933934989462e-05,'kcat':9.174417463278722,'km':4.777372487256253e-05,'ki':2.0921044815624033e-05,'i_type':'n','k2aebsf':3.0756264469580783},
'X5FX87':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.95266826439055e-05,'kcat':11.789268600290177,'km':5.58468122174051e-05,'ki':3.1855951319526476e-05,'i_type':'u','k2aebsf':2.0458927928518547},
'FG188G':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.285031188273903e-05,'kcat':13.047612493354922,'km':7.177787853319616e-05,'ki':2.2387336355080515e-05,'i_type':'c','k2aebsf':2.5569285418417063},
'34P10Q':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.722682984532362e-05,'kcat':8.145189509187809,'km':6.57837365279514e-05,'ki':2.4766261675168723e-05,'i_type':'u','k2aebsf':3.7500007792456365},
'Y4N6KZ':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.8906484201970237e-05,'kcat':13.614464085817126,'km':5.4379228053721865e-05,'ki':2.8526273760851988e-05,'i_type':'n','k2aebsf':2.373916885321159},
'W5XM03':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.9115719982294164e-05,'kcat':10.075765236194103,'km':3.320531258425417e-05,'ki':1.788466321473838e-05,'i_type':'u','k2aebsf':3.951721032682042},
'9V51PV':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.2972895706886008e-05,'kcat':14.253426350877806,'km':8.949671739010028e-05,'ki':2.242595915972425e-05,'i_type':'u','k2aebsf':2.9026754774137578},
'942913':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.0249547380195524e-05,'kcat':11.135081432311162,'km':7.07376899404837e-05,'ki':1.530979579819587e-05,'i_type':'n','k2aebsf':2.419878129417387},
'N898UN':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.8674877368836247e-05,'kcat':10.097357504977413,'km':6.59893141525897e-05,'ki':1.6104691193010986e-05,'i_type':'c','k2aebsf':3.7578493435838753},
'H4CGP6':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.4074717025273083e-05,'kcat':10.86527728039156,'km':4.0295083099196564e-05,'ki':1.8838579326954804e-05,'i_type':'u','k2aebsf':2.5753654110654987},
'13KE9N':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.0654600749048573e-05,'kcat':14.476740111724716,'km':4.664199652900124e-05,'ki':3.565278871613589e-05,'i_type':'c','k2aebsf':2.416169532527277},
'31PQ53':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.264345369791618e-05,'kcat':6.560328970813622,'km':3.930321207228756e-05,'ki':1.7996658903832847e-05,'i_type':'c','k2aebsf':3.027494799911106},
'KK644G':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.9346499463477278e-05,'kcat':8.322469408595582,'km':4.5568979770163385e-05,'ki':2.786600023760229e-05,'i_type':'n','k2aebsf':3.8406155198096887},
'2TNA45':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.9246819164209123e-05,'kcat':5.953190657380047,'km':3.994947194229087e-05,'ki':3.118850349923123e-05,'i_type':'n','k2aebsf':3.3292057548084224},
'N6AADQ':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.8630368266346355e-05,'kcat':8.425285215458262,'km':8.304450919324063e-05,'ki':3.275462952212665e-05,'i_type':'n','k2aebsf':2.043910942913139},
'SV22HX':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.7310317193021016e-05,'kcat':11.54988636685996,'km':5.4691251633663635e-05,'ki':1.4258000433727466e-05,'i_type':'n','k2aebsf':2.7928271592636262},
'VS8S0J':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.1921188687159537e-05,'kcat':11.169575003686369,'km':6.197424343338799e-05,'ki':3.4772457082954824e-05,'i_type':'u','k2aebsf':2.896016126282032},
'4U2RCD':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.876088862624062e-05,'kcat':11.746442846771568,'km':5.739471754772193e-05,'ki':2.7617474463042558e-05,'i_type':'n','k2aebsf':2.6015673358114046},
'ZCRTWU':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.9224581361271966e-05,'kcat':5.076806311887225,'km':3.228842227365505e-05,'ki':2.641539836528339e-05,'i_type':'n','k2aebsf':2.082179293635174},
'7182Y1':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.47216027558941e-05,'kcat':8.241979108276192,'km':6.0074402918688364e-05,'ki':2.9141558444201385e-05,'i_type':'c','k2aebsf':2.763782291732746},
'W8Y4P3':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.7782485501855382e-05,'kcat':10.195874314801054,'km':3.488329626913995e-05,'ki':2.6688208538208135e-05,'i_type':'u','k2aebsf':3.3156359342254533},
'J9PWB4':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.475736161044849e-05,'kcat':6.754889828781962,'km':8.773579280310646e-05,'ki':3.7817954389229254e-05,'i_type':'u','k2aebsf':3.2475775452027933},
'43479S':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.6621708935755493e-05,'kcat':13.144983394351692,'km':5.9336652102587744e-05,'ki':1.2109968155410305e-05,'i_type':'c','k2aebsf':2.101901970702785},
'MYX1AX':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.6766972738830726e-05,'kcat':12.914367456489144,'km':4.940114234055595e-05,'ki':2.3969134784314207e-05,'i_type':'c','k2aebsf':2.426506564801504},
'S0E0YV':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.7032357040088922e-05,'kcat':10.957824559421038,'km':3.289894725028064e-05,'ki':3.7799881099811013e-05,'i_type':'u','k2aebsf':2.317476189522253},
'DFKPU9':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.723282359923739e-05,'kcat':7.466998500516203,'km':6.51627417368447e-05,'ki':3.141311275224014e-05,'i_type':'n','k2aebsf':2.12220666540577},
'9RFXYW':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.5000509553011084e-05,'kcat':6.705684564747556,'km':5.8051980187978164e-05,'ki':3.193666437729011e-05,'i_type':'n','k2aebsf':2.321114542381777},
'88PTV8':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.4524217499362522e-05,'kcat':5.011219927285401,'km':8.251030817940819e-05,'ki':3.075851375645226e-05,'i_type':'n','k2aebsf':3.4749436702803305},
'H0X54M':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.4139816960349272e-05,'kcat':6.589695629876994,'km':6.600131868852241e-05,'ki':1.31444625377903e-05,'i_type':'u','k2aebsf':2.557925418572501},
'KD1K2N':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.7172667254962533e-05,'kcat':10.800375363792174,'km':4.161401188579533e-05,'ki':1.6146814125369517e-05,'i_type':'n','k2aebsf':3.8487277594720775},
'23W0N6':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.922648717519026e-05,'kcat':10.434092819204855,'km':8.777019172064786e-05,'ki':3.765713498947328e-05,'i_type':'n','k2aebsf':3.5945905424214617},
'GQ5P11':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.7288023178577137e-05,'kcat':8.027464722293182,'km':8.77400879268201e-05,'ki':3.871522144226405e-05,'i_type':'c','k2aebsf':2.865635423999882},
'597J70':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.912745303888913e-05,'kcat':10.458568211196791,'km':4.246737812426825e-05,'ki':2.2091709053964623e-05,'i_type':'c','k2aebsf':2.8561055227197865},
'77YE98':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.6706669601780035e-05,'kcat':7.330432197837356,'km':8.891603561232728e-05,'ki':2.385063694003913e-05,'i_type':'n','k2aebsf':3.149992146329768},
'994A4U':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.8895005256200494e-05,'kcat':5.174640178640072,'km':5.320770050272746e-05,'ki':3.484928283677721e-05,'i_type':'c','k2aebsf':3.3935777441032755},
'22NZ8S':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.1267935215025052e-05,'kcat':9.340617525524213,'km':8.084998120581375e-05,'ki':1.9846990411649675e-05,'i_type':'c','k2aebsf':3.977405526302869},
'33VZHV':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.588140524849908e-05,'kcat':11.929996897914258,'km':4.824483178683697e-05,'ki':1.7953941761962762e-05,'i_type':'n','k2aebsf':3.1173189298940516},
'YD34E7':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.1705054520364497e-05,'kcat':10.27610221982453,'km':3.781178868193927e-05,'ki':3.679368703360593e-05,'i_type':'u','k2aebsf':3.643297534636481},
'B4EV54':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.0354460994888705e-05,'kcat':7.021725135847429,'km':5.7035565773548506e-05,'ki':3.4492201250642305e-05,'i_type':'c','k2aebsf':2.080642313124938},
'QXQEA0':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.3323423105185772e-05,'kcat':6.929654495543255,'km':3.181108783085965e-05,'ki':1.329762648384744e-05,'i_type':'u','k2aebsf':3.8249402421942125},
'RCE9Z2':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.01296550430366e-05,'kcat':13.410636428482128,'km':6.436577355205234e-05,'ki':2.9553712571334308e-05,'i_type':'u','k2aebsf':3.867029011846259},
'W382SW':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.774481028180708e-05,'kcat':12.769638907644534,'km':7.359061292718445e-05,'ki':2.857701690770212e-05,'i_type':'c','k2aebsf':2.1432721546280664},
'Y1UUUA':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.0828543359469805e-05,'kcat':6.72929920464161,'km':8.86483930276227e-05,'ki':2.8642829571428845e-05,'i_type':'n','k2aebsf':2.4690982070117036},
'240125':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.7918021956761915e-05,'kcat':5.844744273832838,'km':4.588117735847368e-05,'ki':1.1957994609795895e-05,'i_type':'u','k2aebsf':3.4201212841230206},
'0P20E8':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.9706742739803737e-05,'kcat':11.3167024699186,'km':8.655867671649303e-05,'ki':3.677451188680347e-05,'i_type':'c','k2aebsf':3.2511311962353737},
'CTZKSB':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.6678519754892104e-05,'kcat':14.698116904941546,'km':7.633417818129455e-05,'ki':2.3006367565448628e-05,'i_type':'n','k2aebsf':2.3344780449502913},
'K60820':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.7891470882886813e-05,'kcat':5.1724040679813585,'km':8.540103081102389e-05,'ki':1.5968880094004856e-05,'i_type':'u','k2aebsf':3.4364501187667256},
'WE21H5':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':1.8244941876266545e-05,'kcat':9.019636410141747,'km':8.204223957035615e-05,'ki':2.1798577252831622e-05,'i_type':'n','k2aebsf':3.8098962164574193},
'N180MF':{'pip_sigma':0.015,'abs_sigma':0.001,'e_conc':2.3419204687993863e-05,'kcat':7.10770397148994,'km':5.528682797277228e-05,'ki':1.8279751160378784e-05,'i_type':'u','k2aebsf':2.1463055653327103}}

environment.yml

name: exp_4b_sim
channels:
  - conda-forge
  - defaults
  - conda-forge/label/broken
dependencies:
  - python=3.8.3
  - numpy=1.19.2
  - scipy = 1.5.2
  - matplotlib=3.3.2
  - ipython=7.19.0
  - ipywidgets=7.5.1
  - voila=0.2.6

exp4b_sim.ipynb

exp4b_sim.py

## Module for import into Jupyter for simulation of Experiment 4, part B
## Irreversible inhibition of trypsin by AEBSF
## in Biology 3515/Chem 3515 at the University of Utah, Spring 2021
## https://goldenberg.biology.utah.edu/courses/biol3515/
## David P. Goldenberg, January 2021
## goldenberg@biology.utah.edu

import random as rand
import numpy as np
import matplotlib.pyplot as plt
import ipywidgets as widgets
from IPython.display import display, HTML


from time import sleep, time
import threading
from scipy.integrate import solve_ivp
import functools
from scipy.stats import linregress



from code_dict_exp4b import code_dict
codes = list(code_dict)

display(HTML("<style>div.output_scroll { height: 600ex; }</style>"))
##----------Global Parameters--------------------##
 # delay time while filling the absorbance table
 # Use 0 for testing and 0.2 for production to make the simulation run about
 # 5-x the actual speed. 
t_sleep = 0.2
# initial values of absorbance reading and background absorbance
abs_read = 0.0 
zero_set= 0.0



# Total time and number of steps for abs reading to settle
t_tot = 2
steps = 25
# Title for graph
graph_title = 'Experiment 4, Part B'
style = {'description_width': 'initial'}


##----------------Classes----------------------##

class Tube():
    '''Tube class for putting stuff in'''
    def __init__(self,vol=0.0,vol_n=0,max_vol=1.0,conc={}):
        self.vol = vol # actual volume
        self.vol_n= vol_n # nominal volume, reflecting pipette settings, vs actual delivered volumes
        self.max_vol = max_vol # max volume of tube
        self.conc = conc # concentrations of compounds
        

class Cuvette():
    '''Cuvette class, like Tube but with additional 
    attributes for sample name and reactions start time, t0'''
    def __init__(self):
        self.vol = 0.0
        self.vol_n = 0.0
        self.conc = {}
        self.t0 =0.0

class VolTable(widgets.HTML):
    def __init__(self,tube_dict,head):
        super().__init__(
        value='',
        layout=widgets.Layout(width='250px'))
        self.tube_dict = tube_dict
        self.head = head
        
        self.update()

    def update(self):
        '''function to update the table of tube or cuvette volumes'''
        html_str = '''
        <style>
        table, th, td {
          border: 1px solid black;
        }
        th, td {
          padding: 5px;
        }
        table, {border-collapse: collapse;}
        </style>
        <table>
        <tr>'''
        html_str += f'<th style="width:100px"> {self.head} </th>'       
        html_str += '''<th style="width:100px"> Volume (&mu;L)</th></tr>'''

        for tube in self.tube_dict:
            vol = self.tube_dict[tube].vol_n
            html_str += f'<tr><td>{tube}</td><td>{vol:.0f} </td></tr>\n'
        html_str += '</table>'
        self.value=html_str

class AbsTable(widgets.HTML):
    
    def __init__(self,cuv_dict,t_int,t_tot):
        super().__init__(
            value='',
            layout=widgets.Layout(width='600px'))
        self.cuv_dict = cuv_dict
        self.t_int = t_int
        self.t_tot = t_tot
        self.abs_data = []        
        self.n_meas = int(t_tot/t_int)+1
        self.n_cuv = len(self.cuv_dict)
        
        self.refresh()
        self.update()
        
    def refresh(self):
        self.abs_data=[['Time (min)']]
        for cuv in self.cuv_dict:
            self.abs_data[0].append('Cuvette ' + str(cuv))
        for i in range(self.n_meas):
            t = i*self.t_int
            self.abs_data.append([t]+[None]*self.n_cuv)
        self.update()

    def update(self):
        html_str = '''
        <style>
        table, th, td {
          border: 1px solid black;
        }
        th, td {
          padding: 5px;
        }
        table, {border-collapse: collapse;}
        </style>
        <table>
        <tr>
        <th style="width:100px"> Time (min) </th>'''
        for i in range(self.n_cuv):
            html_str += f'<th style="width:100px"> {self.abs_data[0][i+1]} </th>'
        html_str += '</tr>\n'
        for i in range(self.n_meas):
            html_str += f'<tr><td> {self.abs_data[i+1][0]}</td>'
            for j in range(self.n_cuv):
                if self.abs_data[i+1][j+1] != None:
                    html_str += f'<td>{self.abs_data[i+1][j+1]:0.3f}</td>'
                else:
                    html_str += '<td></td>'
        html_str += '</tr>\n'
        html_str += '</table>'
        self.value=html_str

class RegTable(widgets.HTML):
    def __init__(self,reg_results):
        super().__init__(
        value='',
        layout=widgets.Layout(width='500px'))
        self.reg_results = reg_results      
        
        self.update()
        
    def update(self):
       
        '''function to update the table of results from linear regression'''
        n_cuv = len(self.reg_results)
        html_str = '''
        <style>
        table, th, td {
          border: 1px solid black;
        }
        th, td {
          padding: 5px;
        }
        table, {border-collapse: collapse;}
        </style>
        <table>
        <tr>'''
        html_str += '''<th style="width:100px"> Cuvette </th>'''
        html_str += '''<th style="width:100px"> Rate (min<sup>-1</sup>) </th>'''
        html_str += '''<th style="width:100px"> A<sub>0</sub> </th>'''
        html_str += '''<th style="width:100px"> R<sup>2</sup> </th></tr>'''

        for cuv in range(n_cuv):
            html_str += f'<tr><td> {cuv+1}</td>'
            slope = self.reg_results[cuv].slope
            html_str += f'<td>{slope:.4f}</td>'
            a0 = self.reg_results[cuv].intercept
            html_str += f'<td>{a0:.4f}</td>'
            rsq = self.reg_results[cuv].rvalue**2
            html_str += f'<td>{rsq:.3f}</td></tr>'
        html_str += '</table>'
        self.value=html_str

#

## --------------- Create Dictionaries ------------------##
# This has to come after the Tube and Cuvette classes are defined!  


tube_conc_dict = {'trypsin':0.0, 'hepes':0.0, 'cacl':0.0,'aebsf':0.0, 'substr':0.0,'benz':0.0}

cuv_conc_dict = {'trypsin':0.0, 'tris':0.0, 'cacl':0.0,'substr':0.0,'prod':0.0}


tube_dict ={}
for n in range(1,5):
    tube_dict[n] = Tube()
    tube_dict[n].conc = tube_conc_dict.copy()

cuv_dict = {}
for n in range(1,5):
    cuv_dict[n] = Cuvette()
    cuv_dict[n].conc = cuv_conc_dict.copy()
    

solns_dict1={} # used to store stock solution concentrations
# for reaction tubes
solns_dict1['trypsin'] =0.0
solns_dict1['cacl'] = 20.0*1e-3 # M
solns_dict1['aebsf'] = 5.0e-3
solns_dict1['substr'] = 2.0*1e-3 # M
solns_dict1['benz'] = 1.0e-3
solns_dict1['hepes'] = 0.2 # M

    
# for cuvettes
solns_dict2 = {}
solns_dict2['tris'] = 0.2  
solns_dict2['substr'] = 2.0*1e-3 # M


#########---------Widgets and Their Functions --------------########

##----------------Pipettes -----------------------##
# Used for multiple parts of experiment
# The deliver button is specific to each part
def on_pipette_ch(change):
    '''Function to changes volume parameters when pipette is changed.'''
    pip_vol.max = 1000.0
    if pipette.value == 1000.0:
        pip_vol.min = 200.0  
        pip_vol.max = 1000.0        
        pip_vol.step = 10.0
    elif pipette.value == 200.0:
        pip_vol.min = 20.0
        pip_vol.max = 200.0               
        pip_vol.step = 1.0
    elif pipette.value == 20.0:
        pip_vol.min = 1.0
        pip_vol.max = 20.0              
        pip_vol.step = 0.1
    pip_vol.value = pip_vol.max
    
pipette = widgets.Dropdown(
    # Choose pipette size
    options = [('P1000',1000.0),('P200',200.0),('P20',20.0)],
    description = 'Pipette:',
    style=style,
    layout=widgets.Layout(width='150px',margin='0px 0px 0px 50px')
    )
pipette.observe(on_pipette_ch,names=['value'])


pip_vol = widgets.BoundedFloatText(
    # Pipette volume setting
    value = 1000.0,
    min = 200.0,
    max = 1000.0,
    step = 10.0,
    description = 'Volume set (uL):',
    style = style,
    layout=widgets.Layout(width='200px',margin='0px 0px 0px 50px')
    )

def pip_deliver(soln_widget, soln_dict, tube_widget,tube_dict):
    
    tube_list = list(tube_dict)
    conc_list = list(tube_dict[tube_list[0]].conc)    
    pip_sigma = code_dict[lab_code.value]['pip_sigma']
    # get pipette err from normal distr
    err_pipette = pipette.value*rand.normalvariate(0,pip_sigma)
    
    # calculate delivered volume
    vol = pip_vol.value+err_pipette
    # save old volume and calculate new
    vol_old = tube_dict[tube_widget.value].vol
    vol_new = vol_old + vol

    tube_list = list(tube_dict)
    reag_list = list(tube_dict[tube_list[0]].conc)
    
    incr = {}
    for reag in reag_list:
        incr[reag]=0.0
    # calculate increment in solute amount (mg, moles,etc)
    for reag in reag_list:
        if reag == soln_widget.value:
            incr[reag] = vol*soln_dict[reag]
        
        if 'trypsin' == soln_widget.value:
            # special provision for trypsin solution conaining 20 mM CaCl2
            incr['cacl'] =vol*0.02
  
    # update concentrations
    for reag in reag_list:
        conc_old = tube_dict[tube_widget.value].conc[reag]       
        conc_new = (conc_old*vol_old + incr[reag])/vol_new      
        tube_dict[tube_widget.value].conc[reag] = conc_new
    
    #update volumes
    tube_dict[tube_widget.value].vol = vol_new
    tube_dict[tube_widget.value].vol_n += pip_vol.value
    
##----------------Lab Code Entry ------------------##

def on_code_ch(value):
    '''Respond to change in the code entered in the code box'''
    
    if lab_code.value != '' and lab_code.value not in codes:

        code_warn.value = '<span style="color:red;">Invalid code</span>'
    elif lab_code.value in codes:
    
        solns_dict1['trypsin']=code_dict[lab_code.value]['e_conc']/10
        
        code_warn.value =''

        deliver_butt1.button_style = 'success'
        deliver_butt1.description='Pipette!'
        deliver_butt2.button_style = 'success'
        deliver_butt2.description='Pipette!'

#         run_butt.button_style = 'success'
#         run_butt.description='Run!'
        
code_label = widgets.HTML(
    value = ''' <h3>Lab code: </h3>'''
    )

lab_code = widgets.Text(
    # text-entry widget to enter lab code
    value = '',
    placeholder='',
    #description = 'Lab code',
    layout=widgets.Layout(width='100px',margin='20px 0px 0px 15px')
    )
lab_code.observe(on_code_ch,names=['value'])   


code_warn = widgets.HTML(
    # warning when invalid lab code is entered
    value = '',
    layout=widgets.Layout(width='200px',margin='15px 50px 15px 0px')
    )
    
row_code = widgets.HBox([code_label,lab_code,code_warn])   




###-------------Reaction Tubes------------##

def deliver1(change):
    if lab_code.value not in codes:
        deliver_butt1.description='Enter valid lab code'
        deliver_butt1.button_style = 'warning'
        return
    pip_deliver(solns1_widget, solns_dict1, tubes_widget, tube_dict)
    tube_vol_table.update()

def empty1(change):
    tube = tube_dict[tubes_widget.value]

    for conc in tube.conc:
        tube.conc[conc]=0.0
    tube.vol = 0.0
    tube.vol_n = 0.0
    tube_vol_table.update()

solns1_widget = widgets.RadioButtons(
    # solutions for reaction tubes
    options=[('H2O','H2O'),('0.2 M HEPES, pH 8', 'hepes'),('20 mM CaCl2','cacl'),('5 mM AEBSF','aebsf'),('2 mM substrate','substr'),('1 mM benzamidine','benz'),('Trypsin','trypsin')],
    description='Solutions'
    )

empty_butt1 = widgets.Button(
    # button to empty tube for bsa dilution
    description = 'Empty',
    button_style = 'danger',
    )
empty_butt1.on_click(empty1)

tubes_widget=widgets.RadioButtons(
    # Tubes for BPTIf-trypsin incubation
    options=[1,2,3,4],
    description = 'Tubes:'
    )
tube_vol_table = VolTable(tube_dict,'Tube')


deliver_butt1 = widgets.Button(
    # Button to deliver volume for BSA dilution
    description = 'Pipette!',
    button_style = 'success',
    )
deliver_butt1.on_click(deliver1)

tubeVb=widgets.VBox([tubes_widget,empty_butt1],
                     layout=widgets.Layout(width='40%',margin='0px 0px 0px 00px'))

row_tubes = widgets.HBox([solns1_widget,tubeVb,tube_vol_table],
                    layout=widgets.Layout(margin='0px 0px 50px 00px'))
                    
row_pip1 = widgets.HBox([deliver_butt1,pipette,pip_vol])

box_rxn_tubes = widgets.VBox([row_tubes, row_pip1])


###---------------Start Reactions-------------------###


def irrev_de(t,y,k2,b_conc,b_ki,s_conc,km,kcat):
    '''Differential eqns for irreversible inhibition of
    trypsin by aebsf, with effects of substrate and benzamidine'''
    e_conc=y[0]
    i_conc=y[1]
    s_conc=y[2]
    if b_conc > 0.0:
        km = km*(1 + b_ki/b_conc)
    e_avail = e_conc/(1+b_conc/b_ki + s_conc/km)
    ds_conc = -e_conc*kcat*s_conc/(km + s_conc)
    de_conc = -k2*e_avail*i_conc
    di_conc = de_conc
    return [de_conc,di_conc,ds_conc]


rxn_kin_solns = []

def start_rxns(change):

    start_rxn_butt.disabled = True

    # kinetic parameters for reactions of trypsin with AEBSF
    # k2 for reaction with AEBSF
    k2 = code_dict[lab_code.value]['k2aebsf']
    # Ki for benzamidine
    b_ki = 5e-6 # M
    km = code_dict[lab_code.value]['km']
    # kcat for substrate under these conditions
    # inferred from the actual experiment, about 1/15 of value
    # under normal conditions
    kcat = code_dict[lab_code.value]['kcat']/15.0
    min_tot = 150
    sec_tot = min_tot*60
    pts = min_tot + 1
    for tube in tube_dict:
        e_conc = tube_dict[tube].conc['trypsin']
        i_conc = tube_dict[tube].conc['aebsf']
        b_conc = tube_dict[tube].conc['benz']
        s_conc = tube_dict[tube].conc['substr']
        soln = solve_ivp(irrev_de,[0.0,sec_tot],[e_conc,i_conc,s_conc],
                args=[k2,b_conc,b_ki,s_conc,km,kcat],
                method = 'Radau',t_eval=np.linspace(0.0,sec_tot,pts))
        rxn_kin_solns.append(soln)
    reset_rxn_butt.disabled = False
    deliver_butt3.disabled = False
        
def reset_rxns(change):
    global rxn_kin_solns
    rxn_kin_solns.clear()
    tube_reset(tube_dict)  
    tube_vol_table.update() 
    start_rxn_butt.disabled=False
    deliver_butt3.disabled = True
    reset_rxn_butt.disabled = True
    
    
start_rxn_butt = widgets.Button(
    # Button to start simulated kinetics run
    description = 'Start Reactions!',
    button_style = 'success',
    disabled = False,
    layout=widgets.Layout(margin='0px 0px 0px 0px')
    )
start_rxn_butt.on_click(start_rxns)

reset_rxn_butt = widgets.Button(
    # Button to start simulated kinetics run
    description = 'Reset Reactions',
    button_style = 'danger',
    disabled = True,
    layout=widgets.Layout(margin='0px 0px 0px 20px')
    )
reset_rxn_butt.on_click(reset_rxns)

row_rxn_butt = widgets.HBox([start_rxn_butt,reset_rxn_butt])


##----------------Cuvette Setup --------------------------##

def deliver2(change):
    if lab_code.value not in codes:
        deliver_butt2.description='Enter valid lab code'
        deliver_butt2.button_style = 'warning'
        return

    pip_deliver(solns_widget2, solns_dict2, cuv_widget, cuv_dict)
    c_trypsin = cuv_dict[cuv_widget.value].conc['trypsin']
    c_substr = cuv_dict[cuv_widget.value].conc['substr']
    if c_trypsin >0 and c_substr >0:
        cuv_dict[cuv_widget.value].t0 = time()
    cuv_vol_table.update()
    

def empty_cuv(change):
    cuv = cuv_dict[cuv_widget.value]
    for conc in cuv.conc:
        cuv.conc[conc]=0.0
    cuv.vol = 0.0
    cuv.vol_n = 0.0
    cuv.t0=0.0
    cuv_vol_table.update()

solns_widget2 = widgets.RadioButtons(
    # solutions for cuvettes for part A
    options =[('H20','H2O'), ('0.2 M Tris-Cl, pH 8','tris'),
         ('2 mM substrate','substr')],
    description='Solutions',
    layout=widgets.Layout(width='30%',margin='0px 0px 0px 0px')
    )

cuv_widget = widgets.RadioButtons(
    # Cuvettes for part A
    options=[1,2,3,4],
    description = 'Cuvettes:'
    )

empty_cuv_butt = widgets.Button(
    # button to empty cuvettes for part A
    description = 'Empty',
    button_style = 'danger',
    )   
empty_cuv_butt.on_click(empty_cuv)


cuv_vol_table = VolTable(cuv_dict,'Cuvette')

deliver_butt2 = widgets.Button(
    # Button to deliver volume for BSA dilution
    description = 'Pipette!',
    button_style = 'success',
    )
deliver_butt2.on_click(deliver2)   


cuvVb=widgets.VBox([cuv_widget,empty_cuv_butt],
                     layout=widgets.Layout(width='40%',margin='0px 0px 0px 00px'))

row_cuv = widgets.HBox([solns_widget2,cuvVb,cuv_vol_table])

row_pip = widgets.HBox([deliver_butt2,pipette,pip_vol],
    layout=widgets.Layout(margin='15px 0px 0px 0px'))

box_cuv = widgets.VBox([row_cuv,row_pip])



## -------------- Final Cuvette additions _________##
# The tubes from the AEBSF reactions serve as the solutions for the final addition.


def deliver3(change):
    if lab_code.value not in codes:
        deliver_butt3.description='Enter valid lab code'
        deliver_butt3.button_style = 'warning'
        return
    if len(rxn_kin_solns)<4:
        deliver_butt3.description='Start reactions'
        deliver_butt3.button_style = 'warning'
        return 
    
    if not (0 <= rxn_time.value <= 150):
        deliver_butt3.description='Enter valid rxn time'
        deliver_butt3.button_style = 'warning'
        return    
    
    pip_sigma = code_dict[lab_code.value]['pip_sigma']
    tube = tubes_widget.value
    cuv = cuv_widget.value
    
    # get pipette err from normal distr
    err_pipette = pipette.value*rand.normalvariate(0,pip_sigma)
    
    # calculate delivered volume
    vol = pip_vol.value+err_pipette
    # save old volume and calculate new
    vol_old = cuv_dict[cuv].vol
    vol_new = vol_old + vol
    
    # active enzyme concentration comes from the simulation of
    # the AEBSF reaction
    # we ignore everything else in the reaction tubes! 
    t_rxn= rxn_time.value
    e_conc = rxn_kin_solns[tubes_widget.value-1].y[0][t_rxn]

    incr = vol*e_conc
    conc_old = cuv_dict[cuv].conc['trypsin']
    cuv_dict[cuv].conc['trypsin'] = (conc_old*vol_old + incr)/vol_new 
        
    #update volumes
    cuv_dict[tube].vol = vol_new
    cuv_dict[tube].vol_n += pip_vol.value

    c_trypsin = cuv_dict[cuv].conc['trypsin']
    c_substr = cuv_dict[cuv].conc['substr']
    if c_trypsin >0 and c_substr >0:
        cuv_dict[cuv].t0 = time()
    
    cuv_vol_table.update()
    
def on_time_ch(change):
    if 0 <= rxn_time.value <= 150: 
        deliver_butt3.description='Pipette!'
        deliver_butt3.button_style = 'success'


rxn_time = widgets.IntText(
    # text box for reaction time
    description = 'Reaction Time (min):',
    value= 0,
    layout=widgets.Layout(width='200px',margin='20px 0px 0px 15px'),
    style=style,
    disabled = False
    )
rxn_time.observe(on_time_ch,names=['value'])   



deliver_butt3 = widgets.Button(
    # Button to deliver volume for BSA dilution
    description = 'Pipette!',
    button_style = 'success',
    disabled = True
    )
deliver_butt3.on_click(deliver3)   



row_cuv2 = widgets.HBox([tubes_widget,cuv_widget])

row_pip3 = widgets.HBox([deliver_butt3,pipette,pip_vol],
    layout=widgets.Layout(margin='15px 0px 0px 0px'))
    
box_final_add = widgets.VBox([row_cuv2,row_pip3])



##---------------Kinetic Run --------------------=##
def mm_de(t,y,e_conc,km,kcat):
    s_conc = y[0]
    p_conc = y[1]
    dp_conc = e_conc*kcat*s_conc/(km+s_conc)
    ds_conc = -dp_conc
    return [ds_conc,dp_conc]
    
    
def kin_sim(cuv_dict,t_tot):
    # simulation is run for twice t_tot, to allow for starting delay
    # and continued absorbance readings after the run
    pts = int(2*t_tot*60)
    kin_sols =[]
    km=code_dict[lab_code.value]['km']
    kcat=code_dict[lab_code.value]['kcat']
    
    for cuv in cuv_dict:
        s_conc = cuv_dict[cuv].conc['substr']
        p_conc = 0.0
        e_conc =cuv_dict[cuv].conc['trypsin']
        
        if cuv_dict[cuv].conc['tris'] < 0.09:
             # activity is reduced if tris concentration isn't adequate
            kcat *= 0.5
        if cuv_dict[cuv].conc['cacl'] < 0.0009:
            # some of the enzyme is lost if CaCl2 concentration isn't adequate
            e_conc *= 0.5

        kin_sols.append(solve_ivp(mm_de,[0.0,float(pts)],[s_conc,p_conc],
                args=[e_conc,km,kcat],t_eval=np.linspace(0.0,float(pts),pts+1)))
        # return kcat to its original value
        kcat=code_dict[lab_code.value]['kcat'] 
    return kin_sols
        
        
def kin_run(abs_table,change):
    if lab_code.value not in codes:
        run_butt.description='Enter valid lab code'
        run_butt.button_style = 'warning'
        return

    run_butt.disabled = True
    abs_sigma = code_dict[lab_code.value]['abs_sigma']
    
    abs_table.refresh()
    
    if wl.value == '402 nm':
        ext_coef=0.9e4
    elif wl.value == '405 nm':
        ext_coef=1e4
    else:
        ext_coef=0.0

    t_int = abs_table.t_int
    t_tot = abs_table.t_tot
    n_cuv = abs_table.n_cuv
    n_meas = abs_table.n_meas
    cuv_dict = abs_table.cuv_dict
    abs_data = abs_table.abs_data
    
    # a bit to introduce some variation from run to run,
    # as might arise from loss of enzyme activity   
    e_var = 0.9 + 0.2 * rand.random()
    for cuv in cuv_dict:
        cuv_dict[cuv].conc['trypsin'] *= e_var
    
    kin_sols = kin_sim(cuv_dict,t_tot)
        
    sleep(1)
    cuv_int =int(60*t_int/n_cuv)

    delay_t = []
    for cuv in cuv_dict:
        if cuv_dict[cuv].t0 > 0:
            delay = int(time()-cuv_dict[cuv].t0)
            delay_t.append(delay)
        else:
            delay_t.append(0)
            
    t=0
    tcuv=0
    meas = 1
    cuv = 1
    cuv_show(cuv)
    abs_start = abs_read-zero_set
    pts_total = int((t_tot+t_int)*60+cuv_int)
    for i in range(pts_total):
        sleep(t_sleep)
        read_t = t + delay_t[cuv-1]     
        absorb = kin_sols[cuv-1].y[1][read_t]*ext_coef + abs_start
        abs_show(absorb)
        
        if tcuv>=cuv_int:
            
            err = rand.normalvariate(0,abs_sigma)
            
            abs_data[meas][cuv] = absorb + err
            abs_table.update()
                     
            if cuv < n_cuv:
                cuv+=1
            else:
                cuv=1
                meas +=1
            cuv_show(cuv)
            tcuv=0

        tcuv+=1
        t += 1
        
    make_plot(abs_table.abs_data)
    
    reset_butt.disabled = False
def make_plot(abs_data):
    global reg_table   
    prop_cycle = plt.rcParams['axes.prop_cycle']
    colors = prop_cycle.by_key()['color']
    colors.pop(2) # remove green
    #colors.pop(4) # remove brown
    #colors.pop(5) # remove grey
    
    plot_data = [[]]
    n_meas = abs_table.n_meas
    n_cuv = abs_table.n_cuv
    abs_data = abs_table.abs_data
    for j in range(n_meas):
        plot_data[0].append(abs_data[j+1][0])
    for i in range(n_cuv):
        plot_data.append([])
        for j in range(n_meas):
            plot_data[i+1].append(abs_data[j+1][i+1])
    plot_data = np.array(plot_data)
    
    
    reg_results = []
    for i in range(n_cuv):
        reg = linregress(plot_data[0],plot_data[i+1])
        reg_results.append(reg)
    reg_x = np.array([0.0,plot_data[0,-1]])
    fig = plt.figure(figsize=(7.5,5))
    ax= fig.add_subplot(1,1,1)
    for i in range(n_cuv):
        reg_yint = reg_results[i].intercept
        reg_slope = reg_results[i].slope
        reg_y = reg_x*reg_slope+reg_yint
        ax.plot(plot_data[0],plot_data[i+1],'o',color=colors[i])
        ax.plot(reg_x,reg_y,color=colors[i], label =f'Cuvette {i+1}')
        
    ax.set_title(graph_title,fontsize=18)
    ax.set_xlabel('Time (min)',fontsize=14)
    ylabel_str = 'Absorbance at ' + wl.value
    ax.set_ylabel(ylabel_str,fontsize=14)
    data_min = plot_data.min()
    if data_min < 0.0:
        ax.set_ylim(data_min,)
    else:
        ax.set_ylim(0,)
    ax.set_xlim(0,)
    
    ax.legend()
    
    # Important note: close the plot so that it doesn't automatically
    # display in Jupyter. Otherwise, it will never go away!
    # display the fig in Output widget, which can be made to go away!
    
    plt.close()
    with fig_output:        
        display(fig)

     
    reg_table = RegTable(reg_results) 
            
    # Important note 2: In order for the regression table (an HTML widget
    # created within this function) to appear in voila, it has to be put
    # in an output widget declared globally.
              
    with reg_table_output:
        display(reg_table)




def cuv_show(cuv):
    '''function to display the cuvette number in the cuv_display HTML widget'''
    cuv_displ.value=f'<h2>Cuvette:<span style="color:red;">\
    {cuv} </span></h2>'
    
    
def on_wl_ch(value):
    '''Respond to change in the wavelength widget'''
    h2O_abs = {'260 nm':0.14,'280 nm':0.3, '402 nm':0.4, '405 nm':0.6,'595 nm':0.8}
    absorb=h2O_abs[wl.value]
    abs_update(absorb)

def zero(change):
    '''Respond to the Zero button'''
    global zero_set
    
    zero_set = abs_read
    abs_update(abs_read)

def damp_sin(t,nu,tau):
    '''damped sine function to simulate settling
    of absorbance reading. Input arguments:
    t: time
    nu: sine-function frequency
    tau: exponential-decay time constant
    '''
    d_sin = np.exp(-t/tau)*np.sin(t*nu*2*np.pi)
    return d_sin    

def abs_update(absorb):
    '''function to set global abs_read2 variable and
    Updates absorbance display, with settling time
    Input arguments:
        absb: settled absorbance value
    global variables used:
        t_tot: total time for reading to settle
        steps: number of times to update display
            as it settles.
    '''
    global abs_read
    displ_absb = absorb - zero_set
    
    tau = 0.2*t_tot
    nu = 5/t_tot
    for i in range(steps+1):
        t = t_tot*i/steps
        abs_d = displ_absb*(1+damp_sin(t,nu,tau))
        sleep(t_tot/steps)
        
        abs_show(abs_d)
    
    abs_read = absorb
 

def abs_show(absorb):
    '''function to displays variable in the spec_dislp HTML widget'''
    if absorb < -0.03:
        spec_displ.value='<h2> Abs: <span style="color:red;"> Err  </span></h2>'
    else:
        spec_displ.value='<h2> Abs: <span style="color:red;"> \
        {:.3f}'.format(absorb) + '</span></h2>'
    
    
def cuv_reset(cuv_dict):
    '''Reset volumes, concentrations and t0 in all of the cuvettes in cuv_dict'''
    for cuv in cuv_dict:
        cuv_dict[cuv].vol = 0.0
        cuv_dict[cuv].vol_n = 0.0
        for c in cuv_dict[cuv].conc:
            cuv_dict[cuv].conc[c] = 0.0
        cuv_dict[cuv].t0=0.0

def on_reset(change):
    abs_table.refresh()
    reg_table.close()
    fig_output.clear_output()
    #cuv_reset(cuv_dict)
    cuv_vol_table.update()
    # reset clock on cuvettes so that a run can be restarted without risk
    # of running out of time points. 
    for cuv in cuv_dict:
        cuv_dict[cuv].t0=0.0
    
    run_butt.disabled = False
    reset_butt.disabled = True

abs_table = AbsTable(cuv_dict, 1.0,5.0)

wl = widgets.Dropdown(
    # Dropdown to select wavelength for spectrophotometer
    options = [('260 nm'),('280 nm'),('402 nm'),('405 nm'),('595 nm')],
    description = 'Wavelength:',
    style = style,
    layout=widgets.Layout(width='200px',margin='0px 0px 20px 0px')
    )
wl.observe(on_wl_ch,names=['value'])




zero_butt = widgets.Button(
    # button to zero absorbance display
    description = 'Zero',
    button_style = 'success',
    layout=widgets.Layout(margin='0px 0px 0px 20px')
    )
zero_butt.on_click(zero)



run_butt = widgets.Button(
    # Button to start simulated kinetics run
    description = 'Run!',
    button_style = 'success',
    layout=widgets.Layout(margin='0px 0px 0px 0px')
    )
run_butt.on_click(functools.partial(kin_run,abs_table))

cuv_displ=widgets.HTML(
    # cuvette number display
    value='1',
    layout=widgets.Layout(margin='-15px 0px 0px 20px')
    )

spec_displ = widgets.HTML(
    # spectrophotometer display
    value='0.0',
    layout=widgets.Layout(width='140px',margin='-15px 0px 0px 20px')
    )

reset_butt = widgets.Button(
    # button to reset kinetic simulation
    description ='Reset spec run',
    button_style = 'danger',
    disabled = True,
    layout=widgets.Layout(margin='0px 0px 0px 20px')
    
    )
reset_butt.on_click(on_reset)

abs_show(0)
cuv_show(1)

row_spec1 =  widgets.HBox([wl,zero_butt])
row_spec2 = widgets.HBox([run_butt, cuv_displ, spec_displ, reset_butt])



fig_output = widgets.Output(layout={'border': '1px solid black','width':'500px'})
reg_table_output=widgets.Output()



##---------------- Special Functions -----------------------##

def tube_reset(tube_dict):
    '''Reset volumes and concentrations in all of the tubes in tube_dict'''
    for tube in tube_dict:
        tube_dict[tube].vol = 0.0
        tube_dict[tube].vol_n = 0.0
        for c in tube_dict[tube].conc:
            tube_dict[tube].conc[c] = 0.0
            

def cuv_reset(cuv_dict):
    '''Reset volumes, concentrations and t0 in all of the cuvettes in cuv_dict'''
    for cuv in cuv_dict:
        cuv_dict[cuv].vol = 0.0
        cuv_dict[cuv].vol_n = 0.0
        for c in cuv_dict[cuv].conc:
            cuv_dict[cuv].conc[c] = 0.0
        cuv_dict[cuv].t0=0.0
            

  
def test_cuv():
    cuv_reset(cuv_dict)
    # A function for quickly setting up cuvettes for testing
    e_stock = 0
    s_stock = 0.002
    for cuv in cuv_dict:
        cuv_dict[cuv].vol = 760.0
        cuv_dict[cuv].vol_n = 760.0       
        cuv_dict[cuv].conc['tris']=0.2*400.0/760
        cuv_dict[cuv].conc['substr']= (80.0/760)*s_stock
        cuv_dict[cuv].t0 = 10*cuv

    cuv_vol_table.update()

    
def test_tube():
    tube_reset(tube_dict)
    # A function for quickly setting up the reaction tubes for testing.
    trypsin_conc= code_dict[lab_code.value]['e_conc']/10.0
    cacl_conc = 0.02 # stock solution
    for tube in tube_dict:
        tube_dict[tube].vol = 800.0
        tube_dict[tube].vol_n = 800.0
        tube_dict[tube].conc['hepes'] = 0.1
        tube_dict[tube].conc['trypsin'] = trypsin_conc/10.0
        tube_dict[tube].conc['cacl'] = cacl_conc/8.0
        if tube != 1:
            tube_dict[tube].conc['aebsf'] = 40.0*5e-3/800.0
    
    tube_dict[3].conc['substr'] = 180.0*2e-3/800.0
    tube_dict[4].conc['benz'] = 80.0*1e-3/800.0
   
   
    
    tube_vol_table.update()
    
##-------------- Widgets ----------------------#

##-------------- Decorative and Informational Widgets ----------------------#
hrule = widgets.HTML(
    # general purpose horizontal rule
    value ='<hr border-width:6px, color:black>')

header_html = """
<h2> Biology 3515/Chemistry 3515
<br>
Biological Chemistry Laboratory 
<br>
University of Utah </h2>
<h3> Spring 2021 </h3>
<h3> Experiment 4, Part B: Irreversible Inhibition of Trypsin</h3>
<p style="font-size:16px">

This web page simulates the procedures to be carried out in Part B of Experiment 4. In this experiment, the goal is to measure the rate of inactivation of trypsin by 4-(2-aminoethyl)-benzenesulfonyl fluoride (AEBSF) and the effects of two other compounds on the inhibition kinetics.
<br><br>
This experiment requires multiple steps, as reflected in the headings below. The first step is to set up four reaction tubes, each containing the same amount of trypsin, with and without AEBSF, a substrate and a competitive inhibitor. The specific contents of the tubes are specified in the lab manual.  After the trypsin has been added to all of the tubes, a button must be pressed to start the simulation of the reactions (something that is not required in the real lab!) At specific times after the reactions are started, samples are withdrawn from the tubes and added to cuvettes already containing buffer and substrate. The absorbance of these cuvettes is then monitored to determine the fraction of the initial trypsin that is still active in the tubes. 

<br><br>
Samples are withdrawn from the reaction tubes immediately after the reactions are started and after 15, 30, 60, 90 and 120 min. However, you do not need to wait so long in the simulated experiment! Instead, there is a text entry box in which to specify the time for each of the assay sets, and they can be carried out sequentially without delays.
<br><br>
As in the last few experiments, you will simulate kinetic runs on the spectrophotometer as would be carried out in the lab.  The simulations will output a table of absorbance values recorded at time intervals and make a plot of the data. The program also prints a table of data from least-squares fit of the data to a straight line. As before, these should be copied to your LabArchives notebook with clear annotations indicating the time points.

<br><br>
The simulation of the kinetic run is sped up by a factor of about 5-fold from what the real experiment takes. 

<br><br>
Like the previous experiments, this simulations requires a lab code to function, and your group should use the same code assigned earlier. If you do not have an assigned code, but want to experiment with this simulation, use the code "0GXY02".

"""

header = widgets.HTML(
    value=header_html
    )

    
footer = widgets.HTML(
    value='''
    <hr border-width:6px, color:black>
    David P. Goldenberg, February 2021<br>
    <a href="mailto:goldenberg@biology.utah.edu" target="new">goldenberg@biology.utah.edu</a><br>
    School of Biological Sciences, University of Utah<br>
    Salt Lake City, Utah 8412-0840<br>
     <a href="https://goldenberg.biology.utah.edu/courses/biol3515/index.shtml" 
     target="new">https://goldenberg.biology.utah.edu/courses/biol3550.</a>
''')

hrule = widgets.HTML(
    # general purpose horizontal rule
    value ='<hr border-width:6px, color:black>')

b1header = widgets.HTML(
    # header for part B, part 1
    value = '<h2> 1. Reaction tube setup</h2>'
    )

b2header = widgets.HTML(
    # header for part B, part 2
    value = '<h2> 2. Reaction start</h2>'
    )

b3header = widgets.HTML(
    # header for part B, part 3
    value = '<h2> 3. Cuvette setup </h2>'
    )

b4header = widgets.HTML(
    # header for part B, part 4
    value = '<h2> 4. Sample transfer from reaction tubes to cuvettes</h2>'
    )

b5header = widgets.HTML(
    # header for part B, part 5
    value = '<h2> 5. Kinetic run </h2>'
    )


##---------------- Display Everything -------------------#

#lab_code.value='0GXY02'

display(header)
display(hrule)

display(row_code)
display(hrule)

display(b1header)
display(box_rxn_tubes)
display(hrule)

display(b2header)
display(row_rxn_butt)
display(hrule)

display(b3header)
display(box_cuv)
display(hrule)

display(b4header)
display(rxn_time)
display(box_final_add)
display(hrule)

display(b5header)
display(row_spec1)
display(row_spec2)

display(abs_table)
display(fig_output)
display(reg_table_output)
display(footer)


#display(footer)