Simulation of Experiment 2, for Biol 3515/Chem 3515

Biol 3515-Chem 3515 Exp 2 simulation

Gist title

codeDictionary.py

code_dict = {'0GXY02': {'bsa_init': 0.6302333104590135,
  'coli_pr': 0.02045782192688574,
  'coli_na': 0.028069149086216168,
  'curve_a': 7.628994080420339,
  'curve_b': 79.97496754863742,
  'brad_bkg': 0.21581014164096682},
 'DD0371': {'bsa_init': 1.4101514851390147,
  'coli_pr': 0.03767113005479135,
  'coli_na': 0.021727273260539227,
  'curve_a': 5.23824112385952,
  'curve_b': 49.18698368309747,
  'brad_bkg': 0.12212849875848655},
 'X5FX87': {'bsa_init': 0.559451632519114,
  'coli_pr': 0.020957560308467255,
  'coli_na': 0.033079965658528755,
  'curve_a': 5.159240302043729,
  'curve_b': 53.65818471296826,
  'brad_bkg': 0.1669654048420614},
 'FG188G': {'bsa_init': 0.6211684083261407,
  'coli_pr': 0.03231224514606566,
  'coli_na': 0.026218962171618555,
  'curve_a': 4.009863518780299,
  'curve_b': 35.88984445266249,
  'brad_bkg': 0.13737469662134283},
 '34P10Q': {'bsa_init': 1.376685391815398,
  'coli_pr': 0.02528454078577475,
  'coli_na': 0.026161032352047427,
  'curve_a': 7.13139579450825,
  'curve_b': 70.80233394254888,
  'brad_bkg': 0.2968686705047867},
 'Y4N6KZ': {'bsa_init': 1.2751079559604972,
  'coli_pr': 0.03820446885747479,
  'coli_na': 0.024273280915330177,
  'curve_a': 2.8301783474888142,
  'curve_b': 21.632619148181345,
  'brad_bkg': 0.2027842300758498},
 'W5XM03': {'bsa_init': 1.1098918536440845,
  'coli_pr': 0.02945901590496184,
  'coli_na': 0.03527986928720504,
  'curve_a': 8.758868767465232,
  'curve_b': 96.11014225234263,
  'brad_bkg': 0.16024179290090854},
 '9V51PV': {'bsa_init': 1.476152886320615,
  'coli_pr': 0.021399381745099116,
  'coli_na': 0.02969956384856809,
  'curve_a': 3.2098048344317665,
  'curve_b': 22.17740636850572,
  'brad_bkg': 0.17408720658127075},
 '942913': {'bsa_init': 1.1354799906443611,
  'coli_pr': 0.038162190388555825,
  'coli_na': 0.028272147919856546,
  'curve_a': 4.284229436479604,
  'curve_b': 41.84982405373382,
  'brad_bkg': 0.18584116162074565},
 'N898UN': {'bsa_init': 0.7268642396965732,
  'coli_pr': 0.02340531599438036,
  'coli_na': 0.03737296299646256,
  'curve_a': 2.8702311632457067,
  'curve_b': 24.509429893330523,
  'brad_bkg': 0.10255978643675266},
 'H4CGP6': {'bsa_init': 0.899176843584752,
  'coli_pr': 0.038362154215435075,
  'coli_na': 0.03077414844871194,
  'curve_a': 4.007799049683165,
  'curve_b': 28.920431744257,
  'brad_bkg': 0.2591649173049998},
 '13KE9N': {'bsa_init': 1.4006400447689598,
  'coli_pr': 0.02128436030706538,
  'coli_na': 0.023598989771235163,
  'curve_a': 1.9842431271785594,
  'curve_b': 9.846622888606351,
  'brad_bkg': 0.21255397035988005},
 '31PQ53': {'bsa_init': 1.3030738346518123,
  'coli_pr': 0.028280419363943814,
  'coli_na': 0.038391045658602754,
  'curve_a': 3.575812623335131,
  'curve_b': 27.90323833988697,
  'brad_bkg': 0.2532292114888188},
 'KK644G': {'bsa_init': 1.44262262813991,
  'coli_pr': 0.024414664331468473,
  'coli_na': 0.03970182089468849,
  'curve_a': 8.295133070123354,
  'curve_b': 90.51583976879485,
  'brad_bkg': 0.18424263040479463},
 '2TNA45': {'bsa_init': 0.6573819881083176,
  'coli_pr': 0.0295529286164187,
  'coli_na': 0.032997819386657995,
  'curve_a': 3.243219996073975,
  'curve_b': 20.58218884087249,
  'brad_bkg': 0.14928077253905697},
 'N6AADQ': {'bsa_init': 0.9165464914272847,
  'coli_pr': 0.0208135230951118,
  'coli_na': 0.0270873260762834,
  'curve_a': 5.126060104627027,
  'curve_b': 49.212607378598726,
  'brad_bkg': 0.14632573829835882},
 'SV22HX': {'bsa_init': 1.2102861771752291,
  'coli_pr': 0.02149718745729806,
  'coli_na': 0.033603419002110536,
  'curve_a': 2.169141768180557,
  'curve_b': 9.187564457478402,
  'brad_bkg': 0.13652892317839213},
 'VS8S0J': {'bsa_init': 0.8210403031893194,
  'coli_pr': 0.03214794331807181,
  'coli_na': 0.03755449581376081,
  'curve_a': 2.7969844949982896,
  'curve_b': 16.4075363572732,
  'brad_bkg': 0.18558565154117743},
 '4U2RCD': {'bsa_init': 0.7469661758621895,
  'coli_pr': 0.03210384852556212,
  'coli_na': 0.03297312294071977,
  'curve_a': 2.156737850263122,
  'curve_b': 14.403610349405195,
  'brad_bkg': 0.2869805591773925},
 'ZCRTWU': {'bsa_init': 1.3020990551424825,
  'coli_pr': 0.036710243358538966,
  'coli_na': 0.029314088966354887,
  'curve_a': 7.289548559659246,
  'curve_b': 79.7497851901377,
  'brad_bkg': 0.20324338496663644},
 '7182Y1': {'bsa_init': 1.1147758578790397,
  'coli_pr': 0.02686741656253151,
  'coli_na': 0.031419781501426165,
  'curve_a': 3.2516262455678944,
  'curve_b': 25.12834609400917,
  'brad_bkg': 0.19758276403588176},
 'W8Y4P3': {'bsa_init': 1.2173774020841588,
  'coli_pr': 0.02387166620444361,
  'coli_na': 0.029855130181537716,
  'curve_a': 8.528339986272549,
  'curve_b': 94.60510182724437,
  'brad_bkg': 0.29618691038962786},
 'J9PWB4': {'bsa_init': 0.764189959208705,
  'coli_pr': 0.020779208498265186,
  'coli_na': 0.026119937104039558,
  'curve_a': 7.10698263726603,
  'curve_b': 71.09173203849825,
  'brad_bkg': 0.16283605321341776},
 '43479S': {'bsa_init': 0.6405217918195514,
  'coli_pr': 0.020302646047041423,
  'coli_na': 0.03664699312309894,
  'curve_a': 6.593018254224056,
  'curve_b': 74.08008540507063,
  'brad_bkg': 0.1480061012211324},
 'MYX1AX': {'bsa_init': 1.324833083691523,
  'coli_pr': 0.037507549113220434,
  'coli_na': 0.02750541064719787,
  'curve_a': 6.272254329896093,
  'curve_b': 58.12404333640464,
  'brad_bkg': 0.26349046432563117},
 'S0E0YV': {'bsa_init': 0.5519978390278825,
  'coli_pr': 0.020219007481144108,
  'coli_na': 0.022951831385046556,
  'curve_a': 6.727483299840219,
  'curve_b': 64.3491054091928,
  'brad_bkg': 0.2109578898211646},
 'DFKPU9': {'bsa_init': 0.5780804111841383,
  'coli_pr': 0.035962532226912314,
  'coli_na': 0.03865254889537133,
  'curve_a': 4.083122690178636,
  'curve_b': 35.137770058310714,
  'brad_bkg': 0.1099716479937468},
 '9RFXYW': {'bsa_init': 0.5840088935776985,
  'coli_pr': 0.025060748749074303,
  'coli_na': 0.028553407441499038,
  'curve_a': 1.8180500300948523,
  'curve_b': 8.173002694225502,
  'brad_bkg': 0.23280671380526333},
 '88PTV8': {'bsa_init': 0.6231275554173443,
  'coli_pr': 0.02883746390785842,
  'coli_na': 0.027125170963581857,
  'curve_a': 7.570713178623864,
  'curve_b': 85.2025846227128,
  'brad_bkg': 0.24376978590583756},
 'H0X54M': {'bsa_init': 1.1321608009884556,
  'coli_pr': 0.0385521238979127,
  'coli_na': 0.03492765707915852,
  'curve_a': 4.80734250970189,
  'curve_b': 47.48176109145393,
  'brad_bkg': 0.17255058087818656},
 'KD1K2N': {'bsa_init': 0.93302708835257,
  'coli_pr': 0.03810359867424335,
  'coli_na': 0.039373415170982154,
  'curve_a': 6.971818997674599,
  'curve_b': 74.67099883372816,
  'brad_bkg': 0.1309919905971541},
 '23W0N6': {'bsa_init': 0.6482481699668515,
  'coli_pr': 0.03597725617249658,
  'coli_na': 0.027584702873477467,
  'curve_a': 4.967113767289612,
  'curve_b': 44.45956548525093,
  'brad_bkg': 0.2810893702596993},
 'GQ5P11': {'bsa_init': 1.1277885478456056,
  'coli_pr': 0.03941397156292144,
  'coli_na': 0.03461178123080865,
  'curve_a': 8.161992763569723,
  'curve_b': 91.65048116557341,
  'brad_bkg': 0.2107638583476281},
 '597J70': {'bsa_init': 1.1365077115146103,
  'coli_pr': 0.027385812947625533,
  'coli_na': 0.02622429133424256,
  'curve_a': 7.3277594095638445,
  'curve_b': 81.98070594169553,
  'brad_bkg': 0.18827152305933278},
 '77YE98': {'bsa_init': 0.5963367750165631,
  'coli_pr': 0.032655092026546456,
  'coli_na': 0.024988468904814275,
  'curve_a': 8.502338778781453,
  'curve_b': 87.69796000054274,
  'brad_bkg': 0.17526926659291908},
 '994A4U': {'bsa_init': 0.570985042171707,
  'coli_pr': 0.025353537885538697,
  'coli_na': 0.021490311974125587,
  'curve_a': 8.52267011879738,
  'curve_b': 99.50445959145006,
  'brad_bkg': 0.24570163717107646},
 '22NZ8S': {'bsa_init': 0.9509898167137367,
  'coli_pr': 0.03143947404778345,
  'coli_na': 0.024006452599770123,
  'curve_a': 2.3281500642172497,
  'curve_b': 5.7608664652106185,
  'brad_bkg': 0.20818558044013602},
 '33VZHV': {'bsa_init': 1.4058631822395942,
  'coli_pr': 0.0373458404174298,
  'coli_na': 0.024709811656972162,
  'curve_a': 5.982193055726704,
  'curve_b': 54.507989580099796,
  'brad_bkg': 0.12465571443314515},
 'YD34E7': {'bsa_init': 1.4251831768823449,
  'coli_pr': 0.03979283010807402,
  'coli_na': 0.023466399008471604,
  'curve_a': 5.662020644704536,
  'curve_b': 51.946138776999106,
  'brad_bkg': 0.1000674305851464},
 'B4EV54': {'bsa_init': 1.0613831943977985,
  'coli_pr': 0.03412782658362859,
  'coli_na': 0.0365328039154178,
  'curve_a': 5.480578184396049,
  'curve_b': 59.22235384904483,
  'brad_bkg': 0.24923821797427856},
 'QXQEA0': {'bsa_init': 1.452191010481251,
  'coli_pr': 0.03749655741528499,
  'coli_na': 0.0206458168695719,
  'curve_a': 7.61201780339441,
  'curve_b': 85.99366245627897,
  'brad_bkg': 0.1663318114344157},
 'RCE9Z2': {'bsa_init': 1.4604226493305035,
  'coli_pr': 0.03165903021438017,
  'coli_na': 0.025043850037061718,
  'curve_a': 2.346241287267522,
  'curve_b': 17.1769935120656,
  'brad_bkg': 0.2833063738696384},
 'W382SW': {'bsa_init': 1.038445633316786,
  'coli_pr': 0.038586439441352136,
  'coli_na': 0.02681400144547896,
  'curve_a': 3.73871352496779,
  'curve_b': 32.58280973396393,
  'brad_bkg': 0.24368297263640382},
 'Y1UUUA': {'bsa_init': 0.8729008931178693,
  'coli_pr': 0.03157452594746815,
  'coli_na': 0.021987245586348642,
  'curve_a': 4.37913797898254,
  'curve_b': 33.19143710008858,
  'brad_bkg': 0.14328566320524383},
 '240125': {'bsa_init': 1.1580376473676264,
  'coli_pr': 0.03154744238990789,
  'coli_na': 0.025978305481204698,
  'curve_a': 2.1520860602697325,
  'curve_b': 10.922141767168352,
  'brad_bkg': 0.2471519026095803},
 '0P20E8': {'bsa_init': 1.0222939756638887,
  'coli_pr': 0.03882095525311787,
  'coli_na': 0.02490080412321647,
  'curve_a': 4.116207451793762,
  'curve_b': 37.88070290591054,
  'brad_bkg': 0.2276461792673584},
 'CTZKSB': {'bsa_init': 0.9043556567257972,
  'coli_pr': 0.02071372149014222,
  'coli_na': 0.03533266822319614,
  'curve_a': 6.551683617811493,
  'curve_b': 73.40920582461186,
  'brad_bkg': 0.20424716060973047},
 'K60820': {'bsa_init': 1.0268399981969911,
  'coli_pr': 0.0322084380814433,
  'coli_na': 0.033458076385320765,
  'curve_a': 5.74675831527346,
  'curve_b': 50.39276748870875,
  'brad_bkg': 0.2569968969963384},
 'WE21H5': {'bsa_init': 1.1047891362709161,
  'coli_pr': 0.030276340460969622,
  'coli_na': 0.020162556978298336,
  'curve_a': 7.028432486851976,
  'curve_b': 73.01961704325916,
  'brad_bkg': 0.2299952113925479},
 'N180MF': {'bsa_init': 1.1881707717833925,
  'coli_pr': 0.0378287611835832,
  'coli_na': 0.02999539373677519,
  'curve_a': 5.623675669865823,
  'curve_b': 54.45278003042385,
  'brad_bkg': 0.14742752267277526}}

environment.yml

name: exp_2_sim
channels:
  - conda-forge
  - defaults
  - conda-forge/label/broken
dependencies:
  - python=3.7.3
  - numpy=1.16.4
  - ipython=7.6.1
  - ipywidgets=7.5.0
  - voila = 0.2.6

exp2_sim.ipynb

exp2_sim.py

## Module for import into Jupyter for simulation of Experiment 2
## 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 numpy as np
import random as rand
import ipywidgets as widgets
from IPython.display import display, HTML
display(HTML("<style>div.output_scroll { height: 100ex; }</style>"))

from time import sleep
import threading
from multiprocessing import Process
from labcodes import codes
from codeDictionary import code_dict

def make_code_dict():
    '''Function to build code dictionary specific to this experiment
    Don't actually call this function when loading the module, or else
    the dictionary will change with every execution. Instead save value
    of dictionary in this module.'''
    for code in codes:
        bsa_init = 0.5 + rand.random()
        coli_pr = 0.02 + 0.02*rand.random()
        coli_na = 0.02 + 0.02*rand.random()
        brad_bkg = 0.1 + 0.2*rand.random()
        b = 5 + 95*rand.random()
        a = 0.075*b + 1 + rand.random()
        code_dict[code]={}
        code_dict[code]['bsa_init']=bsa_init
        code_dict[code]['coli_pr'] = coli_pr
        code_dict[code]['coli_na']=coli_na
        code_dict[code]['curve_a']=a
        code_dict[code]['curve_b']=b
        code_dict[code]['brad_bkg']=brad_bkg
        
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
        

##-------------Create the tube dictionary-------------------#

tube_names = ['std 1','std 2','std 3','std 4','std 5','std 6','std 7','std 8','std 9',
              'E.coli 1', 'E.coli 2','E.coli 3']

tube_dict = {}
conc_dict = {'BSA':0.0, 'coliExtr':0.0,'bradford':0.0}

for name in tube_names:
    tube_dict[name] = Tube()
    tube_dict[name].conc = conc_dict.copy()

# A special tube for the dilute BSA
dil_bsa = Tube(conc=0,vol=0)

##--------------Some global variables ----------------#
# standard deviation for pipette errors
# Errors are based on max volume of the pipette used
pip_sigma = 0.04
# Total time and number of steps for abs reading to settle
t_tot = 2
steps = 25
# Background absorbance of blank solutions
a260_bkg = 0.07
a280_bkg = 0.03

##----------------Functions-----------------##

def tube_reset():
    '''Reset volumes and concentrations in all of the tubes'''
    for tube in tube_dict:
        tube_dict[tube].vol = 0
        tube_dict[tube].vol_n = 0
        tube_dict[tube].conc['BSA'] = 0
        tube_dict[tube].conc['coliExtr'] = 0
        tube_dict[tube].conc['bradford'] = 0
    dil_bsa.vol = 0
    dil_bsa.vol_n = 0
    dil_bsa.conc = 0
    vol_table_update()
    dilbsa_vol_update(0)
    


def a260_280(prot_conc,na_conc):
    '''Calculate absorbance for protein and nucleic acid
    solutions, using Warburg/Christian values'''
    e_p260=0.512
    e_p280 = 0.894
    e_na260=22.1
    e_na280=10.8
    a260= prot_conc*e_p260 + na_conc*e_na260
    a280 = prot_conc*e_p280 + na_conc*e_na280
    return a260,a280


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>'
    else:
        code_warn.value =''
        read_uvabs_butt.button_style = 'success'
        read_uvabs_butt.description='Read Absorbance'
        deliver_butt1.button_style = 'success'
        deliver_butt1.description='Pipette!'
        deliver_butt2.description='Pipette!'
        deliver_butt2.button_style = 'success'
        read_bradford_butt.button_style = 'success'
        read_bradford_butt.description='Read Absorbance'
        
def on_wl_ch_a(value):
    '''Respond to change in the wavelength widget'''
    global zero_set
    read_uvabs(0)

def on_wl_ch_b(value):
    '''Respond to change in the wavelength widget'''
    global zero_set
    read_bradford(0)

       
def zero(change):
    '''Respond to the Zero button'''
    global zero_set
    zero_set += abs_read
    abs_update(0)



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(absb):
    '''function to set global abs_read 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
    abs_read = absb
    
    tau = 0.2*t_tot
    nu = 5/t_tot
    for i in range(steps+1):
        t = t_tot*i/steps
        abs_d = absb*(1+damp_sin(t,nu,tau))
        sleep(t_tot/steps)
        
        abs_show(abs_d)
    
def abs_show(absb):
    '''function to displays variable in the spec_dislp HTML widget'''
    spec_displ.value='<h2> Abs: <span style="color:red;">\
    {:.3f}'.format(absb) + '</span></h>'

def read_uvabs(change):   
    '''function to responds to Read Abs button for Part A, uv abs'''
    # check to see if there is a valid lab code
    if lab_code.value not in codes:
        read_uvabs_butt.description='Enter valid lab code'
        read_uvabs_butt.button_style = 'warning'
        return
    a595 = 0
    if UV_samp.value == 'BSA':
        # for BSA sample use specific extinction coefficients
        pr = code_dict[lab_code.value]['bsa_init']
        e280 = 0.67 # mg/ml ext coef
        e260 = 0.6*e280
        a260 = pr*e260
        a280 = pr*e280
    if UV_samp.value=='E. coli extract':
        # for coli extract, use Warburg/Christian estimate
        pr = code_dict[lab_code.value]['coli_pr']
        na = code_dict[lab_code.value]['coli_na']        
        a260,a280 = a260_280(pr,na)
    if UV_samp.value == 'H2O':
        a260 = 0.0
        a280 = 0.0
    if wl_a.value == '260 nm':
        abs_update(a260+a260_bkg-zero_set)
    elif wl_a.value == '280 nm':
        abs_update(a280+a280_bkg-zero_set)
    elif wl_a.value == '595 nm': 
        abs_update(a595)
        
def dilbsa_vol_update(vol):
    '''function to update dilute bsa HTML widget'''
    vol = vol/1000
    html_str = '''
    <style>
    table, th, td {
      border: 1px solid black;
    }
    th, td {
      padding: 5px;
    }
    table, {border-collapse: collapse;}
    </style>
    <table>
    <tr>
    <th style="width:150px"> Dilute BSA Volume </th>           
    '''
    
    html_str  += f'<td style="width:100px">{vol:.3f} mL</td></tr>'
    dilbsa_vol.value=html_str  
        
def vol_table_update():
    '''function to update the table of volumes for the bradford assay'''
    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"> Tube </th>
    <th style="width:100px"> Volume </th>
    </tr>       
    '''
    
    for name in tube_names:
        vol = tube_dict[name].vol_n
        html_str += f'<tr><td>{name}</td><td>{vol:.0f} </td></tr>\n'
    html_str += '</table>'
    vol_table.value=html_str
    
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
    
def deliver1(change):
    '''function for deliver button for bsa dilution'''
    # check for valid lab code
    if lab_code.value not in codes:
        deliver_butt1.description='Enter valid lab code'
        deliver_butt1.button_style = 'warning'
        return

    bsa_conc = code_dict[lab_code.value]['bsa_init']
    # get pipette err from normal distr
    err_pipette = pipette.value*rand.normalvariate(0,pip_sigma)
    vol = pip_vol.value+err_pipette

    # save old volumes and calculate new volume
    vol_old = dil_bsa.vol
    vol_new = vol_old + vol
    dil_bsa.vol = vol_new
    dil_bsa.vol_n += pip_vol.value
    
    # calculate increment to amount of BSA in tube
    bsa_incr = 0
    if solns1.value == 'BSA':
        bsa_incr = bsa_conc*pip_vol.value  
    
    # update concentration
    conc_old = dil_bsa.conc
    dil_bsa.conc = (conc_old*vol_old + bsa_incr)/vol_new
    
    # update displayed volume of dilute bsa solution
    dilbsa_vol_update(dil_bsa.vol_n) 
    
def empty1(change):
    '''Respond to Empty button for BSA dilution'''
    dil_bsa.vol = 0
    dil_bsa.vol_n = 0
    dil_bsa.conc = 0
    dilbsa_vol_update(dil_bsa.vol)
    

def deliver2(change):
    '''function for bradford tubes deliver button'''
    # check for valid lab coed
    if lab_code.value not in codes:
        deliver_butt2.description='Enter valid lab code'
        deliver_butt2.button_style = 'warning'
        return

    # concentrations of stock soulions
    bsa_conc = dil_bsa.conc
    coli_conc = code_dict[lab_code.value]['coli_pr']
    bradford_conc = 5

    # 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[tubes.value].vol
    vol_new = vol_old + vol
    
    
    # calculate increments of bsa, coli extract and bradford reagent
    # as volume_delivered*conc
    bsa_incr = 0
    coli_incr = 0
    bradford_incr = 0
    if solns2.value == 'Dilute BSA':
        bsa_incr = bsa_conc*vol
    elif solns2.value == 'E. coli extract':
        coli_incr = coli_conc*vol
    elif solns2.value == 'Bradford reagent':
        bradford_incr = bradford_conc*vol
    
    
    # update BSA conc
    conc_old = tube_dict[tubes.value].conc['BSA']
    conc_new = (conc_old*vol_old + bsa_incr)/vol_new
    tube_dict[tubes.value].conc['BSA'] = conc_new
    
    # update E. coli extract conc
    conc_old = tube_dict[tubes.value].conc['coliExtr']
    conc_new = (conc_old*vol_old + coli_incr)/vol_new
    tube_dict[tubes.value].conc['coliExtr'] = conc_new

    # update bradford reag conc
    conc_old = tube_dict[tubes.value].conc['bradford']
    conc_new = (conc_old*vol_old + bradford_incr)/vol_new
    tube_dict[tubes.value].conc['bradford'] = conc_new
    
    #update volumes
    tube_dict[tubes.value].vol = vol_new
    tube_dict[tubes.value].vol_n += pip_vol.value
    
    vol_table_update()
    

def empty2(change):
    '''Function to empty selected tube for bradford'''
    tube_dict[tubes.value].vol = 0
    tube_dict[tubes.value].vol_n = 0
    tube_dict[tubes.value].conc['BSA'] = 0
    tube_dict[tubes.value].conc['coliExtr'] = 0
    tube_dict[tubes.value].conc['bradford'] = 0
    vol_table_update()
    
def read_bradford(change):   
    '''function to calculate absorbance for bradford
    using rect hyperbola function with parameters from
    code dictionary'''
    # check for valid lab code
    if lab_code.value not in codes:
        read_bradford_butt.description='Enter valid lab code'
        read_bradford_butt.button_style = 'warning'
        return
    # check wavelength. Abs = 3 if uv
    if wl_b.value != '595 nm':
        abs_update(3.000-zero_set)
        return 
    a = code_dict[lab_code.value]['curve_a']
    b = code_dict[lab_code.value]['curve_b']
    
    brad_conc = tube_dict[tubes.value].conc['bradford']   
    bkg = brad_conc*code_dict[lab_code.value]['brad_bkg']
    pr_conc = tube_dict[tubes.value].conc['coliExtr'] + \
        tube_dict[tubes.value].conc['BSA']
    mcg_pr = 1000.0*pr_conc
    absorb = brad_conc*mcg_pr*a/(mcg_pr+b)
    absorb += bkg-zero_set
    abs_update(absorb)
    
def background():
    '''Background task to keep keep the page from timing out on mybinder'''
    while True:
        sleep(0.1)
        abs_show(abs_read)

##----------------------Widgets---------------------------##
header_html = """
<h2> Biology 3515/Chemistry 3515
<br>
Biological Chemistry Laboratory 
<br>
University of Utah </h2>
<h3> Spring 2021 </h3>
<h3> Experiment 2: Spectrophotometry and Measurement of Protein Concentration</h3>
<p style="font-size:16px">

This web page simulates the procedures to be carried out in Experiment 2. In the first part, UV absorbance is measured for two samples, a solution of bovine serum albumin and an extract prepared from <i>E. coli</i> bacteria. The second part uses the Bradford dye-binding assay to determine protein concentration. For this part, the BSA solution is diluted and used as a calibration standard, and the protein concentration of the <i>E. coli</i> is estimated using the calibration curve.

<hr border-width:6px, color:black>
<p style="font-size:16px">

For this and the subsequent experiments, each lab group will be assigned a six-character code, which must be entered in the box below in order for the simulation to function. The same code will be used for all of the experiments. This code specifies parameters of the experiment, such as solution concentrations, which will generally be different for different groups. Thus, members of different groups are likely to see significant differences among their results. It is as if, in the lab, everyone was using different sets of reagents.  When different members of the same group carry out the simulations, they should obtain similar, but not identical results. Just as in the lab, there will be inevitable experimental errors, particularly in the pipetting operations. The pipetting errors will generally be on the order of 1-2% of the maximum volume of the pipette used.

<br>
For different parts of the experiment, sets of radio buttons are used to select solutions to pipette from and the tubes to be pipetted into. The tables show the nominal volumes in the tubes as reagents are added. (The volumes shown in the table do not account the expected small errors in pipetting). The tables are provided to help you keep track of where you are in the process. But, they won't tell you WHAT is in the tubes, just the total volume. It's up to you to keep track of what have done!
<br><br>
If you do not have an assigned code, but want to experiment with this simulation, use the code "0GXY02".
<hr border-width:6px, color:black>
"""
style = {'description_width': 'initial'}
header = widgets.HTML(
    value=header_html
    )
    
footer = widgets.HTML(
    value='''
    <hr border-width:6px, color:black>
    David P. Goldenberg, January 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>')

aheader = widgets.HTML(
    # header for part A
    value = '<h1> Part A: UV absorbance of protein solutions </h1>'
    )

bheader = widgets.HTML(
    # header for part B
    value= '<h1> Part B: Bradford assay </h1>'
)

b1header = widgets.HTML(
    # header for part B, part 1
    value = '<h2> 1. Dilution of BSA solution</h2>'
    )

b2header = widgets.HTML(
    # header for part B, part 2
    value = '<h2> 2. Set up tubes for Bradford assay</h2>'
    )

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

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')
    )

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

# part A UV absorbance

UV_samp = widgets.RadioButtons(
    # radio buttons to select sample for UV measurement
    options = ['H2O','BSA', 'E. coli extract'],
    description='Sample:',
    #layout=widgets.Layout(width='200px',margin='25px 100px 0px 0px')
    )
    
wl_a = widgets.Dropdown(
    # Dropdown to select wavelength for UV measurement
    options = [('260 nm'),('280 nm'),('595 nm')],
    description = 'Wavelength:',
    style = style,
    layout=widgets.Layout(width='200px')
    )

wl_b = widgets.Dropdown(
    # Dropdown to select wavelength for bradford
    options = [('260 nm'),('280 nm'),('595 nm')],
    description = 'Wavelength:',
    style = style,
    layout=widgets.Layout(width='200px')
    )
    
    
read_uvabs_butt = widgets.Button(
    # Button to read absorbance 
    description = 'Read Absorbance',
    button_style = 'success',
    #layout=widgets.Layout(width='200px',margin='25px 100px 15px 50px')
    )

spec_displ = widgets.HTML(
    # spectrophotometer display
    value='',
    layout=widgets.Layout(margin='-15px 50px 0px 50px')
    )

zero_butt = widgets.Button(
    # button to zero absorbance display
    description = 'Zero',
    button_style = 'success'
    )

# part B widgets

# B1 BSA dilution
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')
    )

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')
    )

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


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


solns1 = widgets.RadioButtons(
    # solutions for making dilute bsa
    options=['H20','BSA'],
    description='Solutions'
    )

dilbsa_vol = widgets.HTML(
    # display volume of the dilute bsa solution
    value = ''
    )

#B2 bradford tube set up
tubes= widgets.RadioButtons(
    # radio buttons to select bradford tubes
    options=tube_names,
    description='Tubes:',
    )
    
solns2 = widgets.RadioButtons(
    # radiou buttons to select solutions for bradford tubes
    options = ['H2O','Dilute BSA', 'E. coli extract', 'Bradford reagent'],
    description='Solution:',
    layout=widgets.Layout(width='30%',margin='0px 0px 0px 0px')
    )
empty_butt2 = widgets.Button(
    # button to empty selected bradford tube
    description = 'Empty',
    button_style = 'danger',
    layout=widgets.Layout(width='35%',margin='0px 0px 0px 80px')
    )
tubesVb=widgets.VBox([tubes,empty_butt2],
                     layout=widgets.Layout(width='40%',margin='0px 0px 0px 00px'))

vol_table = widgets.HTML(
    # HTML table of volumes of bradford tubes
    value = '',
    layout=widgets.Layout(width='250px')
    )

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


# B3 Bradford absorbance readings
read_bradford_butt = widgets.Button(
    # Button to read absorbance for bradford
    description = 'Read Absorbance',
    button_style = 'success',
    )



#---------------Layout widgets-------------------------#
# lab code
row0 = widgets.HBox([code_label,lab_code,code_warn])
# uv absorbance
row1 = widgets.HBox([UV_samp,wl_a])
row2 = widgets.HBox([read_uvabs_butt,spec_displ,zero_butt])
# dilute bsa
row3 = widgets.HBox([solns1,dilbsa_vol,empty_butt1])
row4 = widgets.HBox([deliver_butt1,pipette,pip_vol])
# set up bradford tubes

row5 = widgets.HBox([solns2,tubesVb,vol_table])
row6 = widgets.HBox([deliver_butt2,pipette,pip_vol],
                    layout=widgets.Layout(margin='15px 0px 0px 0px'))
# read bradford abs
row7 = widgets.HBox([tubes,wl_b])
row8 = widgets.HBox([read_bradford_butt,spec_displ,zero_butt])



uvabs_box = widgets.VBox([hrule,aheader,row1,row2,hrule])
bsa_dil_box = widgets.VBox([bheader,b1header,row3,row4])
brad_tube_box = widgets.VBox([hrule,b2header,row5,row6])
brad_abs_box = widgets.VBox([hrule,b3header,row7,row8])


## ----------------Widget actions---------------------------##

lab_code.observe(on_code_ch,names=['value'])   
wl_a.observe(on_wl_ch_a,names=['value'])
wl_b.observe(on_wl_ch_b,names=['value'])
pipette.observe(on_pipette_ch,names=['value'])


read_uvabs_butt.on_click(read_uvabs) 
zero_butt.on_click(zero)

deliver_butt1.on_click(deliver1)
empty_butt1.on_click(empty1)
deliver_butt2.on_click(deliver2)
empty_butt2.on_click(empty2)
read_bradford_butt.on_click(read_bradford) 


##----------------Initialize Widgets--------------------------##

tube_reset()
abs_update(0)
zero_set=0
zero(0)
dilbsa_vol_update(0)
vol_table_update()

##----------------Display Widgets --------------------------##
display(header)
display(row0)
display(uvabs_box)
display(bsa_dil_box)
display(brad_tube_box)
display(brad_abs_box)
display(footer)

#-----------------Start Background Process-------------------#

labcodes.py

codes =['0GXY02',
 'DD0371',
 'X5FX87',
 'FG188G',
 '34P10Q',
 'Y4N6KZ',
 'W5XM03',
 '9V51PV',
 '942913',
 'N898UN',
 'H4CGP6',
 '13KE9N',
 '31PQ53',
 'KK644G',
 '2TNA45',
 'N6AADQ',
 'SV22HX',
 'VS8S0J',
 '4U2RCD',
 'ZCRTWU',
 '7182Y1',
 'W8Y4P3',
 'J9PWB4',
 '43479S',
 'MYX1AX',
 'S0E0YV',
 'DFKPU9',
 '9RFXYW',
 '88PTV8',
 'H0X54M',
 'KD1K2N',
 '23W0N6',
 'GQ5P11',
 '597J70',
 '77YE98',
 '994A4U',
 '22NZ8S',
 '33VZHV',
 'YD34E7',
 'B4EV54',
 'QXQEA0',
 'RCE9Z2',
 'W382SW',
 'Y1UUUA',
 '240125',
 '0P20E8',
 'CTZKSB',
 'K60820',
 'WE21H5',
 'N180MF']