def ramp_step_setup(duration, initial_volume, steps, final_concentration, testing=60):
MEDIA_OUT_SPD = 100
LIGAND_OUT_SPD = 20
MEDIA_VOL = 80
SWISH_SPD = 100
#---------------------
total_volume = initial_volume
past_lig = 0
for i in range(steps):
print ("Step "+str(i+1))
partial_concentration = (final_concentration/steps)*(i+1)
print(partial_concentration)
lig_vol = (partial_concentration*(total_volume+MEDIA_VOL)-past_lig)/(1-partial_concentration)
past_lig+=lig_vol
total_volume += (lig_vol+MEDIA_VOL)
print ("lig_vol " + str(lig_vol))
print ("total_vol " + str(total_volume))
print ("================")
#pump ligand
drive.m3(1,int(lig_vol), LIGAND_OUT_SPD)
time.sleep(5)
# #pump media
drive.m1(1,MEDIA_VOL, MEDIA_OUT_SPD)
time.sleep(2)
#swish
drive.m2(0,int(total_volume),SWISH_SPD)
time.sleep(5)
#800 is the estimated tube volume so 600 to be safe
drive.m2(1,int(total_volume)+600/steps, SWISH_SPD)
#sleep
print("Sleeping for "+str(int(duration/steps)) + " seconds")
time.sleep(int(duration/steps))
print ("p= "+str(past_lig))
def ramp_wash_setup(duration, initial_volume, steps, final_concentration):
MEDIA_IN_SPD = 200
LIGAND_OUT_SPD = 20
MEDIA_OUT_SPD = 50
OUT_OFFSET = 40
#Assumed that initial volume is constant total volume
#-------------------
for i in range(steps):
print("Step" + str(i))
#Take off old media
drive.m2(0, int(initial_volume) + OUT_OFFSET, MEDIA_OUT_SPD)
#delay for continued suction
time.sleep(int(int(initial_volume) * 1 / float(MEDIA_OUT_SPD)))
print("wait for old media")
time.sleep(10)
#Calculate new concentration
partial_concentration = (i + 1) * float(final_concentration) / (steps)
in_lig = int(partial_concentration * initial_volume)
print(in_lig)
in_med = initial_volume - in_lig
#Pump out ligand
drive.m3(1, in_lig, LIGAND_OUT_SPD)
time.sleep(5)
#Pump out media
drive.m1(1, in_med, MEDIA_IN_SPD)
print("------End of step------")
print("Wating " + str(int(duration / float(steps))) +
"s for the next step")
time.sleep(int(duration / float(steps)))
# def ramp_setup(iterations, duration, volume, testing=60):
"""
def ramp_setup(iterations, duration, volume, testing=60):
OUT_SPD = 50
IN_SPD = 500
MEDIA_VOL = 500
#The amount of liquid used to flush each mini-pulse (40 minimum)
RAMP_WASH_VOL = 40
#------------------------
for i in range(iterations):
#initial drain
drive.m2(0,MEDIA_VOL+100, OUT_SPD)
time.sleep(30)
drive.m1(1,MEDIA_VOL-volume*2, OUT_SPD)
time.sleep(30)
for k in range(duration):
inc_vol = volume/float(duration)
drive.m3(1, int(inc_vol), int(inc_vol/2.0))
drive.m1(1, 40, int(inc_vol/2.0))
time.sleep(1)
#washes
for k in range(6):
print ("\nSwish/Wash" + str(k))
# swish(3,500,250)
wash(MEDIA_VOL,IN_SPD, OUT_SPD)
for t in range(testing*10):
print (str(testing*10-t)+" Sec Remaining", end = "\r")
time.sleep(1)
for k in range (testing*testing*5):
print (str(testing*testing*5-t)+" Sec Remaining", end = "\r")
time.sleep(1)
print ("PULSE " + str(pulses) + " COMPLETE")
def ramp_step_setup(duration,
initial_volume,
steps,
final_concentration,
testing=60):
"""
We have not been able to get this code to work because of the problem with mixing
Swishing did not fix the issue because air and bubbles would get trapped in the swish
line and the water used to swish would sometimes get mixed in with the cells
"""
MEDIA_OUT_SPD = 500
LIGAND_OUT_SPD = 20
MEDIA_VOL = 80
SWISH_SPD = 100
#---------------------
total_volume = initial_volume
past_lig = 0
for i in range(steps):
print("Step " + str(i + 1))
partial_concentration = (final_concentration / steps) * (i + 1)
print(partial_concentration)
lig_vol = (partial_concentration * (total_volume + MEDIA_VOL) -
past_lig) / (1 - partial_concentration)
past_lig += lig_vol
total_volume += (lig_vol + MEDIA_VOL)
print("lig_vol " + str(lig_vol))
print("total_vol " + str(total_volume))
print("================")
#pump ligand
drive.m3(1, int(lig_vol), LIGAND_OUT_SPD)
time.sleep(5)
# #pump media
drive.m1(1, MEDIA_VOL, MEDIA_OUT_SPD)
time.sleep(2)
#swish
drive.m2(0, int(total_volume), SWISH_SPD)
time.sleep(5)
#800 is the estimated tube volume so 600 to be safe
drive.m2(1, int(int(total_volume) + 600 / steps), SWISH_SPD)
#sleep
print("Sleeping for " + str(int(duration / steps)) + " seconds")
time.sleep(int(duration / steps))
print("p= " + str(past_lig))
def pulse2(wait, bmedia, numpulses, pulse, blank, vol1, spd1, vol2, spd2):
"""
USES TWO SYRINGE PUMPS
Creates a simple pulsing stimulation scheme, where the concentration
changes instantaneously (a square wave).
The scheme starts out with blank media, and ends with blank media.
m1 is ligand, m2 is blank media.
Usage:
...
wait is the seconds before the first pulse starts
bmedia is the initial blank media in the dish in microliters
numpulses is the number of pulses
pulse is the pulse length in seconds
blank is the time between pulses in seconds
...
vol1 is the volume of m1 microliters
spd1 is the speed of m1 microliters/second
vol2 is the volume of m2 microliters
spd2 is the speed of m2 in microliters/second
"""
# SET UP LOGS
global transferLog
global timeLog
transferLog = "transferLog.txt"
timeLog = datetime.datetime.fromtimestamp(
time.time()).strftime('%y%m%d_%H%M%S') + "_timeLog.txt"
updatelog("PULSE EXPERIMENT")
# CALCULATE USEFUL VALUES
trans_time1 = (round(vol1 / spd1) + 1) # how long the fluid transfer takes
trans_time2 = (round(vol2 / spd2) + 1) # how long the fluid transfer takes
# ESTABLISH BASELINE
time.sleep(wait)
# REMOVE INITIAL MEDIA
updatelog("Removing initial media.")
drive.m2(0, bmedia, 100)
time.sleep(bmedia / 100 + 1)
# START THE PULSES
for i in range(numpulses):
# ligand pulse
drive.m1(1, vol1, spd1)
time.sleep(trans_time1)
updatelog("Pulse " + str(i + 1) + " START")
time.sleep(pulse)
updatelog("Pulse " + str(i + 1) + " END")
drive.m1(0, vol1, spd1)
time.sleep(trans_time1)
# blank media
drive.m2(1, vol2, spd2)
time.sleep(trans_time2)
if i != (numpulses - 1):
updatelog("Blank " + str(i + 1) + " START")
time.sleep(blank)
updatelog("Blank " + str(i + 1) + " END")
drive.m2(0, vol2, spd2)
time.sleep(trans_time2)
# if this is the last pulse, don't remove the blank media
else:
updatelog("EXPERIMENT COMPLETE\n")
def alt_pulsesetup(pulses, testing = 60):
OUT_SPD = 50
IN_SPD = 100
LIG_VOL = 60
MEDIA_VOL = 600
#Do not edit below this line
#----------------------------
for i in range(pulses):
#initial drain
drive.m2(0,MEDIA_VOL+50, OUT_SPD)
time.sleep(12)
print ("\nPulse "+str(i))
drive.m3(1,LIG_VOL,OUT_SPD)
drive.m1(1,MEDIA_VOL,IN_SPD)
for t in range(60*testing):
print (str(60*testing-t)+" Sec Remaining", end="\r")
time.sleep(1)
#initial wash for double wash
# swish(3,250,250)
wash(MEDIA_VOL,IN_SPD, OUT_SPD)
time.sleep(12)
#washes
for k in range(5):
print ("\nSwish/Wash" + str(k))
# swish(3,500,250)
wash(MEDIA_VOL,IN_SPD, OUT_SPD)
for t in range(testing*10):
print (str(testing*10-t)+" Sec Remaining", end = "\r")
time.sleep(1)
for t in range (testing*testing*5):
print (str(testing*testing*5-t)+" Sec Remaining", end = "\r")
time.sleep(1)
print ("PULSE " + str(pulses) + " COMPLETE")
print ("EXPERIMENT ENDED")
def alt_pulsesetup(pulses, testing=60):
OUT_SPD = 50
IN_SPD = 500
LIG_VOL = 50
MEDIA_VOL = 500
#Do not edit below this line
#----------------------------
for i in range(pulses):
#initial drain
drive.m2(0, MEDIA_VOL + 100, OUT_SPD)
time.sleep(30)
print("\nPulse " + str(i))
drive.m3(1, LIG_VOL, OUT_SPD)
time.sleep(5)
drive.m1(1, MEDIA_VOL, IN_SPD)
for t in range(60 * testing):
print(str(60 * testing - t) + " Sec Remaining", end="\r")
time.sleep(1)
#initial wash for double wash
# swish(3,250,250)
wash(MEDIA_VOL, IN_SPD, OUT_SPD)
time.sleep(30)
#washes
for k in range(6):
print("\nSwish/Wash" + str(k))
# swish(3,500,250)
wash(MEDIA_VOL, IN_SPD, OUT_SPD)
for t in range(testing * 10):
print(str(testing * 10 - t) + " Sec Remaining", end="\r")
time.sleep(1)
for k in range(testing * testing * 5):
print(str(testing * testing * 5 - t) + " Sec Remaining", end="\r")
time.sleep(1)
print("PULSE " + str(pulses) + " COMPLETE")
print("EXPERIMENT ENDED")
def pulsesetup(pulses):
for i in range(pulses):
drive.m2(0,2000,500)
#pulse
time.sleep(5)
print ("\nPulse "+str(i))
drive.m3(1,80,80)
drive.m1(1,2000, 50)
for t in range(60*60):
print (str(60*60-t)+" Sec Remaining", end="\r")
time.sleep(1)
#initial wash for double wash
swish(3,1000,1000)
wash(2000,50)
#washes
for k in range(6):
print ("\nSwish/Wash" + str(k))
swish(3,1000,1000)
wash(2000,50)
for t in range(60*60):
print (str(60*60-t)+" Sec Remaining", end = "\r")
time.sleep(1)
print ("EXPERIMENT ENDED")
def pulsesetup(pulses):
for i in range(pulses):
drive.m2(0, 2000, 500)
#pulse
time.sleep(5)
print("\nPulse " + str(i))
drive.m3(1, 80, 80)
drive.m1(1, 2000, 50)
for t in range(60 * 60):
print(str(60 * 60 - t) + " Sec Remaining", end="\r")
time.sleep(1)
#initial wash for double wash
swish(3, 1000, 1000)
wash(2000, 50)
#washes
for k in range(6):
print("\nSwish/Wash" + str(k))
swish(3, 1000, 1000)
wash(2000, 50)
for t in range(60 * 60):
print(str(60 * 60 - t) + " Sec Remaining", end="\r")
time.sleep(1)
print("EXPERIMENT ENDED")
def pulse2(wait,bmedia,numpulses,pulse,blank,
vol1,spd1,vol2,spd2):
"""
USES TWO SYRINGE PUMPS
Creates a simple pulsing stimulation scheme, where the concentration
changes instantaneously (a square wave).
The scheme starts out with blank media, and ends with blank media.
m1 is ligand, m2 is blank media.
Usage:
...
wait is the seconds before the first pulse starts
bmedia is the initial blank media in the dish in microliters
numpulses is the number of pulses
pulse is the pulse length in seconds
blank is the time between pulses in seconds
...
vol1 is the volume of m1 microliters
spd1 is the speed of m1 microliters/second
vol2 is the volume of m2 microliters
spd2 is the speed of m2 in microliters/second
"""
# SET UP LOGS
global transferLog
global timeLog
transferLog = "transferLog.txt"
timeLog = datetime.datetime.fromtimestamp(time.time()).strftime('%y%m%d_%H%M%S') + "_timeLog.txt"
updatelog("PULSE EXPERIMENT")
# CALCULATE USEFUL VALUES
trans_time1 = (round(vol1/spd1) + 1) # how long the fluid transfer takes
trans_time2 = (round(vol2/spd2) + 1) # how long the fluid transfer takes
# ESTABLISH BASELINE
time.sleep(wait)
# REMOVE INITIAL MEDIA
updatelog("Removing initial media.")
drive.m2(0,bmedia,100);time.sleep(bmedia/100 + 1)
# START THE PULSES
for i in range(numpulses):
# ligand pulse
drive.m1(1,vol1,spd1);time.sleep(trans_time1)
updatelog("Pulse " + str(i+1) + " START")
time.sleep(pulse)
updatelog("Pulse " + str(i+1) + " END")
drive.m1(0,vol1,spd1);time.sleep(trans_time1)
# blank media
drive.m2(1,vol2,spd2);time.sleep(trans_time2)
if i != (numpulses-1):
updatelog("Blank " + str(i+1) + " START")
time.sleep(blank)
updatelog("Blank " + str(i+1) + " END")
drive.m2(0,vol2,spd2);time.sleep(trans_time2)
# if this is the last pulse, don't remove the blank media
else:
updatelog("EXPERIMENT COMPLETE\n")
def pulse3flow(wait,pulse,blank,wash,numpulses,numwashes,bmedia,
washVOL,washSPD,
bVOL,wVOL,lVOL,
bSPD,wSPD,lSPD):
"""
USES THREE SYRINGE PUMPS WITH CONTINUOUS FLOW WASH
Creates a simple pulsing stimulation scheme, where the concentration
changes instantaneously (a square wave).
The scheme starts out with blank media, and ends with blank media.
m1 is blank media, m2 is waste media, m3 is concentrated ligand
Usage:
...
wait is the seconds before the first pulse starts
pulse is the pulse length in seconds
blank is the time between pulses in seconds
wash is the time between washes in seconds
numpulses is the number of pulses
numwashes is the number of washes
bmedia is the initial blank media in the dish in microliters
...
washVOL is the volume transfer of a single wash in microliters
washSPD is the transfer speed of a wash in microliters/s
...
bVOL is the volume of blank media in microliters
wVOL is the volume of waste media in microliters
lVOL is the volume of concentrated ligand in microliters
...
bSPD is the speed of blank media in microliters/second
wSPD is the speed of waste media in microliters/second
lSPD is the speed of concentrated ligand in microliters/second
"""
params = [wait,pulse,blank,wash,numpulses,numwashes,bmedia,washVOL,washSPD,bVOL,wVOL,lVOL,bSPD,wSPD,lSPD]
### ADJUST PARAMETERS
# we change some of the times so that the total intervals are accurate.
# for example, if the "wash" argument is ten minutes, that does not account
# for the time of the actual washing. We substract that time here.
bTT = (bVOL/bSPD + 0.5) # Transfer Time of blank media
wTT = (wVOL/wSPD + 0.5) # Transfer Time of waste media
lTT = (lVOL/lSPD + 0.5) # Transfer Time of concentrated ligand
washTT = (washVOL/washSPD + 0.5) #Transfer Time of single wash
pulse = pulse - lTT - bTT
blank = blank - wash*(numwashes) - wTT
wash = wash - washTT
# CHECK PARAMETERS
if (pulse < 0) | (blank < 0) | (wash < 0):
print("One or more time intervals are too short.")
print('Pulse:',pulse,' Blank:',blank,' Wash:',wash)
return
# PROJECT FLUID USAGE
print('Projected fluid usage in mcl---',
'Blank:',bVOL*2*numpulses + washVOL*(numpulses-1)*numwashes,
' Waste:',wVOL*(2*numpulses-1) + bmedia + washVOL*(numpulses-1)*numwashes,
' Ligand:',lVOL*numpulses)
# SET UP LOGS
global transferLog
global timeLog
transferLog = "transferLog.txt"
timeLog = datetime.datetime.fromtimestamp(time.time()).strftime('%y%m%d_%H%M%S') + "_timeLog.txt"
updatelog("PULSE EXPERIMENT with params: " + str(params).strip('[]'))
app.destroy() #close GUI
# ESTABLISH BASELINE
time.sleep(wait - (bmedia/bSPD + 0.5))
# REMOVE INITIAL MEDIA
updatelog("Removing initial media.")
drive.m2(0,bmedia,wSPD);time.sleep(bmedia/wSPD + 0.5)
# START THE PULSES
for p in range(numpulses):
# ligand pulse
drive.m3(1,lVOL,lSPD);time.sleep(lTT)
drive.m1(1,bVOL,bSPD);time.sleep(bTT)
updatelog("Pulse " + str(p+1) + " START")
time.sleep(pulse)
updatelog("Pulse " + str(p+1) + " END")
if p != (numpulses-1): # not last pulse
# end of ligand
drive.m2(0,wVOL,wSPD);time.sleep(wTT)
drive.m1(1,bVOL,bSPD);time.sleep(bTT)
for j in range(numwashes):
time.sleep(wash);
drive.m4(1,washVOL,washSPD);time.sleep(washTT)
if j == 0:
updatelog("Blank " + str(p+1) + " START")
time.sleep(blank)
updatelog("Blank " + str(p+1) + " END")
drive.m2(0,wVOL,wSPD);time.sleep(wTT)
else: # last pulse, don't remove the blank media
drive.m2(0,wVOL,wSPD);time.sleep(wTT)
drive.m1(1,bVOL,bSPD);time.sleep(bTT)
updatelog("EXPERIMENT COMPLETE\n")
def swish(times, volume, spd):
"""
uses the waste pump to successively remove and add liquid three times in a row.
"""
drive.m2(0,volume, spd)
drive.m2(1,volume, spd)
drive.m2(0,volume, spd)
drive.m2(1,volume, spd)
drive.m2(0,volume, spd)
drive.m2(1,volume, spd)
def wash(volume, inspd, outspd):
drive.m2(0,volume,int(outspd))
print("wash-sleeping")
time.sleep(12)
print("wash-done-sleeping")
drive.m1(1,volume,int(inspd))
def pulse3flow(wait, pulse, blank, wash, numpulses, numwashes, bmedia, washVOL,
washSPD, bVOL, wVOL, lVOL, bSPD, wSPD, lSPD):
"""
USES THREE SYRINGE PUMPS WITH CONTINUOUS FLOW WASH
Creates a simple pulsing stimulation scheme, where the concentration
changes instantaneously (a square wave).
The scheme starts out with blank media, and ends with blank media.
m1 is blank media, m2 is waste media, m3 is concentrated ligand
Usage:
...
wait is the seconds before the first pulse starts
pulse is the pulse length in seconds
blank is the time between pulses in seconds
wash is the time between washes in seconds
numpulses is the number of pulses
numwashes is the number of washes
bmedia is the initial blank media in the dish in microliters
...
washVOL is the volume transfer of a single wash in microliters
washSPD is the transfer speed of a wash in microliters/s
...
bVOL is the volume of blank media in microliters
wVOL is the volume of waste media in microliters
lVOL is the volume of concentrated ligand in microliters
...
bSPD is the speed of blank media in microliters/second
wSPD is the speed of waste media in microliters/second
lSPD is the speed of concentrated ligand in microliters/second
"""
params = [
wait, pulse, blank, wash, numpulses, numwashes, bmedia, washVOL,
washSPD, bVOL, wVOL, lVOL, bSPD, wSPD, lSPD
]
### ADJUST PARAMETERS
# we change some of the times so that the total intervals are accurate.
# for example, if the "wash" argument is ten minutes, that does not account
# for the time of the actual washing. We substract that time here.
bTT = (bVOL / bSPD + 0.5) # Transfer Time of blank media
wTT = (wVOL / wSPD + 0.5) # Transfer Time of waste media
lTT = (lVOL / lSPD + 0.5) # Transfer Time of concentrated ligand
washTT = (washVOL / washSPD + 0.5) #Transfer Time of single wash
pulse = pulse - lTT - bTT
blank = blank - wash * (numwashes) - wTT
wash = wash - washTT
# CHECK PARAMETERS
if (pulse < 0) | (blank < 0) | (wash < 0):
print("One or more time intervals are too short.")
print('Pulse:', pulse, ' Blank:', blank, ' Wash:', wash)
return
# PROJECT FLUID USAGE
print(
'Projected fluid usage in mcl---', 'Blank:',
bVOL * 2 * numpulses + washVOL * (numpulses - 1) * numwashes,
' Waste:',
wVOL * (2 * numpulses - 1) + bmedia + washVOL *
(numpulses - 1) * numwashes, ' Ligand:', lVOL * numpulses)
# SET UP LOGS
global transferLog
global timeLog
transferLog = "transferLog.txt"
timeLog = datetime.datetime.fromtimestamp(
time.time()).strftime('%y%m%d_%H%M%S') + "_timeLog.txt"
updatelog("PULSE EXPERIMENT with params: " + str(params).strip('[]'))
app.destroy() #close GUI
# ESTABLISH BASELINE
time.sleep(wait - (bmedia / bSPD + 0.5))
# REMOVE INITIAL MEDIA
updatelog("Removing initial media.")
drive.m2(0, bmedia, wSPD)
time.sleep(bmedia / wSPD + 0.5)
# START THE PULSES
for p in range(numpulses):
# ligand pulse
drive.m3(1, lVOL, lSPD)
time.sleep(lTT)
drive.m1(1, bVOL, bSPD)
time.sleep(bTT)
updatelog("Pulse " + str(p + 1) + " START")
time.sleep(pulse)
updatelog("Pulse " + str(p + 1) + " END")
if p != (numpulses - 1): # not last pulse
# end of ligand
drive.m2(0, wVOL, wSPD)
time.sleep(wTT)
drive.m1(1, bVOL, bSPD)
time.sleep(bTT)
for j in range(numwashes):
time.sleep(wash)
drive.m4(1, washVOL, washSPD)
time.sleep(washTT)
if j == 0:
updatelog("Blank " + str(p + 1) + " START")
time.sleep(blank)
updatelog("Blank " + str(p + 1) + " END")
drive.m2(0, wVOL, wSPD)
time.sleep(wTT)
else: # last pulse, don't remove the blank media
drive.m2(0, wVOL, wSPD)
time.sleep(wTT)
drive.m1(1, bVOL, bSPD)
time.sleep(bTT)
updatelog("EXPERIMENT COMPLETE\n")
def swish(times, volume, spd):
"""
uses the waste pump to successively remove and add liquid three times in a row.
"""
drive.m2(0, volume, spd)
drive.m2(1, volume, spd)
drive.m2(0, volume, spd)
drive.m2(1, volume, spd)
drive.m2(0, volume, spd)
drive.m2(1, volume, spd)
def wash(volume, inspd, outspd):
drive.m2(0, volume, int(outspd))
print("wash-sleeping")
time.sleep(30)
print("wash-done-sleeping")
drive.m1(1, volume, int(inspd))
def pulsesetup(numpulses, pulselength, waitlength, numwashes = 5, washinterval = 5, speedup = 1):
"""
pulsesetup(npulses, pulselength, waitlength)
pulsesetup(npulses, pulselength, waitlength, numwashes, testing)
numpulses : number of pulses
pulselength : length of pulses in minutes
waitlength : length of wait after pulse in minutes
numwashes : number of washes after pulse, default 5
washinterval: interval between washes in minutes, default 5
speedup : speedup factor for testing (e.g 60 to make pulselength 1 last 1 minute)
example: 6 pulses, 2 hours with 5 hour wait: pulsesetup(6, 120, 300)
"""
# define motor directions: fluid in or out of dish?
OUT = 0;
IN = 1;
# volume parameters in ul
OUT_SPD = 50
IN_SPD = 100
LIG_VOL = 60
MEDIA_VOL = 600
WASH_VOL = 500;
MINUTE = 60/speedup; # minutes = 60 seconds unless testing is provided
WASHINTERVAL = 5; # time between washes in in minutes
DRAINWAIT = 15; # wait after pumping out, in seconds
# (to let pressures equilibrate so fluid is done flowing out)
# SHOW ESTIMATED TIME AND VOLUME, GIVE 30 SECONDS TO ABORT
# total experiment volume in microliter
Vpercycle = (numwashes + 1)*WASH_VOL + MEDIA_VOL + LIG_VOL;
Vtot = Vpercycle*numpulses;
# total experiment time in hours
Ttot = (pulselength + waitlength)*numpulses/60;
print("Total media volume required : " + str(Vtot) + " ul")
print("Total experiment time : " + str(Ttot) + " hours")
print("Countdown before start")
countdown(30)
print("Starting experiment")
# START EXPERIMENT
for i in range(numpulses):
print ("\nPulse "+str(i+1))
# initial drain
print ("Draining")
drive.m2(OUT, MEDIA_VOL + 50, OUT_SPD)
time.sleep(DRAINWAIT)
# ligand pulse
print ("Ligand dilution in")
drive.m3(IN, LIG_VOL, OUT_SPD)
drive.m1(IN, MEDIA_VOL, IN_SPD)
countdown(pulselength*MINUTE)
print ("Pulse done, starting washes")
# initial quick wash after pulse
# - first take out difference between media and wash vol (so we can use smaller wash vol)
drive.m2(OUT, MEDIA_VOL - WASH_VOL, OUT_SPD)
# - then do initial quickwash
wash(MEDIA_VOL, IN_SPD, OUT_SPD)
time.sleep(DRAINWAIT)
# slower washes
for k in range(numwashes):
print ("Wash " + str(k+1) + " of " + str(numwashes) + " ")
wash(WASH_VOL, IN_SPD, OUT_SPD)
countdown(WASHINTERVAL*MINUTE)
# wait until next pulse
print ("Washes done, waiting for next pulse")
remainingtime = (waitlength - WASHINTERVAL*numwashes)*MINUTE
countdown(remainingtime)
print ("Pulse cycle " + str(i+1) + " of " + str(numpulses) + " complete")
print ("Experiment done")
def pulsesetup(numpulses, pulselength, waitlength, numwashes = 5, washinterval = 5, speedup = 1):
"""
pulsesetup(npulses, pulselength, waitlength)
pulsesetup(npulses, pulselength, waitlength, numwashes, testing)
numpulses : number of pulses
pulselength : length of pulses in minutes
waitlength : length of wait after pulse in minutes
numwashes : number of washes after pulse, default 5
washinterval: interval between washes in minutes, default 5
speedup : speedup factor for testing (e.g 60 to make pulselength 1 last 1 minute)
example: 6 pulses, 2 hours with 5 hour wait: pulsesetup(6, 120, 300)
"""
# define motor directions: fluid in or out of dish?
OUT = 0;
IN = 1;
# volume parameters in ul
OUT_SPD = 50
IN_SPD = 100
LIG_VOL = 60
MEDIA_VOL = 600
WASH_VOL = 500;
MINUTE = 60/speedup; # minutes = 60 seconds unless testing is provided
WASHINTERVAL = 5; # time between washes in in minutes
DRAINWAIT = 15; # wait after pumping out, in seconds
# (to let pressures equilibrate so fluid is done flowing out)
# SHOW ESTIMATED TIME AND VOLUME, GIVE 30 SECONDS TO ABORT
# total experiment volume in microliter
Vpercycle = (numwashes + 1)*WASH_VOL + MEDIA_VOL + LIG_VOL;
Vtot = Vpercycle*numpulses;
# total experiment time in hours
Ttot = (pulselength + waitlength)*numpulses/60;
print("Total media volume required : " + str(Vtot) + " ul")
print("Total experiment time : " + str(Ttot) + " hours")
print("Countdown before start")
countdown(30)
print("Starting experiment")
# START EXPERIMENT
for i in range(numpulses):
print ("\nPulse "+str(i+1))
# initial drain
print ("Draining")
drive.m2(OUT, MEDIA_VOL + 50, OUT_SPD)
time.sleep(DRAINWAIT)
# ligand pulse
print ("Ligand dilution in")
drive.m3(IN, LIG_VOL, OUT_SPD)
drive.m1(IN, MEDIA_VOL, IN_SPD)
countdown(pulselength*MINUTE)
print ("Pulse done, starting washes")
# initial quick wash after pulse
# - first take out difference between media and wash vol (so we can use smaller wash vol)
drive.m2(OUT, MEDIA_VOL - WASH_VOL, OUT_SPD)
# - then do initial quickwash
wash(MEDIA_VOL, IN_SPD, OUT_SPD)
time.sleep(DRAINWAIT)
# slower washes
for k in range(numwashes):
print ("Wash " + str(k+1) + " of " + str(numwashes) + " ")
wash(WASH_VOL, IN_SPD, OUT_SPD)
countdown(WASHINTERVAL*MINUTE)
# wait until next pulse
print ("Washes done, waiting for next pulse")
remainingtime = (waitlength - WASHINTERVAL*numwashes)*MINUTE
countdown(remainingtime)
print ("Pulse cycle " + str(i+1) + " of " + str(numpulses) + " complete")
print ("Experiment done")
