725.sagews

# 8/12/2009
# GSC Hamilton Star DNA pooling methods as used by MP
# Quantitative testing of pipetting accuracy
#
# TEST: Dispense all mode (not dispense 3ul)

# initial weights in g (at time 0 minutes)

plt_dry = 28.039 # test plate
plc_dry = 1. # no ctrl plate
tubeA_dry = 0.945 # test tube
tip50_dry = 80.541 # 50ul tips and rack

# filled quadrant 1 of plt and plc with 10ul green colored h2o
# weights before run (at time 5 minutes)

plt_filled = 28.983
plc_filled = 1.

# measured density by pipette volume 1ml of green water
tubeB_dry = 0.927
tubeB_1ml = 1.935
density = (tubeB_1ml - tubeB_dry) / 1000
print "density =", density, "g/ul"

density = 0.00100800000000000 g/ul

# ran pooling program 96 wells * 3ul from plt into tube A
# weights post-run at time 24 minutes

plt_postrun = 28.705
plc_postrun = 1
tubeA_postrun = 1.171
tip50_postrun = 80.568
num_wells = 96
t_postrun = 24

# measured weights later (at 48 minutes)
plt_later = 1.
plc_later = 1.
t_later = 48

# CALCULATIONS

water_plt_before_run = (plt_filled - plt_dry) / density
water_plt_after_run = (plt_postrun - plt_dry) / density
water_plc_before_run = (plc_filled - plc_dry) / density
water_plc_after_run = (plc_postrun - plc_dry) / density

print "water in plt before run =", water_plt_before_run, "ul"
print "water in plt after run =", water_plt_after_run, "ul"
print "water in plc before run =", water_plc_before_run, "ul"
print "water in plc after run =", water_plc_after_run, "ul"

water in plt before run = 936.507936507936 ul water in plt after run = 660.714285714283 ul water in plc before run = 0.000000000000000 ul water in plc after run = 0.000000000000000 ul

total_water_lost_from_plt = (plt_filled - plt_postrun) / density
print "total water lost from test plate plt = ", total_water_lost_from_plt, "ul"

total water lost from test plate plt = 275.793650793653 ul

water_tubeA_after_run = (tubeA_postrun - tubeA_dry) / density
print "water in tubeA after run =", water_tubeA_after_run, "ul"

water in tubeA after run = 224.206349206349 ul

water_tips_after_run = (tip50_postrun - tip50_dry) / density
print "water in tips after run =", water_tips_after_run, "ul"

water in tips after run = 26.7857142857153 ul

water_evap_24min_plt = \
water_plt_before_run \
- water_plt_after_run \
- water_tips_after_run \
- water_tubeA_after_run

print "water lost to evaporation from test plate plt =", water_evap_24min_plt, "ul"

water lost to evaporation from test plate plt = 24.8015873015884 ul

water_evap_24min_plc = \
water_plc_before_run \
- water_plc_after_run
print "water lost to evaporation from ctrl plate plc =", water_evap_24min_plc, "ul"

water lost to evaporation from ctrl plate plc = 0.000000000000000 ul

# sanity check, this should be zero
print "evaporation sanity check, these should be equal."
print "total water lost from plate =", total_water_lost_from_plt, "ul"

#tube, tips, evap
print "total of calculated losses = ", \
water_tubeA_after_run + water_tips_after_run + water_evap_24min_plt, "ul"

evaporation sanity check, these should be equal. total water lost from plate = 275.793650793653 ul total of calculated losses = 275.793650793653 ul

# Break it all down on a per-well basis

print "PER-WELL CONCLUSIONS FOR A SHORT RUN"
print "water in each well at beginning of run (should be 10ul):"
print water_plt_before_run / num_wells, "ul"
print "water in each well after run (should be 7ul):"
print water_plt_after_run / num_wells, "ul"
print "water removed from plate during run (should be 3ul):"
print (water_plt_before_run - water_plt_after_run) / num_wells, "ul"
print "water per well transferred to tubeA (should be 3ul):"
print water_tubeA_after_run / num_wells, "ul"
print "water per well lost to tips:"
print water_tips_after_run / num_wells, "ul"
print "water per well lost, presumably to evaporation (at 24 minutes):"
print water_evap_24min_plt / num_wells, "ul"

PER-WELL CONCLUSIONS FOR A SHORT RUN water in each well at beginning of run (should be 10ul): 9.75529100529100 ul water in each well after run (should be 7ul): 6.88244047619044 ul water removed from plate during run (should be 3ul): 2.87285052910055 ul water per well transferred to tubeA (should be 3ul): 2.33548280423281 ul water per well lost to tips: 0.279017857142868 ul water per well lost, presumably to evaporation (at 24 minutes): 0.258349867724879 ul

# Evaporation over time as measured after the run
#BROKEN

def water_in_plt_per_well(wt_of_plt):
    return (wt_of_plt - plt_dry) / density / num_wells

water_per_well_plt_over_time = (
    water_in_plt_per_well(28.693),
    water_in_plt_per_well(28.691),
    water_in_plt_per_well(28.684),
    water_in_plt_per_well(28.667),
    )
        
timeseries = (
    24-24, 
    25-24, 
    31-24,
    41-24)
   
print ("Water in control plate over time (per well)", 
water_per_well_plt_over_time, "ul")

('Water in control plate over time (per well)', (6.75843253968254, 6.73776455026452, 6.66542658730158, 6.48974867724868), 'ul')

# now plot evaporation over time for the control plate
xypoints = [(timeseries[i], water_per_well_plt_over_time[i]) for i in range(len(timeseries))]
# xypoints.insert(0, (0,0)) # decomment to base graph at 0,0
print xypoints
show(points(xypoints))

[(0, 6.75843253968254), (1, 6.73776455026452), (7, 6.66542658730158), (17, 6.48974867724868)]

evap_rate = (water_per_well_plt_over_time[0] - water_per_well_plt_over_time[3]) / (timeseries[3] - timeseries[0]) * 60 # evaporation rate in ul / hr
print "evaporation rate: ", evap_rate, "ul/hr"

evaporation rate: 0.948295985060684 ul/hr