def Run(self):
self.set_EvoMode()
self.initialize() # set_defaults ??
Rtv.NumOfSamples = self.NumOfSamples
NumOfSamples = self.NumOfSamples
wt = self.worktable
Itr.comment('Extracting RNA from {:s} samples with the MN-Vet kit'.format(str(NumOfSamples))).exec()
# Get Labwares (Cuvette, eppys, etc.) from the work table
ElutBuf = wt.getLabware(Lab.Trough_100ml, "1-VEL-ElutionBuffer" )
LysBuf = wt.getLabware(Lab.Trough_100ml, "2-Vl Lysis Buffer" )
BindBuf = wt.getLabware(Lab.Trough_100ml, "3-VEB Binding Buffer" )
DiTi1000_1 = wt.getLabware(Lab.DiTi_1000ul, "1000-1")
DiTi1000_2 = wt.getLabware(Lab.DiTi_1000ul, "1000-2")
DiTi1000_3 = wt.getLabware(Lab.DiTi_1000ul, "1000-3")
Reactives = wt.getLabware(Lab.GreinRack16_2mL, "Reactives" )
# Set the initial position of the tips
self.go_first_pos()
# Set volumen / sample
SampleVolume = 200.0
LysisBufferVolume = 180.0 # VL1
IC2Volume = 5.0 # ? 4
BindingBufferVolume = 600.0
B_BeadsVolume = 20.0
VEW1Volume = 600.0
VEW2Volume = 600.0
EtOH80pVolume = 600.0
ProtKVolume = 20.0
cRNAVolume = 4.0
IC_MS2Volume = 20.0
ElutionBufferVolume = 100.0
# Liquid classes used for pippetting. Others liquidClass names are defined in "protocol_steps.py"
SampleLiqClass = "Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
all_samples = range(NumOfSamples)
maxTips = min (self.nTips, NumOfSamples)
maxMask = Rbt.tipsMask[maxTips]
# Define the reactives in each labware (Cuvette, eppys, etc.)
LysisBuffer = Rtv.Reagent("VL - Lysis Buffer ",
LysBuf, volpersample=LysisBufferVolume, defLiqClass=B_liquidClass)
IC2 = Rtv.Reagent("IC2 - synthetic RNA ",
Reactives, pos=11, volpersample= IC2Volume, defLiqClass=W_liquidClass)
VEB = Rtv.Reagent("VEB - Binding Buffer ",
BindBuf, volpersample=BindingBufferVolume, defLiqClass=B_liquidClass)
B_Beads = Rtv.Reagent("B - Beads ", Reactives, initial_vol=1200,
pos=1, volpersample= B_BeadsVolume, replicas=2, defLiqClass=Beads_LC_2)
VEW1 = Rtv.Reagent("VEW1 - Wash Buffer ",
wt.getLabware(Lab.Trough_100ml, "4-VEW1 Wash Buffe"),
volpersample=VEW1Volume, defLiqClass=B_liquidClass)
VEW2 = Rtv.Reagent("VEW2 - WashBuffer ",
wt.getLabware(Lab.Trough_100ml, "5-VEW2-WashBuffer" ),
volpersample=VEW2Volume, defLiqClass=B_liquidClass)
EtOH80p = Rtv.Reagent("Ethanol 80% ",
wt.getLabware(Lab.Trough_100ml, "7-EtOH80p" ),
volpersample=EtOH80pVolume, defLiqClass=B_liquidClass)
ElutionBuffer = Rtv.Reagent("Elution Buffer ",
ElutBuf, volpersample=ElutionBufferVolume, defLiqClass="Eluat")
ProtK = Rtv.Reagent("Proteinase K ",
Reactives, pos=16, volpersample= ProtKVolume, defLiqClass=Small_vol_disp)
cRNA = Rtv.Reagent("Carrier RNA ",
Reactives, pos=15, volpersample= cRNAVolume, defLiqClass=Small_vol_disp)
IC_MS2 = Rtv.Reagent("IC MS2 phage culture ",
Reactives, pos=14, volpersample= IC_MS2Volume, defLiqClass=Small_vol_disp)
pK_cRNA_MS2 = Rtv.preMix ("ProtK+cRNA+IC-MS2 mix " ,
Reactives, pos=12, components=[ ProtK, cRNA, IC2 ]
, defLiqClass=W_liquidClass, replicas=2)
# Waste = Rtv.Reagent("Waste " , self.WashWaste )
# Show the CheckList GUI to the user for posible small changes
self.CheckList()
self.set_EvoMode()
Itr.wash_tips(wasteVol=30, FastWash=True).exec()
with group("Prefill plates with VEW1, VEW2, EtOH and Elution buffer"):
Itr.userPrompt("Put the plates for VEW1, Elution Buffer and VEW2"
" in the worktable defined order").exec()
Plate_VEW1 = wt.getLabware(Lab.MP96deepwell, "Plate VEW1" ) # Plate 12 x 8 ?
Plate_ElutB = wt.getLabware(Lab.MP96well, "Plate ElutB") # Plate 12 x 8 ? MP96well !!
Plate_VEW2 = wt.getLabware(Lab.MP96deepwell, "Plate VEW2" ) # Plate 12 x 8 ?
# Define samples and the place for temporal reactions
for s in all_samples:
Rtv.Reagent("VEW1_{:02d}".format(s + 1), Plate_VEW1, initial_vol=0.0, pos=s + 1,
excess=0) # todo revise order !!!
Rtv.Reagent("VEW2_{:02d}".format(s + 1), Plate_VEW2, initial_vol=0.0, pos=s + 1,
excess=0) # todo revise order !!!
Rtv.Reagent("ElutB_{:02d}".format(s + 1), Plate_ElutB, initial_vol=0.0, pos=s + 1,
excess=0) # todo revise order !!!
with tips(reuse=True, drop=False):
spread(reactive=VEW1, to_labware_region=Plate_VEW1.selectOnly(all_samples))
with tips(reuse=True, drop=False):
spread(reactive=VEW2, to_labware_region=Plate_VEW2.selectOnly(all_samples))
with tips(reuse=True, drop=False):
spread(reactive=ElutionBuffer, to_labware_region=Plate_ElutB.selectOnly(all_samples))
Itr.userPrompt("Retire the plates for VEW1, VEW2 and Elution Buffer, and "
"Put the plates for the lysis -in place of VEW1- and for EtOH80p -in place of VEW2-").exec()
Plate_EtOH = wt.replaceWithNew(Plate_VEW2, "Plate_EtOH") # Plate 12 x 8 ?
for s in all_samples:
Rtv.Reagent("EtOH_{:02d}".format(s + 1), Plate_EtOH, initial_vol=0.0, pos=s + 1,
excess=0) # todo revise order !!!
with tips(reuse=True, drop=False):
spread(reactive=EtOH80p, to_labware_region=Plate_EtOH.selectOnly(all_samples))
with group("Sample Lysis"):
Samples = wt.getLabware(Lab.EppRack6x16, "Proben") # 6x16 = 12 x 8 ?
Plate_lysis = wt.replaceWithNew(Plate_VEW1, "Lysis_Plate") # Plate 12 x 8 ?
# Define samples and the place for temporal reactions
for s in all_samples:
Rtv.Reagent("probe_{:02d}".format(s + 1), Samples, single_use=SampleVolume,
pos=s + 1, defLiqClass=SampleLiqClass, excess=0)
Rtv.Reagent("lysis_{:02d}".format(s + 1), Plate_lysis, initial_vol=0.0, pos=s + 1,
excess=0) # todo revise order !!!
with tips(tipsMask=maxMask, reuse=True, drop=True):
pK_cRNA_MS2.make(NumOfSamples)
spread ( reactive=pK_cRNA_MS2, to_labware_region= Plate_lysis.selectOnly(all_samples))
spread ( reactive=LysisBuffer, to_labware_region= Plate_lysis.selectOnly(all_samples))
with tips(reuse=False, drop=True):
transfer( from_labware_region= Samples,
to_labware_region= Plate_lysis,
volume= SampleVolume,
using_liquid_class= (SampleLiqClass, "Serum Disp postMix3"),
optimizeFrom =False, # optimizeTo= True, # todo Really ??
NumSamples= NumOfSamples)
Itr.wash_tips(wasteVol=4, FastWash=True).exec()
# with tips(reuse=False, drop=True): # better reuse=True, drop=False, with normal Liquid Class ??
# spread ( reactive=LysisBuffer,
# to_labware_region= Plate_lysis.selectOnly(all_samples),
# using_liquid_class=(None,"Serum Disp postMix3"))
with incubation(minutes=15):
Itr.userPrompt("Please Schutteln the plates for lysis in pos 1").exec()
with group("Beads binding"):
with tips(tipsMask=maxMask, reuse=True, drop=False):
for p in [40, 50, 60, 65]:
mix_reactive(B_Beads, LiqClass=Beads_LC_1, cycles=1, maxTips=maxTips, v_perc=p)
with tips(reuse=True, drop=True):
spread( reactive=B_Beads, to_labware_region=Plate_lysis.selectOnly(all_samples))
spread( reactive=VEB, to_labware_region=Plate_lysis.selectOnly(all_samples))
# with tips(reuse=False, drop=True): # better reuse=True, drop=False, with normal Liquid Class ??
# spread ( reactive=VEB,
# to_labware_region= Plate_lysis.selectOnly(all_samples),
# using_liquid_class=(None,"Serum Disp postMix3"))
with incubation(minutes=5):
Itr.userPrompt("Please Schutteln the plates for lysis in pos 1").exec()
self.done()
def Run(self):
self.set_EvoMode() # this add: self.iRobot = EvoMode.iRobot(Itr.Pipette.LiHa1, nTips=self.nTips)
# in which: self.robot = Rbt.Robot(index=index, arms=arms, nTips=nTips)
self.initialize() # if needed calls Executable.initialize() and set_EvoMode
# which calls GUI.update_parameters() and set_defaults() from Evo200
Rtv.NumOfSamples = self.NumOfSamples
NumOfSamples = self.NumOfSamples
wt = self.worktable
Itr.comment('Prefill {:d} plates with LysisBufferReact for {:d} samples.'\
.format(self.num_plates,
NumOfSamples )).exec()
# Get Labwares (Cuvette, eppys, etc.) from the work table
BufCuvette = wt.getLabware(Lab.Trough_100ml, "2-Vl Lysis Buffer")
self.go_first_pos() # Set the initial position of the tips
# Set volumen / sample
BufferVolume = 100.0 # VL1 or VL
all_samples = range(NumOfSamples)
maxTips = min (self.nTips, NumOfSamples)
maxMask = Rbt.tipsMask[maxTips]
# Define the reactives in each labware (Cuvette, eppys, etc.)
BufferReact = Rtv.Reagent("Buffer ",
BufCuvette,
volpersample = BufferVolume,
defLiqClass = 'MN VL',
num_of_samples= self.num_plates * NumOfSamples)
# Show the CheckList GUI to the user for possible small changes
self.CheckList()
self.set_EvoMode()
Itr.wash_tips(wasteVol=5, FastWash=True).exec()
LysPlat = [wt.getLabware(Lab.MP96deepwell, "Plate lysis-"+str(i+1)) for i in range(self.num_plates)]
par = LysPlat[0].parallelOrder(self.nTips, all_samples)
# Define place for temporal reactions
for i, LP in enumerate(LysPlat):
for s in all_samples:
Rtv.Reagent("lysis_{:d}-{:02d}".format(i + 1, s + 1),
LP,
initial_vol =0.0,
pos =s + 1,
excess =0)
with group("Prefill plates with BufferReact"):
Itr.userPrompt("Put the plates for BufferReact").exec()
for LP in LysPlat:
with self.tips(reuse=True, drop=False):
self.spread(reactive=BufferReact, to_labware_region=LP.selectOnly(all_samples))
self.dropTips()
self.done()
def Run(self):
self.set_EvoMode()
self.initialize() # set_defaults ??
wt = self.worktable
Itr.comment('Extracting RNA from {:s} samples with the MN-Vet kit'.format(str(NumOfSamples))).exec()
# Get Labwares (Cuvette, eppys, etc.) from the work table
DiTi1000_1 = wt.getLabware(Lab.DiTi_1000ul, "1000-1")
DiTi1000_2 = wt.getLabware(Lab.DiTi_1000ul, "1000-2")
DiTi1000_3 = wt.getLabware(Lab.DiTi_1000ul, "1000-3")
Reactives = wt.getLabware(Lab.GreinRack16_2mL,"Reactives" )
# Set the initial position of the tips
self.go_first_pos()
# Set volumen / sample
SampleVolume = 200.0
EtOH80pVolume = 600.0
SampleLiqClass = "Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
all_samples = range(NumOfSamples)
maxTips = min (self.nTips, NumOfSamples)
maxMask = Rbt.tipsMask[maxTips]
# Define the reactives in each labware (Cuvette, eppys, etc.)
VEB = Rtv.Reagent("VEB - Binding Buffer ",
BindBuf, volpersample=BindingBufferVolume, defLiqClass=B_liquidClass)
EtOH80p = Rtv.Reagent("Ethanol 80% ",
wt.getLabware(Lab.Trough_100ml, "7-EtOH80p" ),
volpersample=EtOH80pVolume, defLiqClass=B_liquidClass)
# Show the CheckList GUI to the user for possible small changes
self.CheckList()
self.set_EvoMode()
Itr.wash_tips(wasteVol=30, FastWash=True).exec()
Plate_lysis = wt.getLabware(Lab.MP96deepwell, "Plate lysis" ) # Plate 12 x 8 ?
Plate_EtOH = wt.getLabware(Lab.MP96deepwell, "Plate EtOH" ) # Plate 12 x 8 ? MP96well !!
Samples = wt.getLabware(Lab.EppRack6x16, "Proben" ) # 6x16 = 12 x 8 ?
# Define samples and the place for temporal reactions
par = Plate_lysis.parallelOrder(self.nTips, all_samples)
for s in all_samples:
Rtv.Reagent("probe_{:02d}".format(s + 1), Samples, single_use=SampleVolume,
pos=s + 1, defLiqClass=SampleLiqClass, excess=0)
Rtv.Reagent("lysis_{:02d}".format(s + 1), Plate_lysis, initial_vol=0.0, pos=par[s] + 1,
excess=0) # todo revise order !!!
Rtv.Reagent("EtOH80p_{:02d}".format(s + 1), Plate_EtOH, initial_vol=0.0, pos=par[s] + 1,
excess=0) # todo revise order !!!
with group("Prefill plate with EtOH80p"):
with tips(reuse=True, drop=False, drop_last=True):
spread(reactive=EtOH80p, to_labware_region=Plate_EtOH.selectOnly(all_samples))
dropTips()
self.done()
PanFla_119 = PrimerMix("PanFLA", ID="119", components=[Primer.IDs[320], Primer.IDs[321]])
WNV_INNT_37 = PrimerMix("WNV_5p", ID="37", components=[Primer.IDs[20], Primer.IDs[21], Primer.IDs[22]])
Exp_300 = PCRexperiment(300, "PanFLA mosq Grecia")
samples = ["Pool-1",
"Pool-2",
"Pool-3",
"Pool-4"]
Exp_300.addReactions(PanFla_119, samples)
Exp_300.addReactions(WNV_INNT_37, samples)
Exp_300.pippete_mix() # Evo75
Exp_300.pippete_samples() # Evo100
def Run(self):
self.set_EvoMode()
self.initialize() # set_defaults ??
Rtv.NumOfSamples = self.NumOfSamples
NumOfSamples = self.NumOfSamples
wt = self.worktable
Itr.comment('Extracting RNA from {:s} samples with the MN-Vet kit'.format(str(NumOfSamples))).exec()
# Get Labwares (Cuvette, eppys, etc.) from the work table
LysBuf = wt.getLabware(Lab.Trough_100ml, "2-Vl Lysis Buffer" )
BindBuf = wt.getLabware(Lab.Trough_100ml, "3-VEB Binding Buffer" )
DiTi1000_1 = wt.getLabware(Lab.DiTi_1000ul, "1000-1")
DiTi1000_2 = wt.getLabware(Lab.DiTi_1000ul, "1000-2")
DiTi1000_3 = wt.getLabware(Lab.DiTi_1000ul, "1000-3")
Reactives = wt.getLabware(Lab.GreinRack16_2mL, "Reactives" )
# Set the initial position of the tips
self.go_first_pos()
# Set volumen / sample
ProtKVolume = 20.0
cRNAVolume = 4.0
LysisBufferVolume = 100.0 # VL1 or VL
IC_MS2Volume = 10.0 # IC2
IC2Volume = 5.0 # ? 4
BindingBufferVolume = 350.0 # VEB
B_BeadsVolume = 20.0 # B-Beads
EtOH80pVolume = 600.0
SampleVolume = 100.0
InitLysisVol = 0.0
if self.version == 'in-VL inactivated':
InitLysisVol = SampleVolume + LysisBufferVolume
elif self.version == 'pre Inactivated':
InitLysisVol = SampleVolume + ProtKVolume + cRNAVolume + IC_MS2Volume + LysisBufferVolume
# Liquid classes used for pippetting.
# Others liquidClass names are defined in "protocol_steps.py"
SampleLiqClass = "Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
all_samples = range(NumOfSamples)
maxTips = min (self.nTips, NumOfSamples)
maxMask = Rbt.tipsMask[maxTips]
# Define the reactives in each labware (Cuvette, eppys, etc.)
if self.version != 'pre Inactivated': # we need to add ProtK+cRNA+MS2 mix
ProtK = Rtv.Reagent("Proteinase K ",
Reactives,
replicas = 2,
pos = [15, 16],
volpersample = ProtKVolume,
defLiqClass = Small_vol_disp)
cRNA = Rtv.Reagent("Carrier RNA ", Reactives, pos=14, volpersample= cRNAVolume, defLiqClass=Small_vol_disp)
IC_MS2 = Rtv.Reagent("IC MS2 phage culture ", Reactives, pos=13, volpersample= IC_MS2Volume, defLiqClass=Small_vol_disp)
# IC2 = Rtv.Reagent("IC2 - synthetic RNA " , Reactives, pos=13, volpersample= IC2Volume ,defLiqClass=W_liquidClass)
pK_cRNA_MS2 = Rtv.preMix ("ProtK+cRNA+IC-MS2 mix " ,
Reactives,
pos=8,
components=[ cRNA, ProtK, IC_MS2] ,
defLiqClass=W_liquidClass,
excess=20)
if self.version != 'in-VL inactivated':
LysisBuffer = Rtv.Reagent("VL - Lysis Buffer ", LysBuf, volpersample=LysisBufferVolume, defLiqClass='MN VL')
B_Beads = Rtv.Reagent("B - Beads ",
Reactives,
pos = [1,2],
initial_vol = 1200,
volpersample = B_BeadsVolume,
defLiqClass = Beads_LC_2,
maxFull = 70)
VEB = Rtv.Reagent("VEB - Binding Buffer ", BindBuf, volpersample=BindingBufferVolume, defLiqClass=B_liquidClass)
EtOH80p = Rtv.Reagent("Ethanol 80% ", wt.getLabware(Lab.Trough_100ml, "7-EtOH80p"), volpersample=EtOH80pVolume, defLiqClass=B_liquidClass)
# Show the CheckList GUI to the user for possible small changes
self.CheckList()
self.set_EvoMode()
# Define the reactives not shown in the CheckList GUI
# Define samples and the place for temporal reactions
Plate_lysis = wt.getLabware(Lab.MP96deepwell, "Plate lysis" ) # Plate 12 x 8 ?
Plate_EtOH = wt.getLabware(Lab.MP96deepwell, "Plate EtOH" ) # Plate 12 x 8 ? MP96well !!
if self.version != 'original samples':
Samples = wt.getLabware(Lab.EppRack6x16, "Proben" ) # 6x16 = 12 x 8 ?
par = Plate_lysis.parallelOrder(self.nTips, all_samples)
for s in all_samples:
if self.version == 'original samples':
Rtv.Reagent("probe_{:02d}".format(s + 1), Samples, single_use=SampleVolume,
pos=s + 1, defLiqClass=SampleLiqClass, excess=0)
Rtv.Reagent("lysis_{:02d}".format(s + 1), Plate_lysis, initial_vol=InitLysisVol, pos=s + 1,
excess=0)
Rtv.Reagent("EtOH80p_{:02d}".format(s + 1), Plate_EtOH, initial_vol=0.0, pos=par[s] + 1,
excess=0) # todo revise order !!!
Itr.wash_tips(wasteVol=30, FastWash=True).exec()
with group("Prefill plate with EtOH80p"):
with self.tips(reuse=True, drop=False, drop_last=True):
self.spread(reactive=EtOH80p, to_labware_region=Plate_EtOH.selectOnly(all_samples))
with group("Sample Lysis"):
if self.version != 'pre Inactivated': # add ProtK+cRNA+MS2 mix
with self.tips(tipsMask=maxMask, reuse=True, drop=False, drop_last=True):
self.makePreMix(pK_cRNA_MS2)
self.spread ( reactive=pK_cRNA_MS2, to_labware_region= Plate_lysis.selectOnly(all_samples))
if self.version != 'in-VL inactivated': # add LysisBuffer
with self.tips(tipsMask=maxMask, reuse=True, drop=False, drop_last=True):
self.spread ( reactive=LysisBuffer, to_labware_region= Plate_lysis.selectOnly(all_samples))
if self.version == 'original samples': # add samples
Itr.userPrompt("Please make sure the samples are in place").exec()
with self.tips(reuse=False, drop=True):
self.transfer( from_labware_region= Samples,
to_labware_region= Plate_lysis,
volume= SampleVolume,
using_liquid_class= (SampleLiqClass, "Serum Disp postMix3"),
optimizeFrom = False,
optimizeTo = False, # todo Really ??
NumSamples = NumOfSamples)
Itr.wash_tips(wasteVol=4, FastWash=True).exec()
if self.version != 'pre Inactivated':
Itr.userPrompt("Please Schutteln the plates for lysis in pos 1").exec()
with incubation(minutes=5): pass
if self.version != 'prefill inactivation':
Itr.userPrompt("Please make sure the samples are back in place").exec()
with group("Beads binding"):
with self.tips(tipsMask=maxMask, reuse=True, drop=False):
for p in [40, 50, 60, 65]:
self.mix_reactive(B_Beads, LiqClass=Beads_LC_1, cycles=1, maxTips=maxTips, v_perc=p)
with self.tips(reuse=True, drop=False):
self.spread( reactive=B_Beads, to_labware_region=Plate_lysis.selectOnly(all_samples))
self.dropTips()
with self.tips(reuse=True, drop=False):
self.spread( reactive=VEB, to_labware_region=Plate_lysis.selectOnly(all_samples))
Itr.userPrompt("Please Schutteln the plates for lysis in pos 1").exec()
self.dropTips()
self.done()
def Run(self):
self.set_EvoMode()
self.initialize() # set_defaults ??
Rtv.NumOfSamples = self.NumOfSamples
NumOfSamples = self.NumOfSamples
wt = self.worktable
Itr.comment('Prefill plates with VEW1, Elution buffer and VEW2 for {:s} samples.'.format(str(NumOfSamples))).exec()
# Get Labwares (Cuvette, eppys, etc.) from the work table
ElutBuf = wt.getLabware(Lab.Trough_100ml, "1-VEL-ElutionBuffer" )
DiTi1000_1 = wt.getLabware(Lab.DiTi_1000ul, "1000-1")
DiTi1000_2 = wt.getLabware(Lab.DiTi_1000ul, "1000-2")
DiTi1000_3 = wt.getLabware(Lab.DiTi_1000ul, "1000-3")
Plate_VEW1 = wt.getLabware(Lab.MP96deepwell, "Plate VEW1" ) # Plate 12 x 8 ?
Plate_VEW2 = wt.getLabware(Lab.MP96deepwell, "Plate VEW2" ) # Plate 12 x 8 ?
Plate_Eluat = wt.getLabware(Lab.MP96well, "Plate ElutB" ) # Plate 12 x 8 ? MP96well !!
# Set the initial position of the tips
self.go_first_pos()
# Set volumen / sample
VEW1Volume = 600.0
VEW2Volume = 600.0
ElutionBufferVolume = 100.0
# Liquid classes used for pippetting. Others liquidClass names are defined in "protocol_steps.py"
# SampleLiqClass = "Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
all_samples = range(NumOfSamples)
maxTips = min (self.nTips, NumOfSamples)
maxMask = Rbt.tipsMask[maxTips]
# Define the reactives in each labware (Cuvette, eppys, etc.)
VEW1 = Rtv.Reagent("VEW1 - Wash Buffer ",
wt.getLabware(Lab.Trough_100ml, "4-VEW1 Wash Buffe"),
volpersample = VEW1Volume,
defLiqClass = B_liquidClass)
VEW2 = Rtv.Reagent("VEW2 - WashBuffer ",
wt.getLabware(Lab.Trough_100ml, "5-VEW2-WashBuffer" ),
volpersample =VEW2Volume,
defLiqClass =B_liquidClass)
ElutionBuffer = Rtv.Reagent("Elution Buffer ",
ElutBuf,
volpersample =ElutionBufferVolume,
defLiqClass =B_liquidClass)
# Show the CheckList GUI to the user for posible small changes
self.CheckList()
self.set_EvoMode()
Itr.wash_tips(wasteVol=30, FastWash=True).exec()
par = Plate_VEW1.parallelOrder(self.nTips, all_samples)
# Define samples and the place for temporal reactions
for s in all_samples:
Rtv.Reagent("VEW1_{:02d}".format(s + 1),
Plate_VEW1,
initial_vol = 0.0,
pos = par[s]+1,
excess = 0) # todo revise order !!!
Rtv.Reagent("VEW2_{:02d}".format(s + 1),
Plate_VEW2,
initial_vol = 0.0,
pos = par[s] + 1,
excess = 0)
Rtv.Reagent("Eluat_{:02d}".format(s + 1),
Plate_Eluat,
initial_vol = 0.0,
pos = par[s] + 1,
excess = 0)
with group("Prefill plates with VEW1, Elution buffer and VEW2"):
Itr.userPrompt("Put the plates for VEW1, Elution buffer and VEW2 in that order").exec()
with self.tips(reuse=True, drop=False):
self.spread(reactive=ElutionBuffer, to_labware_region=Plate_Eluat.selectOnly(all_samples) ) # ,optimize=False
with self.tips(reuse=True, drop=False):
self.spread(reactive=VEW2, to_labware_region=Plate_VEW2.selectOnly(all_samples) ) # , optimize=False
with self.tips(reuse=True, drop=False):
self.spread(reactive=VEW1, to_labware_region=Plate_VEW1.selectOnly(all_samples)) # , optimize=False
self.dropTips()
self.done()
def Run(self):
self.set_EvoMode()
self.initialize()
Rtv.NumOfSamples = self.NumOfSamples
NumOfSamples = self.NumOfSamples
wt = self.worktable
Itr.comment('Prefill {:d} plates with LysisBufferReact for {:d} samples.'\
.format(self.num_plates,
NumOfSamples )).exec()
# Get Labwares (Cuvette, eppys, etc.) from the work table
LysBufCuvette = wt.getLabware(Lab.Trough_100ml, "2-Vl Lysis Buffer")
DiTi1000_1 = wt.getLabware(Lab.DiTi_1000ul, "1000-1")
DiTi1000_2 = wt.getLabware(Lab.DiTi_1000ul, "1000-2")
DiTi1000_3 = wt.getLabware(Lab.DiTi_1000ul, "1000-3")
self.go_first_pos() # Set the initial position of the tips
# Set volumen / sample
LysisBufferVolume = 100.0 # VL1 or VL
all_samples = range(NumOfSamples)
maxTips = min (self.nTips, NumOfSamples)
maxMask = Rbt.tipsMask[maxTips]
# Define the reactives in each labware (Cuvette, eppys, etc.)
LysisBufferReact = Rtv.Reagent("VL - Lysis Buffer ",
LysBufCuvette,
volpersample = LysisBufferVolume,
defLiqClass = 'MN VL',
num_of_samples= self.num_plates * NumOfSamples)
# Show the CheckList GUI to the user for possible small changes
self.CheckList()
self.set_EvoMode()
Itr.wash_tips(wasteVol=5, FastWash=True).exec()
LysPlat = [wt.getLabware(Lab.MP96deepwell, "Plate lysis-"+str(i+1)) for i in range(self.num_plates)]
par = LysPlat[0].parallelOrder(self.nTips, all_samples)
# Define place for temporal reactions
for i, LP in enumerate(LysPlat):
for s in all_samples:
Rtv.Reagent("lysis_{:d}-{:02d}".format(i + 1, s + 1),
LP,
initial_vol =0.0,
pos =s + 1,
excess =0)
with group("Prefill plates with LysisBufferReact"):
Itr.userPrompt("Put the plates for LysisBufferReact").exec()
for LP in LysPlat:
with self.tips(reuse=True, drop=False):
self.spread(reactive=LysisBufferReact, to_labware_region=LP.selectOnly(all_samples))
self.dropTips()
self.done()
def waste(self, from_labware_region=None, using_liquid_class=None, volume=None, to_waste_labware=None, optimize=True):
"""
:param from_labware_region:
:param using_liquid_class:
:param volume:
:param to_waste_labware:
:param optimize:
:return:
"""
to_waste_labware = to_waste_labware or self.worktable.def_WashWaste
assert isinstance(from_labware_region, Lab.Labware), 'A Labware expected in from_labware_region to transfer'
if not volume or volume< 0.0 : volume = 0.0
assert isinstance(volume, (int, float))
oriSel = from_labware_region.selected()
nt = self.robot.curArm().nTips # the number of tips to be used in each cycle of pippeting
if not oriSel:
oriSel = range(Rtv.NumOfSamples)
if optimize:
oriSel = from_labware_region.parallelOrder(nt, oriSel)
NumSamples = len(oriSel)
SampleCnt = NumSamples
if nt > SampleCnt:
nt = SampleCnt
tm = Rbt.tipsMask[nt]
nt = to_waste_labware.autoselect(maxTips=nt)
mV = self.worktable.def_DiTi.maxVol # todo revise !! What tip tp use !
Rest = 50 # the volume we cannot more aspire with liquid detection, to small, collisions
RestPlus = 50
CtrVol = 0.5
if volume:
v = volume
else:
v = from_labware_region.Wells[oriSel[0]].vol
Asp = Itr.aspirate(tm, Te_Mag_LC, volume, from_labware_region)
# Asp = Itr.aspirate(tm, using_liquid_class[0], volume, from_labware_region)
Dst = Itr.dispense(tm, using_liquid_class, volume, to_waste_labware)
# Ctr = Itr.moveLiha(Itr.moveLiha.y_move, Itr.moveLiha.z_start, 3.0, 2.0, tm, from_labware_region)
lf = from_labware_region
msg = "Waste: {v:.1f} µL of {n:s}".format(v=v, n=lf.label)
with group(msg):
msg += " [grid:{fg:d} site:{fs:d}] in order:".format(fg=lf.location.grid, fs=lf.location.site+1) \
+ str([i+1 for i in oriSel])
Itr.comment(msg).exec()
while SampleCnt:
curSample = NumSamples - SampleCnt
if nt > SampleCnt:
nt = SampleCnt
tm = Rbt.tipsMask[nt]
Asp.tipMask = tm
Dst.tipMask = tm
sel = oriSel[curSample:curSample + nt]
spl = range(curSample, curSample + nt)
Asp.labware.selectOnly(sel)
if volume:
r = volume # r: Waste_available yet; volume: to be Waste
else:
vols = [w.vol for w in Asp.labware.selected_wells()]
r_min, r_max = min(vols), max(vols)
assert r_min == r_max
r = r_max
if not using_liquid_class:
if sel:
Dst.liquidClass = Asp.labware.selected_wells()[0].reactive.defLiqClass
with self.tips(tm, drop=True, preserve=False, selected_samples=spl):
while r > Rest: # dont aspire Rest with these Liq Class (Liq Detect)
dV = r if r < mV else mV
if dV < Rest: break # ??
dV -= Rest # the last Rest uL have to be aspired with the other Liq Class
Asp.volume = dV # with Liq Class with Detect: ">> AVR-Serum 1000 << 365"
Dst.volume = dV
Asp.liquidClass = Te_Mag_LC # ">> AVR-Serum 1000 << 365" # "No Liq Detect"
Asp.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Centre
with self.tips(allow_air=CtrVol):
Asp.exec()
if dV + Rest + RestPlus + 2*CtrVol > mV:
Dst.exec()
r -= dV
Dst.volume = 0
else:
break
Asp.volume = Rest
Asp.liquidClass = Te_Mag_Rest # ">> AVR-Serum 1000 << 367" # "No Liq Detect"
with self.tips(allow_air=Rest):
Asp.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Force_Centre
with self.tips(allow_air=CtrVol):
Asp.exec()
Asp.volume = RestPlus
Asp.liquidClass = Te_Mag_RestPlus # ">> AVR-Serum 1000 << 369" # "No Liq Detect"
with self.tips(allow_air=RestPlus):
Asp.exec()
#Ctr.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Force_Centre
Dst.volume += Rest + RestPlus
with self.tips(allow_air=CtrVol):
Asp.exec()
with self.tips(allow_air=Rest + RestPlus):
Dst.exec()
SampleCnt -= nt
Asp.labware.selectOnly(oriSel)
Itr.wash_tips(wasteVol=4).exec()
return oriSel
def waste(from_labware_region=None,
using_liquid_class=None,
volume=None,
to_waste_labware=None,
optimize=True):
"""
:param from_labware_region:
:param using_liquid_class:
:param volume:
:param to_waste_labware:
:param optimize:
:return:
"""
to_waste_labware = to_waste_labware or Lab.def_WashWaste
assert isinstance(
from_labware_region,
Lab.Labware), 'A Labware expected in from_labware_region to transfer'
if not volume or volume < 0.0: volume = 0.0
assert isinstance(volume, (int, float))
oriSel = from_labware_region.selected()
nt = Rbt.Robot.current.curArm(
).nTips # the number of tips to be used in each cycle of pippeting
if not oriSel:
oriSel = range(Rtv.NumOfSamples)
if optimize:
oriSel = from_labware_region.parallelOrder(nt, oriSel)
NumSamples = len(oriSel)
SampleCnt = NumSamples
if nt > SampleCnt:
nt = SampleCnt
tm = Rbt.tipsMask[nt]
nt = to_waste_labware.autoselect(maxTips=nt)
mV = Lab.def_DiTi.maxVol # todo revise !! What tip tp use !
Rest = 50 # the volume we cannot more aspire with liquid detection, to small, collisions
RestPlus = 50
CtrVol = 0.5
if volume:
v = volume
else:
v = from_labware_region.Wells[oriSel[0]].vol
Asp = Itr.aspirate(tm, Te_Mag_LC, volume, from_labware_region)
# Asp = Itr.aspirate(tm, using_liquid_class[0], volume, from_labware_region)
Dst = Itr.dispense(tm, using_liquid_class, volume, to_waste_labware)
# Ctr = Itr.moveLiha(Itr.moveLiha.y_move, Itr.moveLiha.z_start, 3.0, 2.0, tm, from_labware_region)
lf = from_labware_region
msg = "Waste: {v:.1f} µL of {n:s}".format(v=v, n=lf.label)
with group(msg):
msg += " [grid:{fg:d} site:{fs:d}] in order:".format(fg=lf.location.grid, fs=lf.location.site+1) \
+ str([i+1 for i in oriSel])
Itr.comment(msg).exec()
while SampleCnt:
curSample = NumSamples - SampleCnt
if nt > SampleCnt:
nt = SampleCnt
tm = Rbt.tipsMask[nt]
Asp.tipMask = tm
Dst.tipMask = tm
sel = oriSel[curSample:curSample + nt]
spl = range(curSample, curSample + nt)
Asp.labware.selectOnly(sel)
if volume:
r = volume # r: Waste_available yet; volume: to be Waste
else:
vols = [w.vol for w in Asp.labware.selected_wells()]
r_min, r_max = min(vols), max(vols)
assert r_min == r_max
r = r_max
if not using_liquid_class:
if sel:
Dst.liquidClass = Asp.labware.selected_wells(
)[0].reactive.defLiqClass
with tips(tm, drop=True, preserve=False, selected_samples=spl):
while r > Rest: # dont aspire Rest with these Liq Class (Liq Detect)
dV = r if r < mV else mV
if dV < Rest: break # ??
dV -= Rest # the last Rest uL have to be aspired with the other Liq Class
Asp.volume = dV # with Liq Class with Detect: ">> AVR-Serum 1000 << 365"
Dst.volume = dV
Asp.liquidClass = Te_Mag_LC # ">> AVR-Serum 1000 << 365" # "No Liq Detect"
Asp.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Centre
with tips(allow_air=CtrVol):
Asp.exec()
if dV + Rest + RestPlus + 2 * CtrVol > mV:
Dst.exec()
r -= dV
Dst.volume = 0
else:
break
Asp.volume = Rest
Asp.liquidClass = Te_Mag_Rest # ">> AVR-Serum 1000 << 367" # "No Liq Detect"
with tips(allow_air=Rest):
Asp.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Force_Centre
with tips(allow_air=CtrVol):
Asp.exec()
Asp.volume = RestPlus
Asp.liquidClass = Te_Mag_RestPlus # ">> AVR-Serum 1000 << 369" # "No Liq Detect"
with tips(allow_air=RestPlus):
Asp.exec()
#Ctr.exec()
Asp.volume = CtrVol
Asp.liquidClass = Te_Mag_Force_Centre
Dst.volume += Rest + RestPlus
with tips(allow_air=CtrVol):
Asp.exec()
with tips(allow_air=Rest + RestPlus):
Dst.exec()
SampleCnt -= nt
Asp.labware.selectOnly(oriSel)
Itr.wash_tips(wasteVol=4).exec()
return oriSel
def Run(self):
self.set_EvoMode()
self.initialize()
Rtv.NumOfSamples = self.NumOfSamples
NumOfSamples = self.NumOfSamples
wt = self.worktable
Itr.comment((self.version + 'for extracting RNA from {:s} samples with the MN-Vet kit').format(str(NumOfSamples))).exec()
# Get Labwares (Cuvette, eppys, etc.) from the work table
if self.add_VL:
LysBuf = wt.getLabware(Lab.Trough_100ml, "2-Vl Lysis Buffer" )
if self.do_extraction:
BindBuf = wt.getLabware(Lab.Trough_100ml, "3-VEB Binding Buffer" )
ElutBuf = wt.getLabware(Lab.Trough_100ml, "1-VEL-ElutionBuffer" )
Eluat = wt.getLabware(Lab.EppRack3x16R, "Eluat")
Samples = wt.getLabware(Lab.EppRack3x16, "Proben")
Lysis = Samples
DiTi1000_1 = wt.getLabware(Lab.DiTi_1000ul, "1000-1")
DiTi1000_2 = wt.getLabware(Lab.DiTi_1000ul, "1000-2")
DiTi1000_3 = wt.getLabware(Lab.DiTi_1000ul, "1000-3")
Reactives = wt.getLabware(Lab.GreinRack16_2mL, "Reactives" )
if self.do_extraction:
self.TeMg_Heat = wt.getLabware(Lab.TeMag48, "48 Pos Heat")
self.TeMag = wt.getLabware(Lab.TeMag48, "48PosMagnet")
TeMag = self.TeMag
Lysis = TeMag
# Set the initial position of the tips
self.go_first_pos()
# Set volumen / sample
SampleVolume = 200.0
LysisBufferVolume = 180.0 # VL
IC2Volume = 4.0 # IC2
BindingBufferVolume = 600.0 # VEB
B_BeadsVolume = 20.0 # B-Beads
VEW1Volume = 600.0 # VEW1
VEW2Volume = 600.0 # VEW2
EtOH80pVolume = 600.0
ProtKVolume = 20.0
cRNAVolume = 4.0
IC_MS2Volume = 20.0 # MS2
ElutionBufferVolume = 100.0 # VEL
InitLysisVol = 0.0
if self.do_extraction:
if not self.add_samples: InitLysisVol += SampleVolume
if not self.add_preMix: InitLysisVol += ProtKVolume + cRNAVolume + IC_MS2Volume
if not self.add_VL: InitLysisVol += LysisBufferVolume
# Liquid classes used for pippetting.
# Others liquidClass names are defined in "protocol_steps.py"
SampleLiqClass = "Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
all_samples = range(NumOfSamples)
maxTips = min (self.nTips, NumOfSamples)
maxMask = Rbt.tipsMask[maxTips]
if self.do_extraction:
par = TeMag.parallelOrder(self.nTips, all_samples)
# Define the reactives in each labware (Cuvette, eppys, etc.)
# IC2 = Rtv.Reagent("IC2 - synthetic RNA " , Reactives, pos=13, volpersample= IC2Volume ,defLiqClass=W_liquidClass)
if self.add_preMix:
ProtK = Rtv.Reagent("Proteinase K ",
Reactives,
replicas=2,
pos=[15, 16], # only 16 ? pos=16
volpersample=ProtKVolume,
defLiqClass=Small_vol_disp)
cRNA = Rtv.Reagent("Carrier RNA ", Reactives, pos=14, volpersample=cRNAVolume, defLiqClass=Small_vol_disp)
IC_MS2 = Rtv.Reagent("IC MS2 phage culture ", Reactives, pos=13, volpersample=IC_MS2Volume, defLiqClass=Small_vol_disp)
pK_cRNA_MS2 = Rtv.preMix("ProtK+cRNA+IC-MS2 mix ",
Reactives,
pos=8,
components=[cRNA, ProtK, IC_MS2],
defLiqClass=W_liquidClass,
excess=20)
if self.add_VL:
LysisBuffer = Rtv.Reagent("VL - Lysis Buffer ", LysBuf, volpersample=LysisBufferVolume, defLiqClass='MN VL')
if self.do_extraction:
B_Beads = Rtv.Reagent("B - Beads ",
Reactives,
pos = [1,2],
initial_vol = 1200,
volpersample = B_BeadsVolume,
defLiqClass = Beads_LC_2,
maxFull = 70)
BindingBuffer = Rtv.Reagent("VEB - Binding Buffer ", BindBuf, volpersample=BindingBufferVolume, defLiqClass=B_liquidClass)
VEW1 = Rtv.Reagent("VEW1 - Wash Buffer ",
wt.getLabware(Lab.Trough_100ml, "4-VEW1 Wash Buffe"),
volpersample = VEW1Volume,
defLiqClass = B_liquidClass)
VEW2 = Rtv.Reagent("VEW2 - WashBuffer ",
wt.getLabware(Lab.Trough_100ml, "5-VEW2-WashBuffer" ),
volpersample =VEW2Volume,
defLiqClass =B_liquidClass)
EtOH80p = Rtv.Reagent("Ethanol 80% ",
Lab.getLabware(Lab.Trough_100ml, "7-EtOH80p" ),
volpersample=EtOH80pVolume, defLiqClass=B_liquidClass)
ElutionBuffer = Rtv.Reagent("Elution Buffer ",
ElutBuf,
volpersample =ElutionBufferVolume,
defLiqClass =B_liquidClass) # defLiqClass="Eluat" ??
# Show the CheckList GUI to the user for possible small changes
self.CheckList()
self.set_EvoMode()
# Define the reactives not shown in the CheckList GUI
# Define samples and the place for temporal reactions
for s in all_samples:
Rtv.Reagent("lysis_{:02d}".format(s + 1), Lysis, initial_vol=InitLysisVol,
pos=s + 1, defLiqClass=SampleLiqClass, excess=0)
if self.do_extraction:
Rtv.Reagent("RNA_{:02d}".format(s + 1), Eluat, initial_vol= 0.0,
pos=s+1, defLiqClass=def_liquidClass, excess=0)
if self.add_samples:
Rtv.Reagent("probe_{:02d}".format(s + 1), Samples, single_use=SampleVolume,
pos=s+1, defLiqClass=SampleLiqClass, excess=0)
Itr.wash_tips(wasteVol=30, FastWash=True).exec()
if self.do_extraction:
Te_MagS_ActivateHeater(50).exec()
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Dispense).exec()
if self.add_preMix: # add ProtK+cRNA+MS2 mix
with self.tips(tipsMask=maxMask, reuse=True, drop=False):
self.makePreMix(pK_cRNA_MS2)
self.spread ( reactive=pK_cRNA_MS2, to_labware_region= Lysis.selectOnly(all_samples))
if self.add_samples: # add samples
with self.tips(reuse=True, drop=True, preserve=True):
self.transfer( from_labware_region = Samples,
to_labware_region = Lysis,
volume = SampleVolume,
using_liquid_class = (SampleLiqClass, "Serum Disp postMix3"),
optimizeFrom = False,
optimizeTo = True,
NumSamples = NumOfSamples)
Itr.wash_tips(wasteVol=4, FastWash=True).exec()
if self.add_VL: # add LysisBuffer
with self.tips(reuse=True, drop=False): # better reuse=True, drop=False ??
self.spread ( reactive=LysisBuffer, to_labware_region= Lysis.selectOnly(all_samples))
if not self.do_extraction:
self.done()
return
with incubation(10): pass
with group("Beads binding"):
with self.tips(tipsMask=maxMask, reuse=True, drop=False):
for p in [40, 50, 60, 65]:
self.mix_reactive(B_Beads, LiqClass=Beads_LC_1, cycles=1, maxTips=maxTips, v_perc=p)
with self.tips(reuse=True, drop=True):
self.spread( reactive=B_Beads, to_labware_region=TeMag.selectOnly(all_samples))
with self.tips(reuse=True, drop=False, preserve=True, usePreserved=True):
self.wash_in_TeMag(reactive=BindingBuffer, wells=all_samples)
with self.tips(reuse=True, drop=False, preserve=True):
self.wash_in_TeMag(reactive=VEW1, wells=all_samples)
self.wash_in_TeMag(reactive=VEW2, wells=all_samples)
with self.group("Wash in TeMag with " + EtOH80p.name), self.tips():
self.spread( reactive=EtOH80p, to_labware_region= TeMag.selectOnly(all_samples))
with parallel_execution_of(mix_mag_sub, repeat=NumOfSamples//self.nTips + 1):
self.mix( TeMag.selectOnly(all_samples), EtOH80p.defLiqClass)
with incubation(minutes=0.5):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Aspirate, z_pos=24).exec()
with self.tips(usePreserved=self.preserveingTips()):
self.waste( from_labware_region= TeMag.selectOnly(all_samples))
with incubation(minutes=4):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Incubation).exec()
with incubation(minutes=4):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Aspirate, z_pos=24).exec()
self.spread( reactive=ElutionBuffer, to_labware_region=TeMag.selectOnly(all_samples))
with incubation(minutes=2):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Incubation).exec()
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Dispense).exec()
with parallel_execution_of(mix_mag_eluat, repeat=NumOfSamples//self.nTips+1):
self.mix(TeMag.selectOnly(all_samples), ElutionBuffer.defLiqClass)
with self.tips(usePreserved=self.preserveingTips(), preserve=False, drop=True):
with incubation(minutes=1.0, timer=2):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Aspirate).exec()
self.transfer( from_labware_region= TeMag.selectOnly(all_samples),
to_labware_region= Eluat.selectOnly(all_samples),
volume= ElutionBufferVolume,
optimizeTo= False,
using_liquid_class=(ElutionBuffer.defLiqClass, ElutionBuffer.defLiqClass))
self.done()
def extractRNA_with_MN_Vet_Kit(NumOfSamples, CheckList=None):
Rtv.NumOfSamples = NumOfSamples
import protocols.RNAextractionMN_Mag.RobotInitRNAextraction as RI
Itr.comment('Extracting RNA from {:s} samples with the MN-Vet kit'.format(
str(NumOfSamples))).exec()
# DiTi1000_1.fill('C06')
# DiTi1000_2.fill('A11')
# DiTi1000_3.fill('A10')
Itr.set_DITI_Counter2(RI.DiTi1000_1, posInRack='A01').exec()
SampleVolume = 200.0
LysisBufferVolume = 180.0
IC2Volume = 4.0
BindingBufferVolume = 600.0
B_BeadsVolume = 20.0
VEW1Volume = 600.0
VEW2Volume = 600.0
EtOH80pVolume = 600.0
ProtKVolume = 20.0
cRNAVolume = 4.0
IC_MS2Volume = 20.0
ElutionBufferVolume = 100.0
SampleLiqClass = "Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
all_samples = range(Rtv.NumOfSamples)
maxTips = min(Rbt.nTips, Rtv.NumOfSamples)
maxMask = Rbt.tipsMask[maxTips]
par = RI.TeMag.parallelOrder(Rbt.nTips, all_samples)
LysisBuffer = Rtv.Reactive("VL - Lysis Buffer ",
RI.LysBuf,
volpersample=LysisBufferVolume,
defLiqClass=B_liquidClass)
IC2 = Rtv.Reactive("IC2 - synthetic RNA ",
RI.Reactives,
pos=11,
volpersample=IC2Volume,
defLiqClass=W_liquidClass)
BindingBuffer = Rtv.Reactive("VEB - Binding Buffer ",
RI.BindBuf,
volpersample=BindingBufferVolume,
defLiqClass=B_liquidClass)
B_Beads = Rtv.Reactive("B - Beads ",
RI.Reactives,
initial_vol=1200,
pos=1,
volpersample=B_BeadsVolume,
replicas=2,
defLiqClass=Beads_LC_2)
VEW1 = Rtv.Reactive("VEW1 - Wash Buffer ",
Lab.Cuvette(Lab.Trough_100ml,
Lab.Labware.Location(22, 4),
"4-VEW1 Wash Buffer"),
volpersample=VEW1Volume,
defLiqClass=B_liquidClass)
VEW2 = Rtv.Reactive("VEW2 - WashBuffer ",
Lab.Cuvette(Lab.Trough_100ml,
Lab.Labware.Location(22, 5),
"5-VEW2-WashBuffer"),
volpersample=VEW2Volume,
defLiqClass=B_liquidClass)
EtOH80p = Rtv.Reactive("Ethanol 80% ",
Lab.Cuvette(Lab.Trough_100ml,
Lab.Labware.Location(24, 1),
"7-Ethanol 80%"),
volpersample=EtOH80pVolume,
defLiqClass=B_liquidClass)
ElutionBuffer = Rtv.Reactive("Elution Buffer ",
RI.ElutBuf,
volpersample=ElutionBufferVolume,
defLiqClass="Eluat")
ProtK = Rtv.Reactive("Proteinase K ",
RI.Reactives,
pos=16,
volpersample=ProtKVolume,
defLiqClass=Small_vol_disp)
cRNA = Rtv.Reactive("Carrier RNA ",
RI.Reactives,
pos=15,
volpersample=cRNAVolume,
defLiqClass=Small_vol_disp)
IC_MS2 = Rtv.Reactive("IC MS2 phage culture ",
RI.Reactives,
pos=14,
volpersample=IC_MS2Volume,
defLiqClass=Small_vol_disp)
pK_cRNA_MS2 = Rtv.preMix("ProtK+cRNA+IC-MS2 mix ",
RI.Reactives,
pos=12,
components=[ProtK, cRNA, IC_MS2],
defLiqClass=W_liquidClass,
replicas=2)
Waste = Rtv.Reactive("Waste ", RI.WashWaste)
if CheckList is not None:
CheckList()
for s in all_samples:
Rtv.Reactive("probe_{:02d}".format(s + 1),
RI.Samples,
single_use=SampleVolume,
pos=s + 1,
defLiqClass=SampleLiqClass,
excess=0)
Rtv.Reactive("lysis_{:02d}".format(s + 1),
RI.TeMag,
initial_vol=0.0,
pos=par[s] + 1,
defLiqClass=def_liquidClass,
excess=0)
Rtv.Reactive("RNA_{:02d}".format(s + 1),
RI.Eluat,
initial_vol=0.0,
pos=s + 1,
defLiqClass=def_liquidClass,
excess=0)
Itr.wash_tips(wasteVol=30, FastWash=True).exec()
Te_MagS_ActivateHeater(50).exec()
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Dispense).exec()
with tips(tipsMask=maxMask, reuse=True, drop=False):
pK_cRNA_MS2.make()
spread(reactive=pK_cRNA_MS2,
to_labware_region=RI.TeMag.selectOnly(all_samples))
with tips(reuse=True, drop=True, preserve=True):
transfer(from_labware_region=RI.Samples,
to_labware_region=RI.TeMag,
volume=SampleVolume,
using_liquid_class=(SampleLiqClass, "Serum Disp postMix3"),
optimizeFrom=False,
optimizeTo=True,
NumSamples=Rtv.NumOfSamples)
Itr.wash_tips(wasteVol=4, FastWash=True).exec()
with tips(reuse=False, drop=True):
spread(reactive=LysisBuffer,
to_labware_region=RI.TeMag.selectOnly(all_samples))
with incubation(10):
pass
with tips(tipsMask=maxMask, reuse=True, drop=False):
for p in [40, 50, 60, 65]:
mix_reactive(B_Beads,
LiqClass=Beads_LC_1,
cycles=1,
maxTips=maxTips,
v_perc=p)
# mix_reactive(B_Beads, LiqClass=Beads_LC_2, cycles=3, maxTips=maxTips, v_perc=90)
with tips(reuse=True, drop=True):
spread(reactive=B_Beads,
to_labware_region=RI.TeMag.selectOnly(all_samples))
with tips(reuse=True, drop=False, preserve=True, usePreserved=True):
wash_in_TeMag(reactive=BindingBuffer, wells=all_samples)
with tips(reuse=True, drop=False, preserve=True):
wash_in_TeMag(reactive=VEW1, wells=all_samples)
wash_in_TeMag(reactive=VEW2, wells=all_samples)
with group("Wash in TeMag with " + EtOH80p.name), tips():
spread(reactive=EtOH80p,
to_labware_region=RI.TeMag.selectOnly(all_samples))
with parallel_execution_of(mix_mag_sub,
repeat=Rtv.NumOfSamples // Rbt.nTips +
1):
mix(RI.TeMag.selectOnly(all_samples), EtOH80p.defLiqClass)
with incubation(minutes=0.5):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Aspirate,
z_pos=24).exec()
with tips(usePreserved=preserveingTips()):
waste(from_labware_region=RI.TeMag.selectOnly(all_samples))
with incubation(minutes=4):
Te_MagS_MoveToPosition(
Te_MagS_MoveToPosition.Incubation).exec()
with incubation(minutes=4):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Aspirate,
z_pos=24).exec()
spread(reactive=ElutionBuffer,
to_labware_region=RI.TeMag.selectOnly(all_samples))
with incubation(minutes=2):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Incubation).exec()
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Dispense).exec()
with parallel_execution_of(mix_mag_eluat,
repeat=Rtv.NumOfSamples // Rbt.nTips + 1):
mix(RI.TeMag.selectOnly(all_samples), ElutionBuffer.defLiqClass)
with tips(usePreserved=preserveingTips(), preserve=False, drop=True):
with incubation(minutes=1.0, timer=2):
Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Aspirate).exec()
transfer(from_labware_region=RI.TeMag.selectOnly(all_samples),
to_labware_region=RI.Eluat.selectOnly(all_samples),
volume=ElutionBufferVolume,
optimizeTo=False,
using_liquid_class=(ElutionBuffer.defLiqClass,
ElutionBuffer.defLiqClass))