def reset(self): 'Reset this experiment so we can generate it again after adjusting the reagent initial volumes and total time' totalTime=clock.elapsed() clock.reset(totalTime) #print "After reset, elapsed=%d"%clock.elapsed() worklist.reset() self.e=Experiment() self.e.setreagenttemp(6.0) self.e.sanitize(3,50) # Heavy sanitize reagents.reset() Sample.clearall() decklayout.initWellKnownSamples()
def reset(self): 'Reset this experiment so we can generate it again after adjusting the reagent initial volumes and total time' totalTime = clock.elapsed() clock.reset(totalTime) #print "After reset, elapsed=%d"%clock.elapsed() worklist.reset() self.e = Experiment() self.e.setreagenttemp(6.0) self.e.sanitize(3, 50) # Heavy sanitize reagents.reset() Sample.clearall() decklayout.initWellKnownSamples()
def execute(self,ops): reagents=None for iteration in range(2): print "Iteration ",iteration+1 # Need to clear here trp=TRP() if iteration==0: trp.addTemplates(["IN"],200) # Add a template with stock concentration 200nM else: reagents=Sample.getAllOnPlate(Experiment.REAGENTPLATE) for r in reagents: if r.volume<0: r.initvolume=-r.volume+10 Sample.clearall() ops(self) trp.finish()
reagents=None for iteration in range(2): print "Iteration ",iteration+1 trp=TRP() if iteration==0: trp.addTemplates(input,stockconc=10.0/6.0,units="x",plate=Experiment.EPPENDORFS) # Add a template else: reagents=Sample.getAllOnPlate(Experiment.REAGENTPLATE)+Sample.getAllOnPlate(Experiment.EPPENDORFS) for r in reagents: if r.volume<=0: r.initvolume=-r.volume+r.plate.unusableVolume Sample.clearall() t71=trp.runT7(theo=False,src=srcs,tgt=[],vol=10,srcdil=10.0/6,dur=15,stopmaster=stop) #print t71 t71=trp.diluteInPlace(tgt=t71,dil=5) # Dilute input samples enough to use in qPCR directly (should be 5000/(rnagain*2*5) = 20) qpcrdil1=trp.runQPCRDIL(src=t71,tgt=[],vol=100,srcdil=20,dilPlate=False) rt1=trp.runRT(pos=True,src=t71,tgt=[],vol=30,srcdil=2) rt1=trp.diluteInPlace(tgt=rt1,dil=5) lig=trp.runLig(src=rt1*6,tgt=[],vol=20,srcdil=3,master=ligmaster1*3+ligmaster2*3) prods=trp.diluteInPlace(tgt=lig,dil=10) print "prod=",prods for i in range(len(qpcrdil1)): trp.runQPCR(src=qpcrdil1[i],vol=15,srcdil=10.0/4,primers=[tmplqpcr[i]],nreplicates=3)
input = "BT409" srcprefix = "B" prodprefix = "A" for iteration in range(2): print "Iteration ", iteration + 1 trp = TRP() if iteration == 0: trp.addTemplates([input], 200) # Add a template with stock concentration 200nM else: reagents = Sample.getAllOnPlate(Experiment.REAGENTPLATE) for r in reagents: if r.volume < 0: r.initvolume = -r.volume + 20 Sample.clearall() # Round 1 (Keep uncleaved +theo) t71 = trp.runT7(theo=[False, True], src=[input, input], tgt=[], vol=[16, 18], srcdil=4) sv1t7 = trp.saveSamps(src=t71, tgt=[], vol=10, dil=[4, 4]) rt1 = trp.runRT(pos=[True, True], src=t71, tgt=[], vol=[15, 22], srcdil=2) trp.diluteInPlace(tgt=rt1, dil=2) sv1rt = trp.saveSamps(src=rt1, tgt=[], vol=15, dil=2) pcr1 = trp.runPCR(prefix=[srcprefix], src=rt1[1], tgt=[], vol=50, srcdil=4) trp.diluteInPlace(tgt=pcr1, dil=3) sv1pcr = trp.saveSamps(src=pcr1, tgt=["R1"], vol=125, dil=1)