########################################################################
### FILE:	example.mod
### PURPOSE:	Sample protocols for the Magnum PI instrument
### SCOPE:	"FlowChip<n>" branches
### VERSION:	0.6.2
### HISTORY:
###   2010-01-07	Tor Slettnes
###		Created
###
### Copyrights (C) 2010 Life Technologies.  All rights reserved.
#########################################################################


PROCedure PRIME $PrimerCycle$=1 $PrimerTypes$ $States$ $Lanes$ <quote>

    ### Determine active and inactive lanes
01  SET ActiveLanes   $(FILTer? -mask=active   -inputs=$States$ -outputs=$Lanes$)
02  SET InactiveLanes $(FILTer? -mask=inactive -inputs=$States$ -outputs=$Lanes$)
03  SET ActivePrimers $(FILTer? -mask=active   -inputs=$States$ -outputs=$PrimerTypes$)

    ### Set Temperature to 25 degrees C
04  RAMP 25

    ### Deliver TFE to inactive lanes
06  TRANsfer -volume=50 TFE ${InactiveLanes}

    ### Set temperature to 75 degrees C
07  RAMP 75

    ### Incubate for one minute, while rinsing inside/outside tip in water
08  TIMER Incubate 60 
09  RINSE -part=Inside   -duration=2
10  RINSE -part=Outside  -duration=2
11  SYNC Incubate 

    ### Set temperature to 70 degrees C
12  RAMP 70

    ### Incubate for 2 minutes
13  TIMER Incubate 120
14  SYNC  Incubate

    ### Set temperature to 65 degrees C
15  RAMP 65

    ### Incubate for 2 minutes while pre-mixing ligate
16  TIMER Incubate 120

    ### PREMIX LIGASE BEGIN
17      SET NumLanes $(COUNT? "active" $States$)

18      ASPIRATE -count=${NumLanes} -volume=26 LigaseBuffer
19      ASPIRATE -volume=2  AIR
20      ASPIRATE -count=${NumLanes} -volume=2  FwdProbeA
21      ASPIRATE -volume=2  AIR
22      ASPIRATE -count=${NumLanes} -volume=2  FwdLigase
23      ASPIRATE -volume=2  AIR
24      DISPENSE -count=${NumLanes} -volume=36 FwdLigMixA

25      MIX -count=3 FwdLigMixA

26      RINSE -part=Inside  -duration=2
27      RINSE -part=Outside -duration=2
    ### PREMIX LIGATE END

    ### Wait for Incubation
30  SYNC Incubate

    ### Set temperature to 60 degrees, incubate 2 minutes
31  RAMP 60
32  TIMER Incubate 120
33  SYNC Incubate

    ### Set temperature to 25 degrees
34  RAMP 25

35  TRANsfer -volume=200 TMAX $Lanes$
</quote>




PROCedure TEST $States$ $Lanes$ <quote>

    ### Determine active and inactive lanes
01  SET ActiveLanes   $(FILTer? -mask=active   -inputs=$States$ -outputs=$Lanes$)
02  SET InactiveLanes $(FILTer? -mask=inactive -inputs=$States$ -outputs=$Lanes$)

    ### Set Temperature to 25 degrees C
04  RAMP 25

    ### Acquire robot, prevent use for other flowchip
05  USE Robot

    ### Deliver TMAX to inactive lanes
06  TRANsfer -volume=50 TMAX ${InactiveLanes}

    ### Set temperature to 75 degrees C
07  RAMP 75 -asynchronous

    ### Rinse 
08  RinseInside 2
09  RinseOutside 2

    ### Incubate for one minute, while rinsing inside/outside tip in water
10  TIMER Incubate 60

    ### Release robot while incubating
11  RELEASE Robot

12  SYNC Ramping
13  SYNC Incubate 

    ### Set temperature to 65 degrees C
17  RAMP 65

    ### Incubate for 1 minute while pre-mixing ligate
18  TIMER Incubate 60
   
    ### PREMIX LIGASE BEGIN
        USE Robot 
19      SET NumLanes $(COUNT? "active" $States$)

20      ASPIRATE -count=${NumLanes} -volume=26 LigaseBuffer
21      ASPIRATE -volume=2  AIR
22      ASPIRATE -count=${NumLanes} -volume=2  FwdProbeA
23      ASPIRATE -volume=2  AIR
24      ASPIRATE -count=${NumLanes} -volume=2  FwdLigase
25      ASPIRATE -volume=2  AIR
26      DISPENSE -count=${NumLanes} -volume=36 FwdLigMixA

27      MIX -count=3 -volume=72 FwdLigMixA

28      RINSE -part=Inside  -duration=2
29      RINSE -part=Outside -duration=2
30      RELEASE Robot
    ### PREMIX LIGATE END

    ### Wait for Incubation
31  SYNC Incubate

    ### Set temperature to 25 degrees
34  RAMP 25

35  USE Robot
36  TRANsfer -volume=200 TMAX $Lanes$
37  RELEASE Robot
</quote>