R/procedures.R
In dcangst/rrobot: Useful R functions for the Tecan Freedom Evo
Defines functions
washPinTool
iPTdip
iPTdeactivate
tiptouch
sterile_wash_phage
sterile_wash_TT
sterile_wash_c
sterile_wash
evowait
Documented in
evowait
iPTdeactivate
iPTdip
sterile_wash
sterile_wash_c
sterile_wash_phage
sterile_wash_TT
tiptouch
washPinTool
#' wait for t seconds
#'
#' simpler timer
#'
#' @param timer Number of Timer to (re-)start
#' @param timeSpan duration [0.02 - 86400]
#' @family advanced worklist procedures
#' @export
evowait <- function(timer, timeSpan){
startTimer(timer)
waitTimer(timer, timeSpan)
}
#' Custom Sterile Wash procedure
#'
#' Washes & sterilizes all tips, hopefully.
#'
#' @param wash_solution1 RackLabel containing first wash solution
#' @param wash_solution1_liquidClass LiquidClass used to pipet first wash
#' solution
#' @param wash_solution1_volume volume used in first wash
#' @param wash_solution2 RackLabel containing second wash solution
#' @param wash_solution2_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution2_volume volume used in second wash
#' @param wash_solution3 RackLabel containing second wash solution
#' @param wash_solution3_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution3_volume volume used in third wash
#' @family advanced worklist procedures
#' @export
sterile_wash <- function(
wash_solution1 = "trough_bleach",
wash_solution1_liquidClass = "sterileWash_N_bleach",
wash_solution1_volume = 300,
wash_solution2 = "trough_EtOH",
wash_solution2_liquidClass = "sterileWash_N_EtOH",
wash_solution2_volume = 400,
wash_solution3 = "trough_H2O",
wash_solution3_liquidClass = "sterileWash_N_H2O",
wash_solution3_volume = 450
){
adv_gwl_comment("sterile wash: NORMAL")
gwl_comment("START: sterile wash: NORMAL")
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash2_waste",
RackLabel_cleaner = "wash2_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 0.1, cleanerDelay = 0, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(wash_solution1_volume, 8), RackLabel = wash_solution1, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(wash_solution1_volume, 8), RackLabel = wash_solution1,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 2, cleanerDelay = 500, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(wash_solution2_volume, 8), RackLabel = wash_solution2, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(wash_solution2_volume, 8), RackLabel = wash_solution2,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(wash_solution3_volume, 8), RackLabel = wash_solution3, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(wash_solution3_volume, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
moveLiHa(tipMask = rep(1, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8,
zMove = 0, zTarget = 4, offset = 0, speed = 10,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0, arm = 0)
gwl_comment("END: sterile wash: NORMAL")
}
#' Custom Sterile Wash procedure fro chemicals only
#'
#' Washes & sterilizes all tips, hopefully. skips bleach
#'
#' @param wash_solution1 RackLabel containing first wash solution
#' @param wash_solution1_liquidClass LiquidClass used to pipet first wash
#' solution
#' @param wash_solution1_volume volume used in first wash
#' @param wash_solution2 RackLabel containing second wash solution
#' @param wash_solution2_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution2_volume volume used in second wash
#' @param wash_solution3 RackLabel containing second wash solution
#' @param wash_solution3_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution3_volume volume used in third wash
#' @family advanced worklist procedures
#' @export
sterile_wash_c <- function(
wash_solution1 = "trough_EtOH",
wash_solution1_liquidClass = "sterileWash_N_EtOH",
wash_solution1_volume = 300,
wash_solution2 = "trough_EtOH",
wash_solution2_liquidClass = "sterileWash_N_EtOH",
wash_solution2_volume = 400,
wash_solution3 = "trough_H2O",
wash_solution3_liquidClass = "sterileWash_N_H2O",
wash_solution3_volume = 450
){
adv_gwl_comment("sterile wash: NORMAL")
gwl_comment("START: sterile wash: NORMAL")
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash2_waste",
RackLabel_cleaner = "wash2_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 0.1, cleanerDelay = 0, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(wash_solution1_volume, 8), RackLabel = wash_solution1, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(wash_solution1_volume, 8), RackLabel = wash_solution1,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 2, cleanerDelay = 500, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(wash_solution2_volume, 8), RackLabel = wash_solution2, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(wash_solution2_volume, 8), RackLabel = wash_solution2,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(wash_solution3_volume, 8), RackLabel = wash_solution3, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(wash_solution3_volume, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
moveLiHa(tipMask = rep(1, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8,
zMove = 0, zTarget = 4, offset = 0, speed = 10,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0, arm = 0)
gwl_comment("END: sterile wash: NORMAL")
}
#' Short Sterile Wash procedure for Tip Touch Transfers
#'
#' Washes & sterilizes all tips, hopefully.
#'
#' @param wash_rack Wash station used (default: wash1_shallow)
#' @param wash_waste Waste used (default: wash1_waste)
#' @param wash_solution1 RackLabel containing first wash solution
#' @param wash_solution1_liquidClass LiquidClass used to pipet first wash
#' solution
#' @param wash_solution2 RackLabel containing second wash solution
#' @param wash_solution2_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution3 RackLabel containing second wash solution
#' @param wash_solution3_liquidClass LiquidClass used to pipet
#' second wash solution
#' @family advanced worklist procedures
#' @export
sterile_wash_TT <- function(
wash_solution1="trough_bleach",
wash_solution1_liquidClass = "sterileWash_TT_bleach",
wash_solution2="trough_EtOH",
wash_solution2_liquidClass = "sterileWash_TT_EtOH",
wash_solution3="trough_H2O",
wash_solution3_liquidClass = "sterileWash_TT_H2O"
){
gwl_comment("START: sterile wash: TipTouch")
adv_gwl_comment("sterile wash: TipTouch")
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash2_waste",
RackLabel_cleaner = "wash2_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 0.1, cleanerDelay = 0, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(350, 8), RackLabel = wash_solution1, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(350, 8), RackLabel = wash_solution1,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow", wasteVol = 3, wasteDelay = 500,
cleanerVol = 5, cleanerDelay = 500, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution2, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution2,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution3, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
moveLiHa(tipMask = rep(1, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8,
zMove = 0, zTarget = 4, offset = 0, speed = 10,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0, arm = 0)
gwl_comment("END: sterile wash: TipTouch")
}
#' Custom Sterile Wash procedure for Phage work
#'
#' Washes & sterilizes all tips, hopefully. Kills phages, hopefully.
#'
#' @param wash_rack Wash station used (default: wash1_shallow)
#' @param wash_waste Waste used (default: wash1_waste)
#' @param wash_solution1 RackLabel containing first wash solution
#' @param wash_solution1_liquidClass LiquidClass used to pipet first wash
#' solution
#' @param wash_solution2 RackLabel containing second wash solution
#' @param wash_solution2_liquidClass LiquidClass used to pipet second wash
#' solution
#' @param wash_solution3 RackLabel containing third wash solution
#' @param wash_solution3_liquidClass LiquidClass used to pipet
#' third wash solution
#' @param wash_solution4 RackLabel containing fourth wash solution
#' @param wash_solution4_liquidClass LiquidClass used to pipet
#' fourth wash solution
#' @family advanced worklist procedures
#' @export
sterile_wash_phage <- function(
wash_solution1 = "trough100_bck",
wash_solution1_liquidClass = "sterileWash_N_NaOH",
wash_solution2 = "trough_bleach",
wash_solution2_liquidClass = "sterileWash_N_bleach",
wash_solution3 = "trough_EtOH",
wash_solution3_liquidClass = "sterileWash_N_EtOH",
wash_solution4 = "trough_H2O",
wash_solution4_liquidClass = "sterileWash_N_H2O"
){
adv_gwl_comment("sterile wash: PHAGE")
gwl_comment("START: sterile wash: PHAGE")
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(300, 8), RackLabel = wash_solution1, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(300, 8), RackLabel = wash_solution1,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash2_waste",
RackLabel_cleaner = "wash2_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 0.1, cleanerDelay = 0, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(300, 8), RackLabel = wash_solution2, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(300, 8), RackLabel = wash_solution2,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 2, cleanerDelay = 500, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution3, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution4_liquidClass,
volumes = rep(450, 8), RackLabel = wash_solution4, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution4_liquidClass,
volumes = rep(450, 8), RackLabel = wash_solution4,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
moveLiHa(tipMask = rep(1, 8), RackLabel = wash_solution4,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8,
zMove = 0, zTarget = 4, offset = 0, speed = 10,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0, arm = 0)
gwl_comment("END: sterile wash: PHAGE")
}
#' Tip Touch
#'
#' Transfering by tiptouching using the tips
#'
#' @param tip_mask tip mask for source
#' @param wells Wells source
#' @param rack RackLabel of source
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param speed_move movement speed up to z-dispense
#' @param speed_in movement speed when dipping
#' @param speed_out movement speed when retracting
#' @family advanced worklist procedures
#' @export
tiptouch <- function(
tip_mask,
wells,
rack,
ncol = 24,
nrow = 16,
spacing = 2,
speed_move,
speed_in,
speed_out){
# get innoculum
moveLiHa( # move to z-travel
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 0,
zTarget = 0,
offset = 0,
speed = speed_move)
moveLiHa( # move z to z-dispense
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 4,
zTarget = 1,
offset = 0,
speed = speed_move)
moveLiHa( # move z to z-max
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 4,
zTarget = 3,
offset = 0,
speed = speed_in)
moveLiHa( # move z to z-dispense
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 4,
zTarget = 1,
offset = 0,
speed = speed_out)
moveLiHa( # move to z-travel
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 0,
zTarget = 0,
offset = 0,
speed = speed_move)
}
#' iPinTool deactivate pins
#'
#' generates worklist procedures to deactivate pins. All pins are always activated
#' when the pin tool is dropped onto the carrier.
#'
#' @param pins vector of integers 1:384, designating the pins to be deactivated.
#' @param RackLabel name of carrier as on gwl$worktable
#' @param readyVector name of the vector to move over the stub
#' @param pushVector1 name of the vector that pushes the pins 1-192
#' @param pushVector2 name of the vector that pushes the pins 193-384
#' @family advanced worklist procedures
#' @export
iPTdeactivate <- function(
pins,
RackLabel = "iPT tool",
readyVector = "PT getReady",
pushVector1 = "PT Act 1-192",
pushVector2 = "PT Act 193-384"){
adv_gwl_comment("preparing iPT384...")
adv_gwl_comment(
str_c("deactivating pins: ", str_c(pins, collapse = ", "))
)
grid <- getGridSite(RackLabel)$grid
pins_sorted <- shortestPath(pins)
MCAvector(readyVector, grid, 1, back = 0)
for (i in pins_sorted){
if (i <= 192){
MCAvector(pushVector1, grid, i)
} else {
MCAvector(pushVector2, grid, i - 192)
}
}
MCAvector(readyVector, grid, 1, back = 0, direction = 1)
}
#' iPT384 pin transfer
#'
#' pick up 4 adjacent wells on a 384 well plate with the 4 pins in the back left
#' corner of the iPT384. Make sure all other pins are deactivated!
#'
#' @param rack string, Racklabel of target, as in gwl$worktable
#' @param well int 1:384, which well should be hit with pin 1
#' @param n_dips number of dips in plate
#' @param speed_move movement speed up to z-dispense
#' @param speed_in movement speed when dipping
#' @param speed_out movement speed when retracting
#' @family advanced worklist procedures
#' @export
iPTdip <- function(
rack,
well,
n_dips = 3,
speed_move = 35,
speed_in = 5,
speed_out = 5){
well_row <- (well - 1) %/% 24
well_col <- well - well_row * 24 - 1
adv_gwl_comment(str_c(
"dipping ", n_dips, "x in ", rack))
MCArelative(well_col, well_row)
moveMCA( # move over plate, z-travel
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 0,
zTarget = 0,
offset = 0,
speed = speed_move)
moveMCA( # z-move to z-dispense
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 4,
zTarget = 1,
offset = 0,
speed = speed_move)
for (i in 1:n_dips){
moveMCA( # z-move to z-max
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 4,
zTarget = 3,
offset = 0,
speed = speed_in)
moveMCA( # z-move to z-dispense
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 4,
zTarget = 1,
offset = 0,
speed = speed_out)
}
moveMCA( # z-move to global z-travel
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 4,
zTarget = 4,
offset = 0,
speed = speed_move)
MCArelative() # reset offset
}
#' Wash pin tool
#'
#' Procedure to wash pintool
#'
#' @param t_wait integer, time (s) to wait on blotting paper
#' @param t_dry integer, time (s) over dryer
#' @param n_dips_1 integer, number of dips in reagent 1
#' @param n_dips_2 integer, number of dips in reagent 2
#' @param n_dips_3 integer, number of dips in reagents 3
#' @param reservoirs vector of RackLabel of reservoirs to dip
#' @param blots vector of Racklaberl of blotting spots
#' @family advanced worklist procedures
#' @export
washPinTool <- function(
t_wait = 2,
t_dry = 90,
n_dips_1 = 3, n_dips_2 = 3, n_dips_3 = 3,
reservoirs = c("Bleach", "ddH2O", "EtOH"),
blots = c("Blot_frt", "Blot_mid", "Blot_bck")){
adv_gwl_comment("washing tips...")
#dip 3x in first reservoir
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 0,
zTarget = 2,
speed = 10)
for (i in 1:(n_dips_1 - 1)){
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 3,
speed = 60)
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 2,
speed = 60)
}
# retract slowly
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 3,
speed = 60)
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 2,
speed = 5)
# blot 1
moveMCA(
RackLabel = blots[1],
zMove = 0,
zTarget = 3,
speed = 10)
# wait t_wait seconds
evowait(1, t_wait)
#dip 3x in 2nd reservoir
moveMCA(
RackLabel = reservoirs[2],
ncol = 12,
nrow = 8,
zMove = 0,
zTarget = 2,
speed = 10)
for (i in 1:n_dips_2){
moveMCA(
RackLabel = reservoirs[2],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 3,
speed = 60)
moveMCA(
RackLabel = reservoirs[2],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 2,
speed = 60)
}
# blot 2
moveMCA(
RackLabel = blots[2],
zMove = 0,
zTarget = 3,
speed = 10)
# wait t_wait seconds
evowait(1, t_wait)
#dip 3x in 3nd reservoir
moveMCA(
RackLabel = reservoirs[3],
ncol = 12,
nrow = 8,
zMove = 0,
zTarget = 2,
speed = 10)
for (i in 1:n_dips_3){
moveMCA(
RackLabel = reservoirs[3],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 3,
speed = 60)
moveMCA(
RackLabel = reservoirs[3],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 2,
speed = 60)
}
# blot 3: EtOH
moveMCA(
RackLabel = blots[3],
zMove = 0,
zTarget = 3,
speed = 10)
# wait t_wait seconds
evowait(1, t_wait)
#dry
moveMCA(
RackLabel = "PT dryer",
zMove = 0,
zTarget = 3,
speed = 10)
fwCommand("O1SLO3,1")
evowait(1, t_dry)
fwCommand("O1SLO3,0")
moveMCA(
RackLabel = "PT dryer",
zMove = 0,
zTarget = 4,
speed = 10)
}
dcangst/rrobot documentation built on April 10, 2024, 1:59 a.m.
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Defines functions washPinTool iPTdip iPTdeactivate tiptouch sterile_wash_phage sterile_wash_TT sterile_wash_c sterile_wash evowait
Documented in evowait iPTdeactivate iPTdip sterile_wash sterile_wash_c sterile_wash_phage sterile_wash_TT tiptouch washPinTool
#' wait for t seconds
#'
#' simpler timer
#'
#' @param timer Number of Timer to (re-)start
#' @param timeSpan duration [0.02 - 86400]
#' @family advanced worklist procedures
#' @export
evowait <- function(timer, timeSpan){
startTimer(timer)
waitTimer(timer, timeSpan)
}
#' Custom Sterile Wash procedure
#'
#' Washes & sterilizes all tips, hopefully.
#'
#' @param wash_solution1 RackLabel containing first wash solution
#' @param wash_solution1_liquidClass LiquidClass used to pipet first wash
#' solution
#' @param wash_solution1_volume volume used in first wash
#' @param wash_solution2 RackLabel containing second wash solution
#' @param wash_solution2_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution2_volume volume used in second wash
#' @param wash_solution3 RackLabel containing second wash solution
#' @param wash_solution3_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution3_volume volume used in third wash
#' @family advanced worklist procedures
#' @export
sterile_wash <- function(
wash_solution1 = "trough_bleach",
wash_solution1_liquidClass = "sterileWash_N_bleach",
wash_solution1_volume = 300,
wash_solution2 = "trough_EtOH",
wash_solution2_liquidClass = "sterileWash_N_EtOH",
wash_solution2_volume = 400,
wash_solution3 = "trough_H2O",
wash_solution3_liquidClass = "sterileWash_N_H2O",
wash_solution3_volume = 450
){
adv_gwl_comment("sterile wash: NORMAL")
gwl_comment("START: sterile wash: NORMAL")
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash2_waste",
RackLabel_cleaner = "wash2_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 0.1, cleanerDelay = 0, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(wash_solution1_volume, 8), RackLabel = wash_solution1, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(wash_solution1_volume, 8), RackLabel = wash_solution1,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 2, cleanerDelay = 500, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(wash_solution2_volume, 8), RackLabel = wash_solution2, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(wash_solution2_volume, 8), RackLabel = wash_solution2,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(wash_solution3_volume, 8), RackLabel = wash_solution3, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(wash_solution3_volume, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
moveLiHa(tipMask = rep(1, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8,
zMove = 0, zTarget = 4, offset = 0, speed = 10,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0, arm = 0)
gwl_comment("END: sterile wash: NORMAL")
}
#' Custom Sterile Wash procedure fro chemicals only
#'
#' Washes & sterilizes all tips, hopefully. skips bleach
#'
#' @param wash_solution1 RackLabel containing first wash solution
#' @param wash_solution1_liquidClass LiquidClass used to pipet first wash
#' solution
#' @param wash_solution1_volume volume used in first wash
#' @param wash_solution2 RackLabel containing second wash solution
#' @param wash_solution2_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution2_volume volume used in second wash
#' @param wash_solution3 RackLabel containing second wash solution
#' @param wash_solution3_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution3_volume volume used in third wash
#' @family advanced worklist procedures
#' @export
sterile_wash_c <- function(
wash_solution1 = "trough_EtOH",
wash_solution1_liquidClass = "sterileWash_N_EtOH",
wash_solution1_volume = 300,
wash_solution2 = "trough_EtOH",
wash_solution2_liquidClass = "sterileWash_N_EtOH",
wash_solution2_volume = 400,
wash_solution3 = "trough_H2O",
wash_solution3_liquidClass = "sterileWash_N_H2O",
wash_solution3_volume = 450
){
adv_gwl_comment("sterile wash: NORMAL")
gwl_comment("START: sterile wash: NORMAL")
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash2_waste",
RackLabel_cleaner = "wash2_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 0.1, cleanerDelay = 0, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(wash_solution1_volume, 8), RackLabel = wash_solution1, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(wash_solution1_volume, 8), RackLabel = wash_solution1,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 2, cleanerDelay = 500, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(wash_solution2_volume, 8), RackLabel = wash_solution2, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(wash_solution2_volume, 8), RackLabel = wash_solution2,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(wash_solution3_volume, 8), RackLabel = wash_solution3, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(wash_solution3_volume, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
moveLiHa(tipMask = rep(1, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8,
zMove = 0, zTarget = 4, offset = 0, speed = 10,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0, arm = 0)
gwl_comment("END: sterile wash: NORMAL")
}
#' Short Sterile Wash procedure for Tip Touch Transfers
#'
#' Washes & sterilizes all tips, hopefully.
#'
#' @param wash_rack Wash station used (default: wash1_shallow)
#' @param wash_waste Waste used (default: wash1_waste)
#' @param wash_solution1 RackLabel containing first wash solution
#' @param wash_solution1_liquidClass LiquidClass used to pipet first wash
#' solution
#' @param wash_solution2 RackLabel containing second wash solution
#' @param wash_solution2_liquidClass LiquidClass used to pipet
#' second wash solution
#' @param wash_solution3 RackLabel containing second wash solution
#' @param wash_solution3_liquidClass LiquidClass used to pipet
#' second wash solution
#' @family advanced worklist procedures
#' @export
sterile_wash_TT <- function(
wash_solution1="trough_bleach",
wash_solution1_liquidClass = "sterileWash_TT_bleach",
wash_solution2="trough_EtOH",
wash_solution2_liquidClass = "sterileWash_TT_EtOH",
wash_solution3="trough_H2O",
wash_solution3_liquidClass = "sterileWash_TT_H2O"
){
gwl_comment("START: sterile wash: TipTouch")
adv_gwl_comment("sterile wash: TipTouch")
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash2_waste",
RackLabel_cleaner = "wash2_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 0.1, cleanerDelay = 0, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(350, 8), RackLabel = wash_solution1, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(350, 8), RackLabel = wash_solution1,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow", wasteVol = 3, wasteDelay = 500,
cleanerVol = 5, cleanerDelay = 500, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution2, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution2,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution3, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
moveLiHa(tipMask = rep(1, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8,
zMove = 0, zTarget = 4, offset = 0, speed = 10,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0, arm = 0)
gwl_comment("END: sterile wash: TipTouch")
}
#' Custom Sterile Wash procedure for Phage work
#'
#' Washes & sterilizes all tips, hopefully. Kills phages, hopefully.
#'
#' @param wash_rack Wash station used (default: wash1_shallow)
#' @param wash_waste Waste used (default: wash1_waste)
#' @param wash_solution1 RackLabel containing first wash solution
#' @param wash_solution1_liquidClass LiquidClass used to pipet first wash
#' solution
#' @param wash_solution2 RackLabel containing second wash solution
#' @param wash_solution2_liquidClass LiquidClass used to pipet second wash
#' solution
#' @param wash_solution3 RackLabel containing third wash solution
#' @param wash_solution3_liquidClass LiquidClass used to pipet
#' third wash solution
#' @param wash_solution4 RackLabel containing fourth wash solution
#' @param wash_solution4_liquidClass LiquidClass used to pipet
#' fourth wash solution
#' @family advanced worklist procedures
#' @export
sterile_wash_phage <- function(
wash_solution1 = "trough100_bck",
wash_solution1_liquidClass = "sterileWash_N_NaOH",
wash_solution2 = "trough_bleach",
wash_solution2_liquidClass = "sterileWash_N_bleach",
wash_solution3 = "trough_EtOH",
wash_solution3_liquidClass = "sterileWash_N_EtOH",
wash_solution4 = "trough_H2O",
wash_solution4_liquidClass = "sterileWash_N_H2O"
){
adv_gwl_comment("sterile wash: PHAGE")
gwl_comment("START: sterile wash: PHAGE")
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(300, 8), RackLabel = wash_solution1, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution1_liquidClass,
volumes = rep(300, 8), RackLabel = wash_solution1,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash2_waste",
RackLabel_cleaner = "wash2_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 0.1, cleanerDelay = 0, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(300, 8), RackLabel = wash_solution2, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution2_liquidClass,
volumes = rep(300, 8), RackLabel = wash_solution2,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_wash(tipMask = rep(1, 8), RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow", wasteVol = 1, wasteDelay = 500,
cleanerVol = 2, cleanerDelay = 500, Airgap = 10, airgapSpeed = 70,
retractSpeed = 30, FastWash = 1, lowVolume = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution3, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution3_liquidClass,
volumes = rep(400, 8), RackLabel = wash_solution3,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
adv_aspirate(tipMask = rep(1, 8), liquidClass = wash_solution4_liquidClass,
volumes = rep(450, 8), RackLabel = wash_solution4, spacing = 1,
wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0, loopName = "",
action = 0, difference = 0, arm = 0)
adv_dispense(tipMask = rep(1, 8), liquidClass = wash_solution4_liquidClass,
volumes = rep(450, 8), RackLabel = wash_solution4,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8, noOfLoopOptions = 0,
loopName = "", action = 0, difference = 0, arm = 0)
moveLiHa(tipMask = rep(1, 8), RackLabel = wash_solution4,
spacing = 1, wellSelection = 1:8, ncol = 1, nrow = 8,
zMove = 0, zTarget = 4, offset = 0, speed = 10,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0, arm = 0)
gwl_comment("END: sterile wash: PHAGE")
}
#' Tip Touch
#'
#' Transfering by tiptouching using the tips
#'
#' @param tip_mask tip mask for source
#' @param wells Wells source
#' @param rack RackLabel of source
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param speed_move movement speed up to z-dispense
#' @param speed_in movement speed when dipping
#' @param speed_out movement speed when retracting
#' @family advanced worklist procedures
#' @export
tiptouch <- function(
tip_mask,
wells,
rack,
ncol = 24,
nrow = 16,
spacing = 2,
speed_move,
speed_in,
speed_out){
# get innoculum
moveLiHa( # move to z-travel
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 0,
zTarget = 0,
offset = 0,
speed = speed_move)
moveLiHa( # move z to z-dispense
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 4,
zTarget = 1,
offset = 0,
speed = speed_move)
moveLiHa( # move z to z-max
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 4,
zTarget = 3,
offset = 0,
speed = speed_in)
moveLiHa( # move z to z-dispense
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 4,
zTarget = 1,
offset = 0,
speed = speed_out)
moveLiHa( # move to z-travel
tipMask = tip_mask,
RackLabel = rack,
spacing = spacing,
wellSelection = wells,
ncol = ncol, nrow = nrow,
zMove = 0,
zTarget = 0,
offset = 0,
speed = speed_move)
}
#' iPinTool deactivate pins
#'
#' generates worklist procedures to deactivate pins. All pins are always activated
#' when the pin tool is dropped onto the carrier.
#'
#' @param pins vector of integers 1:384, designating the pins to be deactivated.
#' @param RackLabel name of carrier as on gwl$worktable
#' @param readyVector name of the vector to move over the stub
#' @param pushVector1 name of the vector that pushes the pins 1-192
#' @param pushVector2 name of the vector that pushes the pins 193-384
#' @family advanced worklist procedures
#' @export
iPTdeactivate <- function(
pins,
RackLabel = "iPT tool",
readyVector = "PT getReady",
pushVector1 = "PT Act 1-192",
pushVector2 = "PT Act 193-384"){
adv_gwl_comment("preparing iPT384...")
adv_gwl_comment(
str_c("deactivating pins: ", str_c(pins, collapse = ", "))
)
grid <- getGridSite(RackLabel)$grid
pins_sorted <- shortestPath(pins)
MCAvector(readyVector, grid, 1, back = 0)
for (i in pins_sorted){
if (i <= 192){
MCAvector(pushVector1, grid, i)
} else {
MCAvector(pushVector2, grid, i - 192)
}
}
MCAvector(readyVector, grid, 1, back = 0, direction = 1)
}
#' iPT384 pin transfer
#'
#' pick up 4 adjacent wells on a 384 well plate with the 4 pins in the back left
#' corner of the iPT384. Make sure all other pins are deactivated!
#'
#' @param rack string, Racklabel of target, as in gwl$worktable
#' @param well int 1:384, which well should be hit with pin 1
#' @param n_dips number of dips in plate
#' @param speed_move movement speed up to z-dispense
#' @param speed_in movement speed when dipping
#' @param speed_out movement speed when retracting
#' @family advanced worklist procedures
#' @export
iPTdip <- function(
rack,
well,
n_dips = 3,
speed_move = 35,
speed_in = 5,
speed_out = 5){
well_row <- (well - 1) %/% 24
well_col <- well - well_row * 24 - 1
adv_gwl_comment(str_c(
"dipping ", n_dips, "x in ", rack))
MCArelative(well_col, well_row)
moveMCA( # move over plate, z-travel
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 0,
zTarget = 0,
offset = 0,
speed = speed_move)
moveMCA( # z-move to z-dispense
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 4,
zTarget = 1,
offset = 0,
speed = speed_move)
for (i in 1:n_dips){
moveMCA( # z-move to z-max
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 4,
zTarget = 3,
offset = 0,
speed = speed_in)
moveMCA( # z-move to z-dispense
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 4,
zTarget = 1,
offset = 0,
speed = speed_out)
}
moveMCA( # z-move to global z-travel
RackLabel = rack,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove = 4,
zTarget = 4,
offset = 0,
speed = speed_move)
MCArelative() # reset offset
}
#' Wash pin tool
#'
#' Procedure to wash pintool
#'
#' @param t_wait integer, time (s) to wait on blotting paper
#' @param t_dry integer, time (s) over dryer
#' @param n_dips_1 integer, number of dips in reagent 1
#' @param n_dips_2 integer, number of dips in reagent 2
#' @param n_dips_3 integer, number of dips in reagents 3
#' @param reservoirs vector of RackLabel of reservoirs to dip
#' @param blots vector of Racklaberl of blotting spots
#' @family advanced worklist procedures
#' @export
washPinTool <- function(
t_wait = 2,
t_dry = 90,
n_dips_1 = 3, n_dips_2 = 3, n_dips_3 = 3,
reservoirs = c("Bleach", "ddH2O", "EtOH"),
blots = c("Blot_frt", "Blot_mid", "Blot_bck")){
adv_gwl_comment("washing tips...")
#dip 3x in first reservoir
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 0,
zTarget = 2,
speed = 10)
for (i in 1:(n_dips_1 - 1)){
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 3,
speed = 60)
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 2,
speed = 60)
}
# retract slowly
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 3,
speed = 60)
moveMCA(
RackLabel = reservoirs[1],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 2,
speed = 5)
# blot 1
moveMCA(
RackLabel = blots[1],
zMove = 0,
zTarget = 3,
speed = 10)
# wait t_wait seconds
evowait(1, t_wait)
#dip 3x in 2nd reservoir
moveMCA(
RackLabel = reservoirs[2],
ncol = 12,
nrow = 8,
zMove = 0,
zTarget = 2,
speed = 10)
for (i in 1:n_dips_2){
moveMCA(
RackLabel = reservoirs[2],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 3,
speed = 60)
moveMCA(
RackLabel = reservoirs[2],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 2,
speed = 60)
}
# blot 2
moveMCA(
RackLabel = blots[2],
zMove = 0,
zTarget = 3,
speed = 10)
# wait t_wait seconds
evowait(1, t_wait)
#dip 3x in 3nd reservoir
moveMCA(
RackLabel = reservoirs[3],
ncol = 12,
nrow = 8,
zMove = 0,
zTarget = 2,
speed = 10)
for (i in 1:n_dips_3){
moveMCA(
RackLabel = reservoirs[3],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 3,
speed = 60)
moveMCA(
RackLabel = reservoirs[3],
ncol = 12,
nrow = 8,
zMove = 4,
zTarget = 2,
speed = 60)
}
# blot 3: EtOH
moveMCA(
RackLabel = blots[3],
zMove = 0,
zTarget = 3,
speed = 10)
# wait t_wait seconds
evowait(1, t_wait)
#dry
moveMCA(
RackLabel = "PT dryer",
zMove = 0,
zTarget = 3,
speed = 10)
fwCommand("O1SLO3,1")
evowait(1, t_dry)
fwCommand("O1SLO3,0")
moveMCA(
RackLabel = "PT dryer",
zMove = 0,
zTarget = 4,
speed = 10)
}
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