I have a simple problem (I hope), but I can’t find a solution. I’m looking to create a pattern dynamically in VBA for conditional and or unique platemaps for things like lib prep, cleanups, etc that can optimize aliquoting with 8ch pods. An example is below:
Let’s say I want to use the 8ch Pod to aliquot diluent to the blue wells, then use the 96ch to mix columns 1-4 simultaneously. How would I create, access, change or otherwise modify a pattern to associate to 8ch pod transfer commands?
I can see that there are .Pattern and .SelectionInfo commands with [96] arrays, but not sure how/where to access for changes and which will modify the info I want. Possibly something like Positions(“P6”).Labware.Pattern arr(i)?
I realize that Biomek counts wells row wise THEN column so I need to figure out a couple functions as well to utilize patterns naturally, but its all WIP. Just finding out how to modify the patterns would be a huge step forward.
Well unfortunately there was not a lot of feedback on this question from the Biomek support line… but I was able to find the following solution. The following group of functions first convert input sample number into your typical well format, column-row wise (biomek uses row-column wise by default), and creates the specified pattern if it doesn’t yet exist. It loads an array with the wells after conversion to col-row and finally loads that array into the existing or created pattern. This can probably be pretty-fied with an additional sub to replace the array redim, but this is the MVP as it stands.
Option Explicit
Dim PatternName, SampleNumber, x, lwpat, pat, col, row
' Reorient well number to col-row wise. e.g., A1, B1, C1... becomes 1, 13, 25... '
function WellNumCountingDown ( wellNum )
col = ((wellNum-1) \ 8)+1
row = (wellNum-1) mod 8+1
WellNumCountingDown = col + ((row-1) * 12)
end function
' Check if pattern exists, create it otherwise. '
sub SafeCreatePattern ( patternName, wellsX, wellsY )
set lwpat = world.lwpatterns.variantdictionary
if not LwPat.isBound ( patternName ) then
set pat = createobject ( "Biomek5.eeor")
pat.Name = patternName
pat.WellsX = WellsX
pat.WellsY = WellsY
redim WellPatSelected (wellsX * wellsY - 1 )
pat.selected = wellpatSelected
world.Lwpatterns (patternName) = pat
end if
end sub
' Designate your desired sample number and pattern name '
SampleNumber = 38
patternName = "WellPattern1"
' Load array x() with sample number and make pattern accessible outside of script. '
redim x(95)
for i = 1 to SampleNumber
x(WellNumCountingDown (i)-1) = i <= SampleNumber
next
SafeCreatePattern "WellPattern1", 12, 8
world.lwpatterns(patternName).selected = x
Extra note, it appears as if patterns cannot be variable within transfer steps. In order to create custom patterns then use them, they have to share a similar name so the strategy is to either modify patterns as needed, or load a generic pattern as needed and refer to it in the transfer steps. Patterns, as I understand, are 0-index 96-item arrays and can be loaded into another pattern very easily.
world.lwpatterns("GenericPattern").selected = world.lwpatterns(PatternVariable).selected
In the above example, GenericPattern is a str, the name of an existing pattern, and PatternVariable is a variable containing the string name of a second pattern, existing or created.
Switching Between Multiple Patterns in a Method Step
The Pattern field in a transfer does not accept expressions
The Pattern field in a transfer only accepts patterns that are listed in the drop-down
To make pattern selection dynamic use scripting to copy a desired pattern to a placeholder pattern
Create a placeholder pattern in either the Define Pattern Step or the Well Pattern Editor
Patterns created in the Define Pattern step are stored as a variable and have a scope of the method only
Patterns created in the Well Pattern Editor are project items and will be available to all methods within that project
Create whatever patterns you intend on using in either the Define Pattern Step or the Well Pattern Editor
Patterns created in the Define Pattern step are referred to using the notation World.Globals.PropertyChanger.LWPatterns.PatternName.selected
Patterns created in the Well Pattern editor are referred to using the notation World.LWPatterns.PatternName.selected
VBScript line to copy your desired pattern to the generic pattern would be World.LWPatterns.GenericPattern.selected = World.LWPatterns.DesiredPattern.selected
After copying your desired pattern to the generic pattern, configure the Transfer Step to use the generic pattern to select the wells
The thought about loading them with an array dynamically was so I could create something akin to Hamilton sequences. My idea was to define the platemap in a pattern for the largest-case number of replicates and samples, then to load it partially for each condition. e.g., if each sample has 7 replicates + 1 control, I would need one full column per sample and a max of 12 samples. However, since I was having issues loading a pattern such as this dynamically, I ended up utilizing the transfer command, replicating the source well x number of times, where x is equal to my 7 replicats + 1 control.
In this image, the l_PatternVolatile is loaded with a step-specific pattern/platemap and then the “Replicate each well” entry is filled with basically [Number_Wells_Per_Sample * Number_of_Samples] such that the source well is replicated following the plate map for as many wells as I need while following the platemap. I don’t think this is the best solution, but its one of many solutions and it works for what I need.
