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Wednesday, November 9, 2011

Parsing 96 / 384 well Plate Maps

In molecular biology and related fields, we use rectangular plastic plates with 96 or 384 wells for many purposes, allowing us to run many experiments in parallel. In particular, they are the standard format for tasks involving laboratory robotics, such as fluid dispensing, DNA sequencing, mass spectrometry, etc.

In setting up a plate of samples, it is common for a researcher to use Excel to create a 'plate map' - a table of 8 rows and 12 columns, for a 96 well plate, with each cell holding information on the sample in that well.

Converting this into a list of individual wells for input into an instrument or a piece of software should be straightforward but variability in manually created plate maps can be an issue. Extraneous text and the placement of the table in the spreadsheet are just two of them.

I have to deal with this problem every year or two and so I decided to write a utility script that implements this conversion and offers several options for the output file.

It is not intended as a complete solution for any one application. Rather it is a starting point that I can customize as needed.

I know other people have to deal with the same type of data, so I've made the script as general as possible and put it up on github under the MIT license. Please adapt this as you see fit for your needs.

The script can take CSV or Tab delimited files as input, containing 96 or 384 well plate maps. The output is a table with one well per row and the columns : plate, row, column, value. Options allow you to specify CSV or Tab delimited as the output format, whether to parse the input in row or column major order, and whether or not to output empty cells in the plate map.

The code is written in Ruby and you can find it at https://github.com/craic/plate_maps

Let me know if you find it useful

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