Plate layout template for recording sample placement in multi-well plates and merging metadata with measurements in KNIME. See Fig. 1 for illustration. (XLSX 24.4 kb)

Importable workflow for the KNIME Analytics Platform to demonstrate the merging of sample metadata (plate-layout-template.xlsx) and Magellan-measured absorbance data (.asc files). See Fig. 2 for illustration. Please note that importing will return an error initially, because the file paths can not match, and have to be corrected as described in section KNIME workflow for data processing . In case of the File Reader nodes, this correction should be conducted with the option Preserve user settings for new location activated. If forgotten, and if the data preview shows a column filled with question marks, please right-click on that column and activate the option DON’T include column in output table. Traffic light symbols below the nodes will indicate whether corrections are still necessary (red), or whether the nodes can be executed (yellow). Upon execution of this workflow, data files are read in and the Expand Well Position nodes ensure equal formatting of the sample metadata and measurement results according to the well coordinates (defined in the .xlsx file and present in the .asc files). Joiner combines these tables per row, discarding incongruencies between plate layouts and measurement data. Concatenate progressively merges two plates’ data tables into one. Plate Heatmap Viewer provides a visual comparison of the data processing result with the visual impression of a plate. In particular, the expected locations of biofilm-negative and -positive controls are easily discernible. In the concatenated table, Plate Row Converter and Column Combiner regenerate the alphanumeric well coordinates so that the data and visual impression of individual wells can be compared. Column Filter and Column Resorter exclude obsolete coordinate metadata and pre-format the remaining table for export by CSV Writer. (TAR 65.0 kb)

Viaflo ( http://www.integra-biosciences.com/sites/viaflo_pipettes.html ) electronic pipetting scripts to successively remove cells, crystal violet staining solution and wash water after steps 1, 3 and 5 (Table 1). See Fig. 1 for experimental context and Vialinkâ s ( http://www.integra-biosciences.com/sites/vialink.html ) built-in help for importing instructions. (TAR 35.5 kb)

R code to demonstrate the plotting of KNIME-processed data. Please note that due to a randomisation function in the plate layout .xlsx file, editing the latter and running the KNIME workflow and this script again may produce a plot with different assignments of data points to the levels X, Y and Z. (R 1.22 kb)

R code and data (.csv format) used to produce the plots in this article. (TAR 45.0 kb)

Plate-reading method for Tecanâ s Magellan software. See section Robotised biofilm quantification for details. (MTH 15.6 kb)

Plate-reading method for Tecanâ s Magellan software. See section Robotised biofilm quantification for details. (MTH 15.6 kb)

R code and data (.csv format) used to produce the plots in this article. (TAR 45.0 kb)

R code to demonstrate the plotting of KNIME-processed data. Please note that due to a randomisation function in the plate layout .xlsx file, editing the latter and running the KNIME workflow and this script again may produce a plot with different assignments of data points to the levels X, Y and Z. (R 1.22 kb)

Viaflo ( http://www.integra-biosciences.com/sites/viaflo_pipettes.html ) electronic pipetting scripts to successively remove cells, crystal violet staining solution and wash water after steps 1, 3 and 5 (Table 1). See Fig. 1 for experimental context and Vialinkâ s ( http://www.integra-biosciences.com/sites/vialink.html ) built-in help for importing instructions. (TAR 35.5 kb)