Normalization workflow processes raw plate data in a matrix format and performs four commonly used HTS data normalization techniques: Z-score, Robust Z-score, Median polish and B-score. Results are written in both simple text (csv) and excel (xls) file formats. The normalizations are implemented using the R programming environment with the R snippet Knime nodes.
Hit identification workflow processes raw plate data in a matrix format and calculates intraplate standard deviations (deviation from plate mean) and median absolute deviations (deviation from plate median). These values then serve for primary HTS hit identification. The hits are selected on the basis of user defined cutoff values (parameters k and l). Results are written in both simple text (csv) and excel (xls) file formats. For both formats there are two files: one with binary matrix representing original plate, where 1 stands for hit and 0 for inactive well; second with coordinate of wells with hits. Also a scatter plot image (png) with highlighted hits is exported together with the text exports.
Chemical space workflow visualizes molecules distance/similarity in a 2D space using 2 most common dimensionality reduction techniques: Principal Component Analysis (PCA) and Multidimensional Scaling (MDS).
Molecules are read from a SDF file and a set of chosen descriptors (e.g., molecular weight, LogP, number of rotatable bonds etc.) is calculated using RDKit Descriptor Calculation node. Then in one branch of the workflow, these descriptors are used to calculate the principal components of the set. In the second branch, Morgan fingerprints with radius 3 and 1024 bits (hashed binary fingerprints) are also calculated for the set and projected in 2D space by MDS.
In both cases the result of projection is visualized using a scatterplot connected with a HiLite Row Splitter node. This node is able to interactively show selected points (molecules) via a 2D/3D Scatterplot node. In the Scatterplot node, the visualized points can be colored and sized by one of the descriptors (dimensions).