Analyzing Flow Cytometry Data Using Knime Workflows: a Report of an Internship at Janssen Pharmaceutica

This document is an extensive report of an internship at Janssen Pharmaceutica. Scientists at Janssen Pharmaceutica perform routine experiments on large amounts of cells using a technique that irradiates cells with laser light called Flow Cytometry. The goal of the internship project was to automate the data analysis of many of these routine experiments. The existing Flow Cytometry machine is able to process the cells and save all its data into files. These files are used as input for the application. Essentially, we created nodes. Nodes are modular units with a very specific task in mind. For instance, it is possible to have a node which handles the conversion of data into a table. These different nodes can be connected to create complex structures. These complex structures, called workflows, aid in the analysis performed on the data. The final goal would be to fully integrate our project with the existing research platform. The internship project used the KNIME tool. KNIME is an easy to use program which contains all the nodes and allows them to be connected. The nodes themselves are programmed in Java 1.6, making use of the KNIME Framework.