The software for the Patchliner comprises PatchControlHT for controlling the actions of the robot and the experimental workflow, and PatchMaster for electrophysiological data acquisition. PatchControlHT is a graphical user interface for straightforward and easy programming of protocols either by using pre-programmed modules, or by setting up customized protocols based on the specific user requirements. PatchControlHT can run fully automated, controlling the experiments from start to finish, but changes can also be made on-the-fly, a particularly useful feature for assay development and academic research. Because of its inherent logical programming capabilities, experimental redundancy is reduced to a minimum, thus maximizing the data throughput. In addition, PatchControlHT is compatible with various document and database formats which makes compound loading and data analysis faster and easier when screening a large number of compounds.

Data can easily be analyzed using Nanion's Data Analysis Package, an efficient and convenient data analysis tool. With a few mouse clicks raw data is loaded, displayed, analyzed and pooled, reducing the effort to a minimum. Current-voltage relationship plots and concentration response curves are automatically calculated and displayed. V_half values and IC₅₀ or EC₅₀ values are shown for each individual well, and the average values for all active wells are calculated. Raw current traces and time courses are displayed, facilitating judgement of data quality of each recorded well. Individual cells can be easily excluded from the data set and average concentration response curves and IC₅₀ or EC₅₀ values recalculated. Data from several chips and over multiple days can be pooled, and cumulative addition or single point addition regimes can be analyzed.