User launches instrument and then runs a specific assay. The user prepares a worklist file that tells the software which are the wells and tubes to acquire. User then places the samples and reagent in those wells and tubes of the instruments and starts the run. The software directs the instrument to follow a protocol specific to the assay concerned. The protocol includes steps such as washing capillary, loading and mixing samples. User adjusts settings that sets the threshold for the events. Data is acquired by the software and is saved to FCS (Flow Cytometry Standard) file for offline analysis. Data is also exported to a comma-separated file (CSV file) that can be viewed in applications like Excel. In offline analysis, FCS files can be viewed and updated. Access privileges can be maintained by administrators. The software conforms to FDA standards and keeps logs along with the data.