Parallel synthesis has been increasingly integrated into the drug discovery process in order to move discovery programs forward quickly and cost effectively. However, developing a chemistry protocol and defining its scope for a given chemistry in a timely manner remains a challenge to medicinal chemists. At ArQule, we have integrated novel technologies and developed processes to address the bottlenecks in chemistry development. In this presentation, we detail the recent advances, including design of experiments, data analysis and data visualization in protocol development for parallel synthesis, and demonstrate the application of those tools in facilitating the process of shortening development cycle time.