This paper presents a new approach to laboratory automation integration with applications in automatic execution of various biotechnology (genomics and proteomics) protocols. The new configuration is called "tower-based configuration". It provides a scalable workcell that also includes instrumentation for sub-processes such as vortexing, shaking, incubation etc. Tower-based automation is a robotic-based configuration that allows improving the throughput of automated system without changing the robotic workspace or increasing the footprint of the system. Tower configuration consists of two arms mounted on a common cylindrical base, and is surrounded by stackers that carry laboratory processing instruments, labwares and other accessories. The requirement of high throughput is satisfied by parallel processing. A conceptual tower-based automated system for magnetic isolation of TAP tagged protein complexes protocol is presented and compared with a traditional automated system. Our performance investigation showed that the tower-based configuration has a high throughput to footprint ratio, high scalability, and wide protocol flexibility in comparison with traditional laboratory automation approaches.