Pharmaceutical companies often exploit the use of high throughput screening (HTS) facilities consisting of robust liquid handling instrumentation to screen thousands of compounds every day for activity against a particular biological target; however, this practice is not so commonplace in the academic environment. At the University of Pennsylvania, we are establishing the Penn Center for Molecular Discovery (PCMD) as one of nine centers in the newly established NIH Molecular Libraries Screening Centers Network (MLSCN) to search the NIH repository of small molecules for new biologically active molecules. From spec'ing out the instrumentation and designing the layout of the HTS line to developing a method to screen a library of 100,000 compounds against various biological targets for inhibitory or activating activity, the entire process of setting up a high throughput screening facility will be discussed. This includes factory and site acceptance testing, statistical validation, compound management, and assay development and optimization. Each center in the MLSCN will screen the compound repository against unique targets of biological interest provided by scientists around the world. Researchers will upload their findings to PubChem, an online database, to share information on the interactions of thousands of chemicals with scores of biological targets, which can then be data-mined. Tools such as the aforementioned have previously been available to university researchers in only a very limited fashion. The PCMD screening line consists of two liquid handlers (PerkinElmer Evolution and Multiprobe Janus), two Thermo Multidrop high-speed reagent dispensers, a PE Envision multilabel plate reader, a Kendro Cytomat 189-plate incubator, a 120-plate storage carousel, as well as a thermal plate sealer, washer, shaker, delidding station, regrip station, and barcode reader – all accessible by a ThermoCRS Catalyst5 articulated robotic arm. For HTS targets, the PCMD is focused on RNA polymerases, serine and cysteine proteases, and promoters of zebrafish oligodendrocyte development. We have developed microarray based screening where chemical compounds can be printed within individual nanoliter droplets of glycerol in numerous copies using pin microarrayers. Using aerosol deposition, subsequent reagents and water are metered into each reaction center in order to rapidly assemble diverse multicomponent reactions without cross-contamination or the need for surface linkage. This method has already been implemented for protease-substrate profiling and for human Cathepsin L HTS in which inhibitors were found to block SARS coronavirus entry in a cellular model.