Computer hardware; sample processor, namely, a robotic handler and fluid management system capable of dispensing, aspirating, transferring, manipulating and handling substances with the target organism and preparing them for final detection and reading and a reader consisting of a light source and spectrometer capable of making a determination on the existence and the amount of a target organism, used to analyze samples of food, beverages, personal care and pharmaceutical products during the manufacturing process; computer software, namely, software for identifying and analyzing the existence and the amount of target organisms or substances in the food, beverage, personal care, and pharmaceutical product sample being tested during the manufacturing process; apparatus for drug development, namely, an assay analysis system comprised of a test kit consisting of disposable vessels, reaction vessels, chemicals and reagents and cuvette for sample preparation and insertion in the reader, sample processor, namely, a robotic handler and fluid management system capable of dispensing, aspirating, transferring, manipulating and handling substances with the target organism and preparing them for final detection and reading, and a reader consisting of a light source and spectrometer capable of making a determination on the existence and the amount of a target organism for clinical and laboratory use