An apparatus for processing and analyzing samples comprising: a system comprising multiple sample processing bays and an assay analysis module configured to analyze sample scan data from the sample processing bay and generate a report, the system including a processor coupled to a non-transitory computer readable medium, the non-transitory computer readable medium storing instructions directing the processor to: receive and read at least two different assay definition files (ADF, 1024) from an external source, the ADFs (1024-1, 1024-2) each comprising at least an OPUS file and an AAM file, wherein each OPUS file comprises parameters that define operations controlled by an execution of the sample processing bay and each AAM file comprises parameters that define an analysis performed by the AAM; send control instructions based on each OPUS file to asample processing bay; generate scan data for the sample from a sample processing bay; send the scan data for the sample to the AAM; apply each AAM file to the scan data by the AAM and generate a detection report based on the analysis; receive a detection report from the AAM; and report the detection report, said apparatus further comprising at least two cartridges configured to be received into any one of the sample processing bays, the cartridges each including a sample preparation module and a sample reaction module wherein the sample reaction module comprises a wide vent top plate, fluid transport electrodes and sense electrodes, wherein each OPUS file comprises control parameters including a first set of control parameters pertaining to the sample preparation module and a second set of control parameters pertaining to the reaction module, and wherein the AAM file parameters define one or more of which sense electrode data is to analyzed, digital processing filters to be applied to sense electrode data, which electrodes are to be processed for a given digital processing filter, a classifier for determining how to interpret digitally processed data, call logic for determining the presence of one or more targets, and aspects of a report generation, wherein the first ADF comprises an OPUS file that further includes bead mixing parameters and an AAM file that utilizes a first digital processing filter for analyzing the scan data received from the processing bay from all of the sense electrodes in the reaction module, and wherein the second ADF comprises an AAM file that utilizes the first digital processing filter for analyzing the scan data from a subset of the sense electrodes in the reaction module and a second digital processing filter for analyzing the scan data received from the remaining sense electrodes. receive and read at least two different assay definition files (ADF, 1024) from an external source, the ADFs (1024-1, 1024-2) each comprising at least an OPUS file and an AAM file, wherein each OPUS file comprises parameters that define operations controlled by an execution of the sample processing bay and each AAM file comprises parameters that define an analysis performed by the AAM; send control instructions based on each OPUS file to asample processing bay; generate scan data for the sample from a sample processing bay; send the scan data for the sample to the AAM; apply each AAM file to the scan data by the AAM and generate a detection report based on the analysis; receive a detection report from the AAM; and report the detection report, wherein each OPUS file comprises control parameters including a first set of control parameters pertaining to the sample preparation module and a second set of control parameters pertaining to the reaction module, and wherein the AAM file parameters define one or more of which sense electrode data is to analyzed, digital processing filters to be applied to sense electrode data, which electrodes are to be processed for a given digital processing filter, a classifier for determining how to interpret digitally processed data, call logic for determining the presence of one or more targets, and aspects of a report generation, wherein the first ADF comprises an OPUS file that further includes bead mixing parameters and an AAM file that utilizes a first digital processing filter for analyzing the scan data received from the processing bay from all of the sense electrodes in the reaction module, and wherein the second ADF comprises an AAM file that utilizes the first digital processing filter for analyzing the scan data from a subset of the sense electrodes in the reaction module and a second digital processing filter for analyzing the scan data received from the remaining sense electrodes.