A system comprising: a fluidic network comprising a sample channel, a reaction chamber, and a reservoir (151, 152), the sample channel being in flow communication with a sample port that is configured to receive a biological sample; a pump assembly configured to be in flow communication with the fluidic network; and a rotary valve comprising a flow channel and being configured to rotate between first and second valve positions, the flow channel fluidically coupling the reaction chamber and the sample channel when the rotary valve is in the first valve position, and fluidically coupling the reservoir and the reaction chamber when the rotary valve is in the second valve position, the system further comprises: a detection assembly to detect light signals generated by a reaction from an array of reaction recesses within the reaction chamber comprising a guide array of light guides and a sensor array of light sensors, the reaction chamber having at least one optically transparent surface to receive illumination light from an optical path; wherein the pump assembly is able to induce a flow of the biological sample toward the reaction chamber when the rotary valve is in the first valve position, and is able to induce a flow of a reaction component from the reservoir (151, 152) toward the reaction chamber when the rotary valve is in the second valve position; and wherein the rotary valve is able to retain the biological sample in the flow channel as the rotary valve rotates from the first valve position to the second valve position, and the pump assembly is able to induce a flow of the biological sample into the reservoir (151, 152) when the rotary valve is in the second valve position. a fluidic network comprising a sample channel, a reaction chamber, and a reservoir (151, 152), the sample channel being in flow communication with a sample port that is configured to receive a biological sample; a pump assembly configured to be in flow communication with the fluidic network; and a rotary valve comprising a flow channel and being configured to rotate between first and second valve positions, the flow channel fluidically coupling the reaction chamber and the sample channel when the rotary valve is in the first valve position, and fluidically coupling the reservoir and the reaction chamber when the rotary valve is in the second valve position, the system further comprises: a detection assembly to detect light signals generated by a reaction from an array of reaction recesses within the reaction chamber comprising a guide array of light guides and a sensor array of light sensors, the reaction chamber having at least one optically transparent surface to receive illumination light from an optical path; wherein the pump assembly is able to induce a flow of the biological sample toward the reaction chamber when the rotary valve is in the first valve position, and is able to induce a flow of a reaction component from the reservoir (151, 152) toward the reaction chamber when the rotary valve is in the second valve position; and wherein the rotary valve is able to retain the biological sample in the flow channel as the rotary valve rotates from the first valve position to the second valve position, and the pump assembly is able to induce a flow of the biological sample into the reservoir (151, 152) when the rotary valve is in the second valve position. a detection assembly to detect light signals generated by a reaction from an array of reaction recesses within the reaction chamber comprising a guide array of light guides and a sensor array of light sensors, the reaction chamber having at least one optically transparent surface to receive illumination light from an optical path; wherein the pump assembly is able to induce a flow of the biological sample toward the reaction chamber when the rotary valve is in the first valve position, and is able to induce a flow of a reaction component from the reservoir (151, 152) toward the reaction chamber when the rotary valve is in the second valve position; and wherein the rotary valve is able to retain the biological sample in the flow channel as the rotary valve rotates from the first valve position to the second valve position, and the pump assembly is able to induce a flow of the biological sample into the reservoir (151, 152) when the rotary valve is in the second valve position.