Abstract: Systems, devices and methods are described herein that are configured for use in the monitoring and detecting of chemical reactions, such as, for example, the monitoring and detection of Polymerase chain reactions (PCR). For example, the systems and devices described herein can be used for accelerated real-time PCR. A fully integrated PCR system is provided that includes a touch screen user interface, eliminating the need for additional computers, keyboards, and related devices. The PCR systems described herein can be network enabled to provide communications between one or more PCR monitoring and detection devices and a central monitoring station. A disposable sample holding device can be placed in the PCR device for testing in an upright vertical orientation, providing improved optical scanning capabilities and rapid heating and cooling capabilities.