Systems and methods for software-reconfigurable chemical process systems useful in a wide range of applications. Embodiments may include software control of internal processes, automated provisions for cleaning internal elements with solvents, provisions for clearing and drying gasses, and multitasking operation. In one family of embodiments, a flexible software-reconfigurable multipurpose reusable “Lab-on-a-Chip” or “embedded chemical processor” is realized that can facilitate a wide range of applications, instruments, and appliances. Through use of a general architecture, a single design can be economically manufactured in large scale and readily adapted to diverse specialized applications. Clearing and cleaning provisions may be used to facilitate reuse of the device, or may be used for decontamination prior to recycling or non-reclaimed disposal. In other embodiments, a flexible software-reconfigurable multipurpose reusable laboratory glassware setup may be realized, sparing talented laboratory staff from repetitive, complex, or low-level tasks occurring in analysis, synthesis, or small-scale chemical manufacturing.