A system for joining a plurality of fluid manipulation components into a flow scheme for directing fluids to and from a chromatographic separation device and for operating said joined fluid manipulation components according to a selected protocol, said system comprising: a plurality of modules, each said module comprising (a) one of said fluid manipulation components and (b) a microcontroller that (i) encodes machine-readable data characterizing the type of said fluid manipulation component, and (ii) transmits operational signals to said fluid manipulation component in response to commands received from outside said module; a mounting frame comprising a plurality of mounting sites, each said mounting site constructed to receive a single module interchangeably with other said modules, and each said mounting site comprising a signal connector that couples to and communicates with the microcontroller of a module mounted at said mounting site; and software communicating with the microcontroller of each module mounted on said mounting frame through said signal connectors, said software being programmed for receiving said machine-readable data, and for recognizing the fluid manipulation components and their locations on the mounting frame by electronic signals transmitted through the couplings, coordinating the components into a flow scheme, instructing a user by a graphical user interface in the making of fluid connections directly between the mounted components by having the modules themselves provide visual cues near the locations between which a tubing connection should be installed, or by turning on virtual indicator lights on a computer display that correspond to each of the sites for the tubing connections, to indicate the connections to be made, and for causing said fluid manipulation components, once joined according to said flow scheme, to direct fluids to and from said chromatographic separation device and in accordance with said protocol. a plurality of modules, each said module comprising (a) one of said fluid manipulation components and (b) a microcontroller that (i) encodes machine-readable data characterizing the type of said fluid manipulation component, and (ii) transmits operational signals to said fluid manipulation component in response to commands received from outside said module; a mounting frame comprising a plurality of mounting sites, each said mounting site constructed to receive a single module interchangeably with other said modules, and each said mounting site comprising a signal connector that couples to and communicates with the microcontroller of a module mounted at said mounting site; and software communicating with the microcontroller of each module mounted on said mounting frame through said signal connectors, said software being programmed for receiving said machine-readable data, and for recognizing the fluid manipulation components and their locations on the mounting frame by electronic signals transmitted through the couplings, coordinating the components into a flow scheme, instructing a user by a graphical user interface in the making of fluid connections directly between the mounted components by having the modules themselves provide visual cues near the locations between which a tubing connection should be installed, or by turning on virtual indicator lights on a computer display that correspond to each of the sites for the tubing connections, to indicate the connections to be made, and for causing said fluid manipulation components, once joined according to said flow scheme, to direct fluids to and from said chromatographic separation device and in accordance with said protocol.