This disclosure generally relates to systems and methods for manipulating chambers and other substrates for chemical, biological, or biochemical samples, such as cell culture and other chambers, within units such as incubators. In certain embodiments, the invention provides a technique for maintaining a plurality of substrates or chambers in a housing within which a predetermined environment is maintained, different from the environment external to the housing, and moving substrates or chambers in and out of the housing, in some cases without creating a large opening in the housing (e.g., by opening a door significantly larger than the substrates). A technique is provided, in certain embodiments, in which a plurality of substrates are mounted in fixed, secured relation to each other within a housing providing a predetermined, controlled environment, and are moved within the housing so that they can be evenly exposed to any differences in environment within the housing. In certain embodiments, the invention provides a technique for agitating a fluid within one or more chambers or substrates within a housing that can provide environmental control, in certain embodiments without physically stirring the fluid, such as with a stir bar or other stirring element in direct contact with the fluid. In still another embodiment, the invention provides a method for rotating a substrate or chamber about a substantially vertical and/or horizontal axis. In some cases, any of the above-described systems can be rotated at a speed sufficient to cause separation of a substance within the chamber or substrate.