Abstract: Apparatus and associated methods relate to cell culture systems having controlled gas concentration boundary conditions around cell culture. In an illustrative example, a programmable cell culture system (PCCS) may include one or more manifolds, each releasably coupled to multiple cell culture modules. The cell culture modules, for example, may include a nutrient capacitive medium (NCM) in fluid communication with a concentration-controlled gas source through at least two gas transfer interfaces. The gas transfer interfaces (GTIs) may, for example, be spatially distributed in relation to a cell growth surface in the NCM. Each GTI, for example, may include a gas permeable membrane (GPM) and a plenum. The GPM may be disposed between the plenum and the NCM. Various embodiments may advantageously selectively control a concentration of at least one target gas in the NCM by maintaining predetermined boundary conditions of the cell growth surface via the GTIs.