A bioreactor control system comprises a batch server for controlling a bioreactor system in response to a recipe, a batch software system for generating a control sequence for the bioreactor system via the batch server for implementing the recipe, and a recipe conversion system that inputs the recipe into the batch software system. Preferably, the recipe conversion system reads a word processor file containing the recipe and interprets styles applied to text in the word processor file as indicating equipment and phases of the recipe to the recipe conversion system. Generally, the bioreactor system includes one or more bioreactors and additional hardware to perform the upstream and downstream processing. The document properties of the word processor file containing the recipe are applied as header information for the recipe input into the batch software system. This system solves a problem associated with traditional batching software systems, in which the authoring of recipes on the systems can be relatively arcane. Here, the recipe can be authored on a common word processor.