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From 1997 to 2001, the third author worked with a team of engineers at JSC to develop the requirements and basic design for the Bioregenerative Planetary Life Support Systems Test Complex, or BIO-Plex. Under the Advanced Integration Matrix (AIM) Project, this earlier effort is extended to an investigation of methods and approaches for Advanced Systems Integration and Control. The intent is to understand and validate the use of software as an integrating function for complex heterogeneous systems, particularly for Advanced Life Support (ALS), in the context of support of mission operations. Preliminary investigations undertaken in the summer of 2004 indicate that integration of controls for the type of dynamic, non-linear, closed-loop biological systems under investigation for ALS systems require a different systems engineering approach than that required for traditional avionics systems.