Scientific Programs (SPs) are large research lines encompassing one or more thematically related research groups (RG). From an organizational standpoint, SPs are comparable to the departments at other CSIC institutes.

Initially the RG at the I²SysBio are thematically organized into five SPs. The SPs are understood to be dynamic and must necessarily evolve to incorporate new research and novel developments in integrative systems biology, open to new perspectives. Therefore, the SPs would be regrouped, modified, expanded or suppressed in order to maintain quality and retain a competitive position following the suggestions of the external Scientific Committee at I²SysBio.