BHIVE: Modeling and Simulation Environment for Large-scale Study of Cellular Community Behavior

The BHIVE project began in 2007 as a collaborative project involving Yale University (Thierry Emonet, PI), the University of Chicago (Rick Stevens), the University of Pittsburgh (James Faeder), and Northwestern University (Gary An). The focus of this project was to develop a multiscale simulator for biological systems (e.g. organs, tissues, cells) that would function on massively parallel platforms. Thus far, the BHIVE project has resulted in significant breakthroughs, including: (i.) the NFsim stochastic simulation environment, (ii.) the initial Model SEED system for automated reconstruction of metabolic models, (iii.) the core BHIVE modular simulation framework, and (iv.) new published models of Bacterial Chemotaxis. More recently, the BHIVE framework has been applied to simulating the behavior of 1 million interacting cells, operating in a shared environment. This simulation was conducted using 1000 cores of the BlueGene/P supercomputer located at Argonne National Laboratory.

Current efforts in the BHIVE project are focused on expanding the set of simulation algorithms available to the framework, and applying the framework to the large scale simulation of microbial communities. Rick Stevens, Christopher Henry, Fangfang Xia, and Scott Devoid in the Computational Biology group at Argonne and UC are currently engineering the BHIVE simulator to run in a petascale computational environment. Gary An and Scott Christley are exploring the application of BHIVE to the simulation of microbial communities in the gut. The team is developing the infrastructure to allow BHIVE to use thousands and even millions of processors to simulate microbial communities with billions of independently functioning and interacting cells. New modules are also being developed for simulating metabolism, chemotaxis, excretion, and signaling of diverse populations of cells interacting in a complex 3D environment. The ultimate goal of this project is to model the interactions of microbial communities within a complex 3D environment to improve our understanding of bioremediation, carbon sequestration, and even cellulose hydrolysis for biofuel production.


Portions of the BHIVE Project were supported by the U.S. National Science Foundation Computer & Information Science & Engineering (CISE) Directorate.

Chicago Systems Participants:

  • Rick Stevens (PI)

  • Gary An

  • Scott Christley

  • Scott Devoid (CI)

  • Fangfang Xia

    UC Partner Participants (ANL):

  • Narayan Desai (ANL)

  • Chris Henry (ANL)