Biocomplexity Institute

• Develop and distribute open-source software frameworks for Virtual Tissue modeling, including long-term stewardship of the CompuCell3D multiscale modeling environment.
• Create, validate, and disseminate Virtual Tissue models that address fundamental and translational biological problems.
• Integrate mechanistic modeling with AI/ML approaches, including generative AI and large language models (LLMs) to accelerate model design, calibration, and interpretation.
• Lead and expand the Medical Digital Twins community, including stewardship of the GLIMPRINT initiative.
• Develop and promote standards and best practices for multiscale simulations, through leadership in the OpenVT interoperability and reproducibility ecosystem.
• Train the next generation of researchers, including undergraduate and graduate students at IU and nationwide, through research opportunities, courses, online video materials, and long-standing workshops such as the CompuCell3D Workshop Series.
• Collaborate on national STEM initiatives, including undergraduate AI research training with the University of Michigan focused on AI/ML methods for accelerating CompuCell3D modeling, and participation in the EMBRIO Institute at Purdue University, where BIOC faculty contribute to curriculum development and instruction in computational modeling.
• Organize and convene national and international workshops, seminars, and symposia, including the CompuCell3D Workshop Series, the IMAG/GLIMPRINT Virtual Seminar Series, and OpenVT community events.

Researchers at the Biocomplexity Institute study a broad range of biological, biomedical, and methodological problems, including:

• Models of viral infection and immune response, including multiscale influenza, SARS-CoV-2, and emerging pathogen simulations.
• Medical digital twins, modeling immune dynamics, patient-specific disease trajectories, therapeutic response, and intervention design.
• Liver toxicology and chemical risk assessment, including integration with NAMs and Virtual Tissue models.
• Angiogenesis, tumor growth, and cancer progression, with applications to diagnosis, therapy, and spatial pattern classification.
• Corneal, skin, and epithelial tissue models, linking biophysics, signaling, mechanical properties, and emergent tissue organization.
• Reproductive research, includes the creation of MOTHER-DB.org, a multispecies ovary histology digital repository that enables comparative biology, alongside NIH-funded studies developing computational models of toxicant effects on ovary follicle development.
• Generative AI and large language models to accelerate multiscale model development, automate documentation, and integrate biological data into mechanistic simulations.
• Community building, education, and leadership in multiscale modeling, including standards development, training programs, seminars, and reproducibility efforts.
• Ongoing development and maintenance of CompuCell3D, one of the world's leading platforms for multiscale and agent-based biological simulation.

Affiliates strengthen BIOC’s expertise across toxicology, developmental biology, engineering, AI/ML, and biomedical applications.

• Dr. Thomas Knudsen, Adjunct ProfessorExpert in toxicology, developmental biology, and computational risk assessment. Provides key leadership in outreach to government and industry, and in federal grant and contract development.
• Dr. Maciej SwatSoftware Developer and lead developer of CompuCell3D
• Dr. Gilberto ThomasCompuCell3D applications and education.
• Dr. Lorenzo VeschiniDeveloper of Virtual Skin (vSkin) models, co-executive of GLIMPRINT, and OpenVT core member.
• Peter FyffeSoftware Developer and extension and maintenance of CompuCell3D.
• Bartholomew JardineSoftware standards and community building.

The Biocomplexity Institute maintains longstanding collaborations with partners across academia, industry, and government, including:

• University of Virginia computational modeling of development, mechanistic modeling/AI integration
• Johns Hopkins University Applied Physics Laboratory (JHU/APL) modeling viral infection and immune response
• University of Florida OpenVT, Tissue Forge modeling framework and immune digital twins
• Purdue University (EMBRIO Institute) STEM training, mechanistic modeling education, developmental biology research
• University of Michigan undergraduate AI/ML research training linked to CompuCell3D and digital twin development
• Universidade Federal do Rio Grande do Sul, Porto Alegre Brazil graduate student training and research exchanges
• University of Nebraska, Omaha models of radiation therapy and oncological medical digital twins
• University of Nebraska, Lincoln medical digital twins and GLIMPRINT
• Utrecht University computational developmental toxicology
• Procter & Gamble toxicology, consumer safety, NAM development
• OpenVT community partners including teams from Dresden Technical University, EMBL-EBI, ETH Zurich, Georgia State University, Goethe University Frankfurt Germany, Indiana University, Institute for System Biology, John Hopkins University, King’s College London, Leiden University, Leipzig University, Radboud University, University of British Columbia, University of Connecticut, University of Florida, University of Melbourne, University of Nottingham, University of Oxford, University of Washington advancing standards for reproducible multiscale modeling

These partnerships enhance BIOC’s capacity to integrate biology, engineering, computation, AI, and education—driving innovation in Virtual Tissues, Medical Digital Twins, and multiscale modeling science.