Open Source Multicellular Modeling

Cross framework Reference Models

Different simulation frameworks, such as CompuCell3D, PhysiCell, Morpheus, Chaste, and others offer varying methodologies and support various concepts and data structures. Creating more robust model exchanges among these frameworks is non-trivial due to several issues, including differences in modeling algorithms, dimensions (2D vs. 3D), and level of detail in representing cells and their interactions. This working group and initiative brings together community members to implement reference models across various frameworks.

Landscape of Modeling Tools

This group works across the entire community to understand and bridge the differing conceptual, quantitative and computational models by sharing best practices. Ultimately reproducibility and reliable standardization hinges on distinguishing among three critical aspects of modeling: conceptual models (addressing model structure), sharing of models, quantitative models (method-independent), and computational models (including computational methodologies). Finally, addressing the archiving and reusability by scientists and practitioners. An important goal of this group is to speed up onboarding of new researchers to multicell modeling, facilitating their choice of an appropriate modeling approach and simulation framework to solve their scientific problem.

Bridging methods and models in multicellular simulations

We are bridging gaps in understanding of how different simulation methods affect models by focusing on development of best practices, standards and schemas, with special emphasis on multi-scale, embedded, and coupled simulation methods. We present a review of best practices and ways to standardize descriptions of framework capabilities for framework developers and users including: workflow standardization, common ways to analyze, share, reproduce simulation results and explore the potential for using Artificial Intelligence and Machine Learning. By doing this, researchers and framework developers will develop a better understanding of how different approaches work (through the use of different simulation frameworks) to solving the same problems.

Developer resource componets

For example, GUI Model Visualization component for use by Scientific Practitioners. We are introducing GUIs that visualize complex models to support scientists and researchers in understanding the intricacies and interconnectedness of various components. Visual representations are particularly beneficial for virtual tissues where complexity can be challenging to grasp without graphical aids and representation. This can include image analysis tools/libraries such as Topological Data Analysis Python libraries, Sensitivity analysis components, VTK components.

Models predicting chemical toxicity

These are crucial models for designing safer chemicals and enhancing biomedical research. They are applied in many areas such as:

Developmental Toxicity Model: Simulates early human development to predict chemical impacts on embryonic growth.

Blood Vessel Development Model: Helps understand chemical effects on the formation and function of blood vessels.

Neurovascular Unit Model: Integrates neurons and blood vessels to study their interaction under chemical exposure, impacting brain health and disease progression.

Virtual Cornea Models

Virtual cornea models allow researchers to study the intricate behaviors of the cornea under various conditions and avoid many of the ethical and logistical complexities of in vivo testing. These models can simulate how the cornea reacts to injuries and inflammation, providing valuable insights into the healing processes and into the efficacy of therapeutic interventions. These help to not only enhance our understanding of ocular health but also to accelerate the path toward innovative, safe, and effective therapies.