Morpheus

Morpheus simulates multiscale and multicellular biological systems by enabling construction, coupling, and execution of cell-based, ODE, PDE, rule-based, SBML, and image-based models to study tissue morphogenesis, gene regulation, metabolism, and their interactions.

Key Features:

• Declarative Modeling: Models are specified declaratively using biological terms and mathematical expressions via a domain-specific language, avoiding manual code compilation.
• Model Formalisms Support: Supports cell-based models, ordinary differential equations (ODEs), partial differential equations (PDEs), rule-based models, Systems Biology Markup Language (SBML) models, and image-based modeling, with the ability to couple these formalisms for multiscale modeling.
• Visualization and Analysis: Produces customizable 2D and 3D images or movies of simulation results and enables feature extraction during simulations.
• Extensibility: Provides a plugin architecture to extend and customize computational capabilities.
• Batch Processing: Supports batch execution of simulations for parameter sweeps and multiple runs.

Scientific Applications:

• Systems Biology: Enables multiscale systems biology studies that integrate molecular, cellular, and tissue-level processes.
• Tissue Morphogenesis: Facilitates modeling of tissue morphogenesis and multiscale feedback mechanisms between cells and fields.
• Gene Regulation and Metabolism: Supports coupling of gene regulatory and metabolic models with cell-based dynamics to study intracellular–intercellular interactions.
• Reaction–Diffusion and Dynamics: Allows integration of reaction–diffusion (PDE) systems with cell-based models to investigate spatiotemporal pattern formation and dynamic behaviors.

Methodology:

Models are expressed declaratively in the domain-specific language MorpheusML; the framework couples cell-based, ODE, PDE, rule-based, SBML, and image-based model components and generates 2D/3D simulation outputs with integrated feature extraction.