ANISE

ANISE configures TiFoSi mechanobiology simulations by constructing gene regulatory network equations and generating TiFoSi-compatible XML configuration files for studies of mechanical forces and signaling in planar epithelia.

Key Features:

• Configurator: Constructs complete configuration files for TiFoSi and outputs XML compatible with TiFoSi execution.
• Equation Builder: Constructs modeling equations for gene regulatory networks and encodes them into the TiFoSi configuration format.
• Module Coverage: Supports specification of initial conditions, mechanical properties, and signaling pathways for TiFoSi simulations.
• TiFoSi Integration: Translates user-defined model components and parameters into the XML format required by TiFoSi for simulation execution.

Scientific Applications:

• Mechanobiology of planar epithelia: Enables simulation of the interplay between mechanical forces and signaling in planar epithelial tissues.
• Tissue morphogenesis: Supports modeling of processes driving tissue shape and pattern formation.
• Wound healing simulations: Facilitates in silico studies of cellular responses during tissue repair.
• Cancer cell migration: Allows simulation of migratory behaviors influenced by mechanical cues and signaling.
• Hypothesis testing and validation: Produces simulation setups that can be used for computational hypothesis testing and experimental comparison.

Methodology:

Constructs modeling equations for gene regulatory networks, configures TiFoSi modules including initial conditions, mechanical properties, and signaling pathways, and translates these configurations into TiFoSi-compatible XML files.