xCellerator

xCellerator models signal transduction networks and converts arrow-based biochemical reaction descriptions into differential equations for simulation and quantitative analysis.

Key Features:

• Implementation: Implemented as a Mathematica® package for computational modeling of biochemical systems.
• Reaction notation: Represents single- and multi-cellular biochemical reactions using a compact, optionally palette-driven, arrow-based notation.
• Kinetic models: Supports mass-action kinetics, enzymatic processes, allosteric regulation, and connectionist models.
• Equation generation: Translates biochemical reaction descriptions into systems of differential equations.
• Numerical simulation: Numerically solves the generated differential equations to produce time-course simulations.
• Export capability: Exports systems of equations for use with other computational tools.
• Multi-compartment modeling: Represents multi-compartmental systems as graphs whose nodes contain embedded signal transduction networks (STNs).
• Model nesting: Allows models to be nested indefinitely within larger data structures.
• Portability: Portable across operating systems that support Mathematica®.

Scientific Applications:

• Signal transduction modeling: Modeling signal transduction networks (STNs) at single-cell and multi-cellular scales.
• Dynamic simulation: Simulating temporal dynamics of biochemical pathways via numerical integration of ODEs.
• Regulatory mechanism analysis: Analyzing enzymatic processes and allosteric regulation within biochemical networks.
• Multi-compartment analysis: Modeling interactions within and between cellular compartments using graph-based representations.
• Model interchange: Exporting equation systems for integration with other computational analyses and tools.

Methodology:

Translates arrow-based reaction representations into systems of differential equations, supports mass-action and other kinetic formulations (enzymatic, allosteric, connectionist), represents compartments as graphs with embedded STNs, numerically solves ODE systems to produce time courses, and exports equation systems; implemented as a Mathematica® package with support for nested model structures.