BioUML

BioUML constructs and simulates modular models of biological pathways and virtual cells to support systems biology analysis and hypothesis testing.

Key Features:

• Modular Modeling: Employs a module concept mirroring computer hardware to define and integrate modules representing distinct biological pathways.
• Virtual cell and physiological system modeling: Supports construction and simulation of virtual cells and virtual physiological systems.
• Database Integration: Integrates data from Reactome and TRANSPATH into models.
• Simulation Capabilities: Performs simulations of complex biological processes and pathway dynamics.
• Validation with Experimental Data: Validates modules against experimental data to ensure model consistency with observations.
• Comprehensive Analysis Tools: Provides visualization, parameter fitting, and analysis of high-throughput data with scripting support in R and JavaScript.

Scientific Applications:

• Systems Biology: Enables analysis and reconstruction of intricate biological networks in systems biology studies.
• Apoptosis Pathway Modeling: Implements a detailed 13-module apoptosis model including modules for TRAIL, CD95L, TNF-α, p53, EGF, NF-κB, caspase activation, and the execution phase.

Methodology:

Modules are defined and automatically converted into plain models for simulation; simulations and parameter fitting are performed and modules are validated against experimental data, with scripting support in R and JavaScript.