JigCell Run Manager

JigCell Run Manager manages hierarchical parameterizations and executes simulation, plotting, and export of biochemical models to support analysis of biomolecular reaction network behavior across multiple parameter sets.

Key Features:

• Hierarchical Parameter Management: Defines structured hierarchies of parameter values, simulations, and plot settings to represent different experimental conditions or genetic modifications such as gene knockouts and overexpression.
• Simulation and Plot Generation: Generates simulation plots for interpreting the dynamic behavior of biochemical networks under different parametrizations.
• Export Capabilities: Exports models to COPASI and SBML (Level 3 Version 1) for interoperability with other bioinformatics tools.
• Model Management and Sharing: Handles the lifecycle of models across multiple parametrizations and supports sharing models before and after publication.
• Implementation: Implements computational functionality using Java and integration with the COPASI API.

Scientific Applications:

• Exploration of mutation and condition effects: Enables systematic exploration of phenotypic outcomes of different mutations and experimental conditions within biochemical networks using multiple parameterizations.
• Model interoperability and integration: Facilitates integration of biochemical models into broader analytical workflows via COPASI and SBML (Level 3 Version 1) export.

Methodology:

Implemented in Java and integrated with the COPASI API to extend COPASI functionality and support hierarchical model management.