CaSQ

CaSQ converts CellDesigner molecular interaction maps into executable Boolean models encoded in SBML-Qual to enable dynamic analysis of biological systems.

Key Features:

• Conversion from Static to Dynamic Models: Infers Boolean rules from the topology and semantics of CellDesigner molecular interaction maps to produce executable dynamic models.
• Adherence to SBGN Standards: Processes molecular maps whether or not they adhere to Systems Biology Graphical Notation (SBGN) standards, enabling use with diverse map formats.
• Output in SBML-Qual Format: Generates Boolean models encoded in Systems Biology Markup Language - qualitative (SBML-Qual) for interoperability with modeling tools.
• Retention of Annotations and Layouts: Preserves references, annotations, and layout information from the original CellDesigner maps during conversion.

Scientific Applications:

• In silico simulation and perturbation studies: Enables systems biologists to perform in silico simulations and perturbation analyses on networks derived from molecular interaction maps.
• Gene regulatory network analysis: Supports exploration of gene regulatory network dynamics by providing executable Boolean representations.
• Signaling pathway and emergent behavior analysis: Facilitates analysis of signaling pathways and emergent behaviors in complex biological networks.

Methodology:

Applies defined conversion rules and logical formulas that translate map topology and annotations into Boolean rules, with validation possible by comparing inferred models to manually constructed logical models.