BioSWITCH

BioSWITCH converts static gene regulatory networks encoded in the BioPAX standard into executable GINML logical models to enable simulation and prediction of cellular behavior.

Key Features:

• BioPAX integration: Processes and interprets networks encoded in the BioPAX standard for downstream conversion.
• GINML conversion and execution: Transforms BioPAX networks into GINML to produce logical models that can be executed for dynamic analysis.
• Automated network processing: Automates the de-coding and re-coding of gene network components during the conversion process.
• Model integration: Integrates BioPAX-derived models into existing GINML graphs to extend or merge network representations.
• Simulation and prediction: Enables simulation-based prediction of cellular behavior from the resulting logical network models.

Scientific Applications:

• Gene regulatory network dynamics: Modeling dynamic behavior of gene regulatory networks as executable logical models.
• Haematopoiesis modeling: Application to gene networks involved in haematopoiesis to study lineage and regulatory dynamics.
• Cellular response prediction: Predicting cellular responses under physiological or pathological conditions, including responses to drug treatments.

Methodology:

Converts BioPAX-formatted gene regulatory networks to GINML; performs automated de-coding and re-coding of network elements; integrates BioPAX-derived models into existing GINML graphs; applied to a previously published haematopoiesis gene network as a case study.