RENCO

RENCO generates ordinary differential equations (ODEs) representing pre-transcriptional combinatorial regulation in artificial gene regulatory networks by incorporating protein–protein interactions and mechanistic features of gene and protein expression and exporting models in SBML.

Key Features:

• Automatic ODE generation: Automatically constructs ordinary differential equations (ODEs) describing regulatory interactions and expression dynamics in artificial networks.
• Explicit modeling of protein-protein interactions: Represents interactions among transcription factors and protein complexes explicitly within generated models.
• Combinatorial control representation: Captures combinatorial control exerted by multiple transcription factors on target genes at the pre-transcriptional level.
• Mechanistic gene and protein expression modeling: Incorporates detailed mechanistic features into models of gene and protein expression.
• SBML output: Exports generated models in Systems Biology Markup Language (SBML) format.

Scientific Applications:

• Gene regulatory network modeling: Provides mechanistic ODE models for studying dynamics of transcriptional regulation in artificial regulatory networks.
• Systems biology and synthetic biology: Supports modeling and analysis tasks in systems biology and synthetic biology that require detailed pre-transcriptional regulation representations.
• Benchmarking network inference algorithms: Facilitates assessment and benchmarking of algorithms for inferring regulatory networks by producing mechanistic simulated models and dynamics.

Methodology:

Generates ordinary differential equations that describe pre-transcriptional combinatorics and protein-protein interactions within artificial regulatory networks and outputs models in SBML.