ecmtool

ecmtool computes Elementary Conversion Modes (ECMs) from metabolic network models to enumerate substrate-to-product conversion modes and characterize how an organism can influence its environment.

Key Features:

• Elementary Conversion Mode calculation: Computes ECMs from metabolic models to characterize all possible conversions a cell can catalyze without detailing intracellular intermediate steps.
• Scalability and parallel vertex enumeration (mplrs): Integrates mplrs, a scalable parallel vertex enumeration method, to reduce memory requirements and accelerate ECM computation for standard and high-performance computing environments.
• Application to large models and redundancy detection: Demonstrated on large-scale models such as the near-complete JCVI-syn3.0 model (≈4.2 billion ECMs) and used to identify redundant sub-networks within metabolic reconstructions.

Scientific Applications:

• Metabolic network analysis: Enumerates the full set of feasible ECMs to explore the range of biochemical transformations represented by a metabolic model.
• Systems biology: Provides metabolic conversion profiles that inform studies of organismal behavior and environmental interactions.
• Model simplification and optimization: Identifies redundant sub-networks to aid simplification and more efficient optimization of metabolic models.

Methodology:

Computation of ECMs using scalable parallel vertex enumeration with mplrs to exhaustively explore steady-state flux distributions and identify redundant sub-networks.