moped

moped constructs, modifies, and analyzes metabolic network models to enable integration of genome- and proteome-derived reconstructions with constraint-based, differential-equation, and topological network analyses.

Key Features:

• Reproducible model construction: Builds metabolic models directly from genome or proteome sequences using pathway/genome databases with Gene-Protein-Reaction (GPR) annotations.
• Multi-paradigm modeling support: Supports differential equation-based modeling, constraint-based modeling, and topological network analysis within a single framework.
• SBML import and Python representation: Imports existing models in SBML format and represents them as Python objects for programmatic manipulation.
• Model modification and curation: Provides methods to add, remove, or alter reactions and to perform gap-filling strategies to identify and inspect missing network components.
• Topological analysis and biosynthetic capacity: Performs topological analyses and computes biosynthetic capacities using network expansion techniques.
• Interoperability with CobraPy: Exports or converts models to CobraPy objects to enable constraint-based analyses.

Scientific Applications:

• Draft genome-scale reconstruction: Reconstruction of draft metabolic networks from genome or proteome sequence data using pathway/genome databases with GPR annotations.
• Model curation and gap-filling: Identification and inspection of missing reactions and components to curate and complete metabolic models.
• Constraint-based and simulation analyses: Preparation and export of models for constraint-based analysis and integration with differential-equation-based simulations.
• Topological and biosynthetic capacity assessment: Analysis of network topology and computation of biosynthetic capabilities via network expansion.

Methodology:

Construction from genome/proteome sequences using pathway/genome databases with GPR annotations; SBML import and representation as Python objects; reaction addition/removal/alteration and gap-filling strategies; topological analysis via network expansion; export/conversion to CobraPy; support for differential-equation, constraint-based, and topological analyses.