RAVEN Toolbox

RAVEN Toolbox enables semi-automated reconstruction, curation, analysis, and visualization of genome-scale metabolic models (GEMs) for de novo model construction, model refinement, simulation, and integration of omics data.

Key Features:

• De Novo Reconstruction: Performs de novo GEM reconstruction from curated pathway databases such as MetaCyc.
• KEGG-based Pipeline: Implements a redesigned pipeline that integrates Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway information into GEMs.
• Integration and Convergence: Supports convergence and integration of metabolic reconstructions derived from multiple sources and existing models.
• Performance Optimization and COBRA Compatibility: Optimizes computational performance and provides compatibility with the COBRA Toolbox for constraint-based modeling and simulation.
• Visualization and Analysis Tools: Provides methods for visualizing simulation results and mapping omics data onto metabolic networks.
• Simulation Capabilities: Includes tools for performing simulations and analyzing outcomes to predict effects of genetic modifications on metabolic pathways.

Scientific Applications:

• Streptomyces coelicolor GEM reconstruction: Applied to reconstruct and compare de novo reconstructions with the manually curated iMK1208, producing the Sco4 model with expanded coverage of primary and secondary metabolism to identify genome-editing targets for optimizing antibiotic production.

Methodology:

Semi-automated reconstruction and curation using MetaCyc and a KEGG-based pipeline, convergence of reconstructions from multiple sources, simulation and outcome analysis, visualization of simulation results and omics data, and model comparison with existing GEMs such as iMK1208.