SuBliMinaL Toolbox

SuBliMinaL Toolbox automates modular generation and refinement of genome-scale metabolic reconstructions to support systems-level metabolic model construction and analysis.

Key Features:

• Modular Design: Consists of independent modules, each tailored to perform specific tasks within the reconstruction process and usable together or individually.
• Automation Capabilities: Automates generation of draft reconstructions, determination of metabolite protonation states, and mass and charge balancing of reactions.
• Intracellular Compartmentalization: Suggests intracellular compartmentalization strategies for more accurate metabolic modeling.
• Transport Reactions and Biomass Functions: Adds transport reactions and biomass functions required for comprehensive metabolic models.
• SBML Compatibility: Manipulates reconstructions encoded in Systems Biology Markup Language (SBML) for interoperability with third-party analysis packages.

Scientific Applications:

• Genome-scale metabolic model reconstruction: Supports construction and refinement of genome-scale metabolic models in systems biology.
• Saccharomyces cerevisiae case study: Has been used to develop a metabolic reconstruction for Saccharomyces cerevisiae and to analyze and suggest improvements for blocked reactions.

Methodology:

Generates initial draft metabolic networks by leveraging KEGG and MetaCyc and refines those drafts through its modules, which can be executed sequentially as a reconstruction pipeline or used selectively during manual curation.