MEMOSys

MEMOSys manages genome-scale metabolic models (GEMs) by providing storage, version control, annotation integration with Systems Biology Markup Language (SBML), and model-hierarchy management to support model reconstruction and analysis.

Key Features:

• Derived Models: Model hierarchies with automatic propagation of modifications across derived models.
• Enhanced Annotations: Extraction and integration of annotations from Systems Biology Markup Language (SBML) files to enrich model components.
• Query Mechanisms and Reaction Search: Query mechanisms and reaction search capabilities for identifying and retrieving model components and reactions.
• Link-out Services to Public Databases: Link-outs to publicly available databases for external referencing of entities within models.
• Public Model Repository: A repository containing 20 publicly available models that can be exported into standardized formats for downstream analysis.
• Version Control and Reconstruction History: A version-control system that records comprehensive reconstruction history of models.

Scientific Applications:

• Model Development: Support for development and refinement of GEMs using version control and recorded reconstruction histories.
• Data Integration and Annotation: Integration of diverse datasets by importing SBML-derived annotations into model components.
• Collaborative Research: Sharing and reuse of models via a public repository and export into standardized formats to support cross-institutional analyses.
• Educational Use: Hands-on training and teaching in metabolic reconstruction through access to models, annotations, and version histories.

Methodology:

Automatic propagation of modifications across derived model hierarchies; extraction and integration of annotations from SBML files; query mechanisms for reaction search; link-outs to external databases; export of models into standardized formats; and a version-control system that records reconstruction history.