Model comparison and matching software tools | Metabolic engineering data analysis
Genome-scale reconstructions and models, as collections of genomic and metabolic information, provide a useful means to compare organisms. Comparison requires that models are similarly notated to pair shared components.
Allows users to set and modify annotations easily. semanticSBML is a comprehensive software combining model annotation, checking and building as well as merging. It helps the human modeller to detect syntactic and semantic conflicts. It was also developed to perform uncritical routine steps and to handle different naming conventions. Its graphical user interface (GUI) provides a simple and intuitive way to edit Systems Biology Ontology (SBO) terms and MIRIAM-compliant RDF annotations.
Facilitates comparing and combining of openCOBRA Toolbox compatible genome-scale metabolic reconstructions. modelBorgifier assists users in the task of reconciling dissimilarly annotated models in an efficient and practical manner, combining oversight, and smart automation. By combining models, users can easily compare as well as share information among models. Additional datasets, such as thermodynamic data, can also be mapped across multiple reconstructions.
Provides an integrated environment for users to perform functions that are required for biological pathways integration (BPI). PINT is a website that provides two useful features, a tolerant integration mode and an online annotation editor, to help manage the exceptions caused by inter-model incompatibilities of the annotation styles and data storage formats, respectively. Technically, PINT integrates pathways at the level of nodes, which may consist of one or multiple entities.
Assists users for difference detection in models of biological systems. BiVeS is a software library that improves the detection of differences between versions of models in SBML or CellML format. It filters the identified differences and drops all but biologically and mathematically relevant modifications. This algorithm produces reports and graphical representations of changes using open formats such as GraphML, HTML or Markdown and thereby helps to communicate the changes.
Analyses large biochemical networks by comparing reactions and involved reactants. ModeRator detects duplicate reactions in a single model. This software works with SBML files and COBRA files. It automatically evaluates comparison results by check of Enzyme Commission (EC) numbers and reaction synonyms if they are available. This algorithm is able to compare reactions by reactant’s abbreviation, neutral or charged formula. The comparison results can be automatically evaluated by additional criteria.
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