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The PathCase-SB Model Composition Interface provides a three-step model composition process for computational models defined in SBML format.
The PathCase-SB Model Composition Interface [ 38] provides a three-step model composition process for computational models defined in SBML format.
Our web-based tool can be iteratively used for both (1) models used for composition, and (2) the composed model in the same window to facilitate the work of the user during the model composition process.
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As previously highlighted in other works [ 6, 7], there is a need for efficient algorithms with user-friendly interfaces during and after the model composition (merging) process.
Our integrated web-based tool presents unique features to facilitate the model composition by an iterative process that also provides visualization of metabolic pathways and simulations.
As of July 2013, the current version of the Pathcase-SB visualization tool allows editing the model only after the composition process.
It is possible to manually add the annotations necessary for the model-to-sequence conversion process after model composition.
An argumentation structure can ensure that the thought processes behind model composition and design decisions are transparent and readily available for scientific scrutiny.
One distinguishing feature of the approach is the adoption of a unique model to represent heterogeneous facets of the composition process.
While the former one provides a system where advanced users can merge complex models published in the BioModels Database, the latter one provides basic models for beginners to practice and learn the composition process, or for any researcher who wants to understand the specifics of the composition algorithm.
In particular, the composed model contains all information of the submodels used in the composition process without any redundancies, although the information related to the relationship between elements of the composed model and the submodel is lost.
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