Curating models from BioModels: Developing a workflow for creating OMEX files.

ABSTRACT: The reproducibility of computational biology models can be greatly facilitated by widely adopted standards and public repositories. We examined 50 models from the BioModels Database and attempted to validate the original curation and correct some of them if necessary. For each model, we reproduced these published results using Tellurium. Once reproduced we manually created a new set of files, with the model information stored by the Systems Biology Markup Language (SBML), and simulation instructions stored by the Simulation Experiment Description Markup Language (SED-ML), and everything included in an Open Modeling EXchange (OMEX) file, which could be used with a variety of simulators to reproduce the same results. On the one hand, the reproducibility procedure of 50 models developed a man

SUBMITTER: Xu J 

PROVIDER: S-EPMC10979985 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature