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

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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 validation procedure of 50 models developed a manual workflow that we would use to build an automatic platform to help users more easily curate and verify models in the future. On the other hand, these exercises allowed us to find the limitations and possible enhancement of the current curation and tooling to verify and curate models. Author summary Public repositories with models deposited using standard formats are an important activity in computational systems biology, which allows scientists to easily find, access, and reuse them to rerun simulations or derive new ones using compatible software or tools. Common standards and public repositories can facilitate the reuse and regeneration of computational biology models beyond the software originally used to perform the simulations. As an exercise to validate and correct the current curation, we examined a selection of models in the BioModels Database. For each model, we reproduced some published results in the corresponding papers by a certain software. Once reproduced we manually created a standard file package using the model and its simulation information stored in the standard formats. These exercises not only allowed us to develop a workflow that we would use to develop an automatic online platform to help users more easily curate models for existing or future databases and repositories but also allowed us to find the limitations and possible enhancement of the current curation and tooling to verify and curate models.
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