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

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.