Models can be submitted by registered users. The submission process can be initiated by clicking on 'Submit'. This takes the user to a guidelines page, with information related to the format and format version supported. If a model is not handled by any of the plugins supported by jummp, the model is stored in the BioModels as an 'unknown' format. The submission process can be stopped at any point by clicking on the 'abort' button.

Submission Guidelines

When continue is clicked, the user is taken to the file upload step. Users can upload 'main' files, which define the model, and 'supplementary' files, which provide information related to it. Examples include code written to demonstrate the model or text describing the model in more detail. Clicking on 'Add a supplementary file' creates a file upload box and an associated text box where a description can be optionally entered. It is not necessary to create as many boxes as needed, any unused file upload boxes are ignored. It is however necessary to provide at least one main file. If this is not provided the user is brought back to the upload page with an error message. When continue is clicked, the format of the model is detected. The model is validated according to it's format. Models failing validation are labelled invalid, however can still be submitted.

Upload Files

Information is extracted from the model, and is displayed when the user clicks upload files. This includes the name and description of the model, and may include the option of editing the model in later versions. In the next step the user is asked to provide a publication link. This can be skipped by leaving the boxes blank. A number of different link types can be provided (such as pubmed, doi, isbn etc). Each of these known types are validated against a pattern stored for their links. If an invalid link is provided an error message is shown and the user is asked to supply a correct link.

Model publication link

If the user supplies a pubmed link, the publication is retrieved using the Europe PMC web service. If an existing publication link is provided, the details are retrieved from the database. The user is then directed to a form that allows editing of any data retrieved based on the link.

Publication details page

Finally, before submission, a submission summary is shown to the user.

Submission Summary

It is possible until this point to go back and forth in the process until the model is finally submitted. For instance, the user can go back to the upload files page and add more files. Files already uploaded are stored on the server and do not need to be uploaded again. It is possible to remove and replace files already uploaded to the server.

When the user finally submits the model by clicking 'Complete Submission' on the summary page, the files are moved from temporary storage into the repository, and a new model is generated with a unique id. A link to the model is provided in the confirmation page.

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