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Instructions to Authors

The main task for a Physiome paper is to provide a citable link between a published, validated model and its instance in the Physiome Model Repository (PMR) or corresponding repository or database. The model files submitted must fulfill the demands of reusibility stated by the Physiome Project. All submissions to Physiome must also be associated with one, or more, articles accepted by peer-reviewed physiology, bioengineering or biophysics journals, here refered to as a primary publication. Authors are encouraged to prepare their Physiome submission(s) in parallel to the primary paper. Submissions will not be curated and evaluated until the primary paper is accepted, but authors will be able to access and share their submission via the PMR. Please contact Physiome (physiome@physiomeproject.org) if you have any queries.

1. Preparing your submission

Submissions should be prepared using the Overleaf template (LINK) or MS Word template (LINK). These templates will provide the main document for the submission, but the submission must include all resources required to evaluate the reproducibility, reusability, and discoverability of the submission. As described in the templates, such resources can be directly included in the Overleaf project or zip archive, or linked to via appropriate online repositories or databases.

A Physiome paper is a description of the model submitted to the repository. If the model code submitted is complete, all parameter values, units, etc will be included in the files and do not to be printed in the article. The paper should include: i) reference(s) to the primary paper(s); ii) figures showing that the code simulates the same graphs as shown in the primary paper; iii) any modifications made to the model, including motivations and origin; iv) references to the origins of the parameter values, if other than the primary paper; v) a brief explanation of the biological system modelled.

It is encouraged that the authors of the primary primary paper are included in the Physiome paper. The Physiome team can help with reaching out to them if needed.

2. Types of submissions

The following types of submissions will be considered for publication in Physiome. Here you can find templates and examples for the different types of submissions. (LINK)