Physiome papers describe the details of mathematical models and computational simulations associated with a ‘primary’ experimental/modelling paper that has recently been accepted to a peer-reviewed physiology, bioengineering or biophysics journal. Submissions to Physiome are evaluated to determine their reproducibility, reusability, and discoverability. At a minimum, accepted submissions are guaranteed to be in an executable state that reproduces the modelling predictions in the primary paper, and are archived for permanent access by the community. Physiome will also publish new papers based on older primary modelling papers where there is substantial value to the physiological modelling community in making a reusable, reproducible, and discoverable version of the model available. Physiome papers are citable with a DOI and published as open access with an author processing charge of US$300.
The purpose of Physiome is to encourage the reproducibility and reuse of models by providing citation credit for papers that describe and document curated and annotated models. The journal will assist authors in making suitable submissions available in the Physiome encoding standards (CellML, FieldML, SBML, NeuroML for encoding the model; SED-ML for encoding the simulation procols, parameters and outputs).
Note that a submission (Original or Retrospective) will only be accepted for Physiome if the primary paper that describes the experiments, data and model(s) has been accepted by a recognised peer-reviewed journal (referred to here as the ‘primary journal’). The exception to this will be submitted and solicited Reviews, that document a range of published models in a given area, and submitted Letters, that provide new insights on published models (see more details under 'Instructions to Authors'). For some primary journals the submission of the companion modelling paper to Physiome may proceed in parallel so that the curated, annotated and documented model is available at the time of publication of the primary paper. Authors are therefore 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 Physiome Model Repository.
Physiome will provide submission templates to ensure consistent documentation of the model and will work with authors to ensure that the published models reproduce the figures of the primary paper.
Physiome articles will be available on the Physiome Figshare portal (..), where the Physiome paper and the zipped collection of models and data are available with DOIs. “Live” models and simulation descriptions will also be available in the Physiome Model Repository. Wherever possible, models encoded in the standard formats are available to run from directly from this website.