Physiome: encouraging the publication and reuse of reproducible models

Presentation given at VPH Conference 2024

Abstract:

Physiome: encouraging the publication and reuse of reproducible models

David Nickerson¹, Weiwei Ai¹, Shelley Fong¹, Karin Lundengård¹, Anand Rampadarath^1,2, Tommy Yu¹, Poul Nielsen¹, Peter Hunter¹

¹Auckland Bioengineering Institute, University of Auckland, New Zealand

²Plant and Food Research, New Zealand

Reproducibility and confirmation of results is crucial for useful science and should be one of the supporting pillars of good research. However, only one third of computational physiological models published in scientific journals provide sufficient information to even attempt reproduction let alone demonstrate reproducibility.

Physiome is a journal committed to reproducibility and reusability of mathematical models of physiological processes. Every model published in Physiome is connected to a curated and permanent version of the model implementation with a persistent identifier. The code necessary to run the model is easily accessible, to be reused as it is or as a module in a novel model. Model validation and scientific value is ensured by being connected to a primary paper published in a domain-specific journal. We have collaborated with supporters of open science Digital Science (figshare and Overleaf) and Curvenote to build an open-source curation and publication system, with all journal articles published open access on a Curvenote powered website and archived in figshare.

Using these systems, Physiome publications are a complement to your primary article that ensures reproducibility, reusability and discoverability of you model. The format encourages modularity that facilitates combination of different models to develop the next level of systems understanding. And all the models are in one place, easy to find and accessible.

Physiome is open access with a low Author Processing Charge. Physiome curators will help authors ensure that models and simulation experiments are made available using appropriate community standards prior to acceptance for publication in Physiome. When aspects of a computational modelling study are not able to be encoded in standard formats, Physiome editors will help authors ensure their work is as open, reproducible, and reusable as possible. We will help as much as is currently possible with model curation and annotation to ensure that the modelling results presented in the primary paper are consistent with the model implementation published in Physiome.

For more information visit: https://journal.physiomeproject.org