Physiome curation system for reproducible models: Reproducibility, Reusability, Discoverability
presentationposted on 2020-12-07, 21:57 authored by Karin LundengardKarin Lundengard, David NickersonDavid Nickerson, Tommy YuTommy Yu, Anand RampadarathAnand Rampadarath
Reproducibility and confirmation of results is crucial for useful science and should be one of the supporting pillars of good research. However, less than 10% of the computational physiological models published in scientific journals reproduce the published results when implemented by another group. 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 code 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. The Physiome Project have collaborated with Digital Science to build an open-source curation system (based on the collaborative knowledge foundation software), with journal articles published open access in figshare. The effort in demonstrating reproducibility by building reproducibility into scientific workflows from the beginning can also be reduced through the use of technologies such as gigantum. Using these systems, Physiome publications are a complement to your primary article that ensures reproducibility, reusability and discoverability of you model.
ABOUT THE AUTHOR(S)
Karin Lundengård is a Post-doc from Linköping University, Sweden. She is an Editor and Curator for the new scientific journal Physiome. She also models the human cervical spine to help whiplash patients.
David Nickerson is a Senior Research Fellow at the Auckland Bioengineering Institute, University of Auckland, where he is involved in several computational physiology projects. David is a co-director of the NIH-funded Center for Reproducible Biomedical Modeling, where he leads a curation service to provide scientific journals an evaluation of reproducibility for modelling manuscripts submitted for publication.
Tommy Yu is a Software Developer at the Auckland Bioengineering Institute, University of Auckland, where he took the role as the lead developer of the Physiome Model Repository and is still the maintainer of the associated infrastructures for its day-to-day operation.
Anand Rampadarath is a Model Curator/Research Assistant at the Auckland Bioengineering Institute, University of Auckland. He is the main curator for Physiome
as well as the NIH-funded Center for Reproducible Biomedical Modeling, and currently serves as a Technical Advisor for a Reproducibility pilot project with PLoS Computational Biology.