Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility
Year: 2022
Type: article
Abstract: During the COVID-19 pandemic, mathematical modeling of disease transmission has become a cornerstone of key state decisions. To advance the state-of-the-art host viral modeling to handle future pandemics, many scientists working on related issues assembled to discuss the topics. These discussions exposed the reproducibility crisis that leads to inability to reuse and integrate models. This document summarizes these discussions, presents difficulties, and mentions existing efforts towards future solutions that will allow future model utility and integration. We argue that without addressing these challenges, scientists will have diminished ability to build, disseminate, and implement high-impact multi-scale modeling that is needed to understand the health crises we face.
Source: Frontiers in Systems Biology
Authors: Jonathan Karr, Rahuman S. Malik-Sheriff, James Osborne, Gilberto Gonzalez-Parra, Eric Forgoston, Ruth Bowness, Yaling Liu, Robin Thompson, Winston Garira, Jacob Barhak, John Rice, Marcella Torres, Hana M. Dobrovolny, Tingting Tang, William Waites, James A. Glazier, James R. Faeder, Alexander Kulesza
Institutions: Icahn School of Medicine at Mount Sinai, European Bioinformatics Institute, The University of Melbourne, New Mexico Institute of Mining and Technology, Montclair State University, University of Bath, Lehigh University, University of Warwick, University of Venda, University of Richmond, Texas Christian University, San Diego State University, San Diego State University, Imperial Valley Campus, University of Strathclyde, London School of Hygiene & Tropical Medicine, Indiana University Bloomington, Indiana University, University of Pittsburgh
Language: English
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
Open Access status: gold
Estimated APC paid: $1,900
Awards: G1288308599, Competitive Renewal of Development, Improvement and Extension of the Tissue Simulation Environment - CompuCell3D, A novel hybrid discrete-continuum cellular automaton model to study tuberculosis disease progression and treatment, Investigating SARS-CoV-2 Transmission in UK Jewish Communities, High Performance Computing for Multiscale Modeling of Biological Systems, Dissemination of libRoadRunner and CompuCell3D, Network for Computational Nanotechnology - Engineered nanoBIO Node, G8805859268, Center for Reproducible Systems for Biomedical Modeling
OpenAlex ID: W4220690841