2021/04/30 by Bilal Shaikh, Gnaneswara Marupilla, Michael Wilson +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Gene Regulatory Network Analysis #Microbial Metabolic Engineering and Bioproduction #Bioinformatics and Genomic Networks
paper · pdf · doi:10.1093/nar/gkab411
openalex publication_date 2021/04/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
Comprehensive, predictive computational models have significant potential for science, bioengineering, and medicine. One promising way to achieve more predictive models is to combine submodels of multiple subsystems. To capture the multiple scales of biology, these submodels will likely require multiple modeling frameworks and simulation algorithms. Several community resources are already available for working with many of these frameworks and algorithms. However, the variety and sheer number of these resources make it challenging to find and use appropriate tools for each model, especially for novice modelers and experimentalists. To make these resources easier to use, we developed RunBioSimulations (https://run.biosimulations.org), a single web application for executing a broad range of models. RunBioSimulations leverages community resources, including BioSimulators, a new open registry of simulation tools. These resources currently enable RunBioSimulations to execute nine frameworks and 44 algorithms, and they make RunBioSimulations extensible to additional frameworks and algorithms. RunBioSimulations also provides features for sharing simulations and interactively visualizing their results. We anticipate that RunBioSimulations will foster reproducibility, stimulate collaboration, and ultimately facilitate the creation of more predictive models.