RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

Graphical Abstract RunBioSimulations is an extensible, standards-driven web application for executing models across a broad range of modeling frameworks, simulation algorithms, and model formats and visualizing and sharing their results

Abstract

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.

Publication
Nucleic Acids Research
Bilal Shaikh
Bilal Shaikh
Biomedical Software Developer

Working on developing tools to enable large scale models of biology