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

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.

Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility

“…If the goal is for non-modelers to be able to interact with models (e.g., to analyze data, to contribute data toward a modeling project, or to apply a model for medicine), it needs to be much easier to find and use these tools. Two initiatives that are trying to address this are BioSimulators (BioSimulators, 2021) and runBioSimulations (Shaikh et al, 2021).…”

BioSimulators: a central registry of simulation engines and services for recommending specific tools

“…Once an investigator has learned BioSimulators' conventions, they can run a broad range of simulations involving a variety of tools. In particular, we believe that simple web applications for using BioSimulators, such as runBioSimulations (15), will empower peer reviewers to review simulations more deeply, leading to better evaluation of modeling studies.…”

libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library

“…or developing new computational approaches such as detecting bistable switches (Reyes et al, 2022) (more???). Tool developers on the other hand use libRoadRunner as a core SBML handling component in their modular software design (Choi et al, 2018), runBiosimulations (Shaikh et al, 2021), MASSPy (Haiman et al, 2021), SBMLUtils (Watanabe et al, 2018), Compucell3D (Swat et al, 2012), PhysiCell (Ghaffarizadeh et al, 2018), pyBioNetFit (Neumann et al, 2021) and DIVIPAC (Nguyen et al, 2015).…”