runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
Creating large and comprehensive predictive models of biological processes will likely require the collaboration of many domain experts, who have various levels of familiarity and technical expertise in biological modeling methods, tools, and standards. Additionally, the complexity of biological systems requires the use of a variety of different frameworks and algorithms to capture different levels of granularity and multiple scales. Currently, many modeling tools have a high barrier to entry, requiring the installation of software, configuration of environments, and management of various files in various formats. Furthermore, different tools are required to run simulations involving different frameworks and algorithms, increasing the complexity and effort required to work collaboratively. To facilitate the use of modeling tools by both experienced and novice modelers, runBiosimulations provides a single, easy-to-use web interface for simulating biological models across a variety of frameworks, algorithms, and formats. The runBiosimulations application currently provides access to 10 simulators that support 6 frameworks, 37 algorithms, and 2 model formats. The modular architecture of the system is designed to enable the community to incorporate nearly any tool for any set of frameworks, algorithms, and formats. We invite the community to use and contribute to runBioSimulations. More information is available at run.biosimulations.org/help/about. By facilitating collaboration and reuse, we anticipate that runBioSimulations will help the community develop more comprehensive and more predictive models.