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

Shaikh, Bilal; Marupilla, Gnaneswara; Wilson, Michael; Blinov, Michael L.; Moraru, Ion I.; Karr, Jonathan R.

doi:10.1093/nar/gkab411

Cited by 15 publications

(13 citation statements)

References 26 publications

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“…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.…”

Section: Use Casesmentioning

confidence: 99%

“…To ensure these resources are used consistently, we also developed tools for integrated validation of simulation projects and tools (Figure 2A ). On top of BioSimulators, we have also developed runBioSimulations and BioSimulations, user-friendly web applications for using BioSimulators to execute and share simulations and visualizations of their results ( 15 ) (Figure 2C ).…”

Section: Introductionmentioning

confidence: 99%

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

Shaikh

Smith

Vasilescu

et al. 2022

Nucleic Acids Research

Self Cite

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Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.

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Section: Use Casesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Shaikh

Smith

Vasilescu

et al. 2022

Nucleic Acids Research

Self Cite

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“…Crucially, multiple user-friendly tools are available for their formulation, numerical simulation, and sharing [3][4][5][6][7], which has contributed to their widespread use in biological research and education [8]. In addition to simulating their dynamics through time, visually analyzing the global behavior of such models is essential for understanding their function.…”

Section: Introductionmentioning

confidence: 99%

Automatic Generation of Interactive Multidimensional Phase Portraits

Ogunsan

Lobo

2022

Preprint

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Mathematical models formally and precisely represent biological mechanisms with complex dynamics. To understand the possible behaviors of such systems, phase portrait diagrams can be used to visualize their overall global dynamics across a domain. However, producing these phase portrait diagrams is a laborious process reserved to mathematical experts. Here, we developed a computational methodology to automatically generate phase portrait diagrams to study biological dynamical systems based on ordinary differential equations. The method only needs as input the variables and equations describing a multidimensional biological system and it automatically outputs for each pair of dependent variables a complete phase portrait diagram, including the critical points and their stability, the nullclines of the system, and a vector space of the trajectories. Crucially, the portraits generated are interactive, and the user can move the visualized planar slice, change parameters with sliders, and add trajectories in the phase and time domains, after which the diagrams are updated in real time. The method is available as a user-friendly graphical interface or can be accessed programmatically with a Mathematica package. The generated portraits and particular views can be saved as computable notebooks preserving the interactive functionality, an approach that can be adopted for reproducible science and interactive pedagogical materials. The method, code, and examples are freely-available at https://lobolab.umbc.edu/autoportrait .

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“…JWS Online [16] supports simulation and steady-state analysis but does not support parameter estimation. The tool suite RunBioSimulations [17] offers time course simulation and steady-state analysis but lacks support for parameter estimation. Additionally, RunBioSimulations offers many third-party analysis tools with many options and is hence most suitable for experienced users.…”

Section: Introductionmentioning

confidence: 99%

SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models

Yamada¹,

Kaito²,

König³

et al. 2021

Preprint

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In systems biology, biological phenomena are often modeled by ODE and distributed in the de facto standard file format SBML. The primary analyses performed with such models are dynamic simulation, steady-state analysis, and parameter estimation. These methodologies are mathematically formalized, and libraries for such analyses have been published. Several tools exist to create, simulate, or visualize models encoded in SBML. However, setting up and establishing analysis environments is a crucial hurdle for non-modelers. Therefore, easy access to perform fundamental analyses of ODE models is a significant challenge. We developed SBMLWebApp, a web-based service to execute SBML-based simulations, steady-state analysis, and parameter estimation directly in the browser without the need for any setup or prior knowledge to address this issue. SBMLWebApp visualizes the result and numerical table of each analysis and provides a download of the results. SBMLWebApp allows users to select and analyze SBML models directly from the BioModels Database. Taken together, SBMLWebApp provides barrier-free access to an SBML analysis environment for simulation, steady-state analysis, and parameter estimation for SBML models. SBMLWebApp is implemented in Java™ based on an Apache Tomcat® web server using COPASI, the SBSCL, and LibSBMLSim as simulation engines. SBMLWebApp is licensed under MIT with source code available from https://github.com/TakahiroYamada/SBMLWebApp. The program runs online at http://simulate-biology.org.

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

Cited by 15 publications

References 26 publications

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

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

Automatic Generation of Interactive Multidimensional Phase Portraits

SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models

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