Online Modeling Services
RunBioSimulations is a web application for running biosimulations.
There is a follow-up link to publishing the results to the repository – validates curation and publishing to the repository.
REST API Swagger page provides developers with a detailed and interactive documentation of our API endpoints, simplifying the integration process and offering an intuitive interface for executing services, which facilitates efficient interaction with our platform’s functionalities and resources.
Create project provides a dynamic interface to craft a COMBINE/OMEX archive for simulating your chosen model, including model selection, format choice, simulation type, parameter and algorithm configurations, as well as specific namespaces, model attributes, and simulation observables
Visualization service employs both Plotly and Vega to offer reproducible, domain-independent and domain-specific visualizations of simulation data, translating complex computations into accessible, intuitive, and insightful graphical representations. (Currently in development. No link yet.)
makeSBML is a web tool that makes it easy to create SBML models or to translate SBML models into the more readable Antimony format. As an example, copy the following text into the left panel and click on the right-arrow button: “A -> B; k1*A; k1 = 0.1”
Ratesb is a web tool that accepts SBML or antimony encoded models and checks the model rate laws for errors or provides warnings for rate laws that are unusual.
Repository Services
BioSimulation Projects is a searchable database of rigorously curated simulation projects from published works. Each project has been meticulously resimulated to accurately reproduce and validate the originally published outcomes, contributing to the advancement of reproducible research in the field.
BioSimulators is a registry of simulation tools with unified interfaces, which ensures consistency with standards such as CellML, SBML, SED-ML, and the COMBINE archive format. With its built-in recommendation services, the platform streamlines tool selection for specific projects, thereby enhancing the exchange, reproduction, and combination of simulations
Reproducibility Portal a user-friendly browser application that leverages our API to provide seamless access to a vast range of published simulation projects
Validation Services
Model Validation (for SBML or CellML) ensures the reliability of model file.
Validate a simulation experiment (SED-ML) ensures consistent simulation workflows.
Validate metadata (Omex metadata files)
Validate a project (Omex archive)
Desktop Modeling Services
Vscode-Antimony is a Visual Studio Code Extension Tool that adds language support for Antimony for building models in Systems Biology, which makes it convenient to work simultaneously with the Antimony and Systems Biology Markup Language (SBML) representations of models.
Iridium Simulator is an interactive SBML compliant desktop simulator (Windows/Mac) for systems biology.
If you are interested in collaborating to provide online modeling services, please contact info@reproduciblebiomodels.org .