BioSimulators
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Verified
More comprehensive and more predictive models have the potential to advance biology, bioengineering, and medicine. Building more predictive models will likely require the collaborative efforts of many investigators. This requires teams to be able to share and reuse model components and modeling tools. Despite extensive efforts to develop standards such as the COMBINE/OMEX archive format, the Kinetic Simulation Algorithm Ontology (KiSAO), the Systems Biology Markup Language (SBML), and the Simulation Experiment Description Markup Language (SED-ML) and repositories such as BioModels and the Physiome Model Repository, it is still often difficult to share, reuse, and combine models and modeling tools. One challenge to sharing and reusing models is the disparate formats, model repositories, and simulation tools for different types of models. The proliferation of numerous similar formats, repositories, and tools makes it difficult, especially for non-experts, to find models and to find an appropriate simulation tool for each model. In addition, the existing model repositories have limited capabilities for sharing associated resources such as training data, simulation experiments, and visualizations. BioSimulators addressses these challenges by making it easier for researchers to share and reuse modeling tools.
- Home page: https://biosimulators.org
- REST API: https://api.biosimulators.org
- Docker images: https://github.com/orgs/biosimulators/packages
- Command-line programs: https://pypi.org/user/biosimulators
- Python APIs: https://pypi.org/user/biosimulators
- Tutorials: https://tutorial.biosimulators.org
- Documentation: https://docs.biosimulations.org
- Example simulation projects: https://github.com/biosimulators/Biosimulators_test_suite/tree/dev/examples
- Template for simulation tools: https://github.com/biosimulators/Biosimulators_simulator_template
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Repositories
- Biosimulators Public
Registry of containerized biosimulation tools that support a standard command-line interface
- Biosimulators_AMICI Public
AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
- Biosimulators_utils Public
Utilities for building standardized command-line interfaces for biosimulation software packages
- Biosimulators_test_suite Public
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
- SimpleProcessBigraphRuntime Public
A simple project demonstrating how to take a process bigraph input file, and run simulations / workflows utilizing a simple registry
- Biosimulators_COPASI Public
COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
- Biosimulators_smoldyn Public
Smoldyn biochemical network stochastic simulation program via BioSimulators-compliant python interface.
- bspil-basico Public
BioSimulators Process Interface Library for COPASI through the Basico python wrapper
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