Physiome Sciences
Publicly hosted, open-source repository and toolset for multiscale computational physiology. Maintains an indexed archive of curated physiological and biophysical models (433 active models listed), distributes a simulation environment and modular model-construction tools, publishes reproducibility and verification guidelines, and provides training materials and course archives for researchers and educators.
Industries
Products
Collections of open model archives and tutorials
Domain-specific collections of open-source models and tutorials (examples include lung, cardiac, vascular, transport and enzymatic kinetics) packaged for download and interactive exploration.
Consolidated model database index
Aggregated index and cross-archive search interface that links models and metadata across multiple external repositories to aid discovery at scale.
Collections of open model archives and tutorials
Domain-specific collections of open-source models and tutorials (examples include lung, cardiac, vascular, transport and enzymatic kinetics) packaged for download and interactive exploration.
Consolidated model database index
Aggregated index and cross-archive search interface that links models and metadata across multiple external repositories to aid discovery at scale.
Services
Distribution of open-source simulation environment
Provision of downloadable binaries and source distributions of a cross-platform simulation environment for building, running and analyzing physiological models.
Model hosting, indexing and web execution
Hosting, searchable indexing and web-based execution of physiological models with facilities for parameter exploration, visualization and archive download.
Standards, templates and training materials
Guidelines, reproducibility templates, validation checklists and archived course materials (daily zip packages) to support reproducible model development and community training.
Distribution of open-source simulation environment
Provision of downloadable binaries and source distributions of a cross-platform simulation environment for building, running and analyzing physiological models.
Model hosting, indexing and web execution
Hosting, searchable indexing and web-based execution of physiological models with facilities for parameter exploration, visualization and archive download.
Standards, templates and training materials
Guidelines, reproducibility templates, validation checklists and archived course materials (daily zip packages) to support reproducible model development and community training.
Expertise Areas
- Multiscale physiological modeling
- Computational modeling of transport and exchange (BTEX/CTEX)
- Cardiopulmonary and circulatory system modeling
- Model interoperability and format conversion
Key Technologies
- Java-based simulation engine
- Declarative mathematical modeling language
- ODE, DAE and PDE numerical solvers
- Stochastic (Gillespie) simulation methods