EBRAINS Model Catalog
What is the EBRAINS Model Catalog?
The EBRAINS Model Catalog contains information about models developed and/or used within the EBRAINS research infrastructure.
It allows you to find information about neuroscience models and about results obtained using those models, in particular about how those models have been validated against experimental findings.
Find
Find, understand and use interesting models
The Model Catalog lets you filter the list of models by:
- what is being modelled (species, brain region, cell type)
- the scope of the model (subcellular, single cell, network, whole brain)
- the abstraction level of the model (cognitive, neural field, biophysical, spiking point neuron, systems biology)
You can also search by author or model name.
The catalog contains a detailed description of each model, a download link for each version of the model, and information about the validation of each model (i.e. comparing simulation results to experimental data).
Some models have links to other EBRAINS applications where the models can be simulated and/or or explored in more detail.
Share
Share models with others
If you are developing your own model and wish to share it through the EBRAINS Knowledge Graph, adding it to the Model Catalog is the first step.
You don't need to wait until the model is published in a journal article, entries can be marked as private and shared only with your chosen collaborators.
When you're ready to share publicly, our team of professional data and model curators will check the model is ready to be shared (code archived, terms of reuse specified, ...) then release it to the public KG Search interface.
(Coming soon: models released through the EBRAINS Knowledge Graph will received their own DOI through DataCite).
Use
Use an existing model with the EBRAINS research infrastructure
Whether you're developing your own model or want to use an existing published model with EBRAINS tools and services, registering it with the Model Catalog is the first step.
Two services are already directly linked from the Model Catalog:
- NEURON As A Service (aka BlueNaaS), for simulations detailed single neuron models in the browser
- Morphology Viewer, for visualizing the morphology of such models.
More services will be linked soon.
Using the Model Catalog Python client, you can access models from within a Jupyter notebook (e.g. in the EBRAINS Jupyter Lab), giving you access to a still wider range of tools and services.
Validate
Compare models to each other and to experimental data
As mentioned above, one of the main aims of the EBRAINS Model Catalog is to show how models compare to experiments.
We use the SciUnit framework to formalize the comparison of models and experiments as "validation tests", and show both information about these tests and the results of the tests in the Model Catalog.
Running the same set of validation tests with different, but related models, is a powerful tool for comparing models and deciding which is best for your purpose.
Links
How is the EBRAINS Model Catalog different to other model databases?
A number of other model databases are available in neuroscience, including ModelDB, BioModels, and Open Source Brain.
The EBRAINS Model Catalog is complementary to these other databases, providing validation results and making it possible to use models with other EBRAINS tools and services.
Where a model is also available in one of these other databases, it is cross-linked.
Knowledge Graph
How does the EBRAINS Model Catalog relate to the EBRAINS Knowledge Graph Search user interface?
The Model Catalog can be used for models at all stages of development, from initial experimentation through to published models.
Models that satisfy certain quality control criteria: verified source code, a detailed description, and a complete set of metadata, can also be found through the EBRAINS Knowledge Graph Search application, where additional information, in particular about links to related experimental datasets, can be found.
Develop
Develop tools and workflows based on the Model Catalog
The Model Catalog Python client provides programmatic access to the database of models, validation tests and test results, and lets you build the catalog into your model development and simulation workflow.
Contact
Any questions?
If you have questions that are not answered here, contact us by e-mail: support@ebrains.eu
Acknowledgements
This open source software code was developed in part or
in whole in the Human Brain Project, funded from the
European Union’s Horizon 2020 Framework Programme for
Research and Innovation under Specific Grant Agreements
No. 720270, 785907 and xyzabc (Human Brain Project SGA1,
SGA2 and SGA3).
