API Catalogue
This page catalogues the web APIs available for users and developers of EBRAINS tools and services.
Core services / Collaboratory
Authentication / Authorization (IAM)
IAM is the EBRAINS Identity and Access Management service which is delivered by the Collaboratory and manages user identification and permission management for all EBRAINS users and services.
Collaboratory wiki
The Wiki service of the Collaboratory hosts the main interface to access all the other Collaboratory services. As such, it embodies the full concept of collab workspaces and most users consider it to be the collab service. The Wiki in itself offers a handy way of documenting a user's work with a simple wiki user interface.
Drive
The Collaboratory offers two storage solutions for collabs: the Drive and the Bucket. The Drive is especially well suited for files and documents that need to be worked on in a more agile manner, possibly also collaboratively. For larger files, datasets, and videos the Bucket offers a better solution.
Bucket (Data Proxy)
The Collaboratory offers two storage solutions for collabs: the Drive and the Bucket. The Drive is especially well suited for files and documents that need to be worked on in a more agile manner, possibly also collaboratively. For larger files, datasets, and videos the Bucket offers a better solution.
Find and share data
Knowledge Graph core
The EBRAINS Knowledge Graph is a multi-modal metadata store which brings together information from different fields on brain research. At the core of the EBRAINS Knowledge Graph, a graph database tracks the linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research than would be possible otherwise.
Knowledge Space
KnowledgeSpace aims to be a globally-used, community-based, data-driven encyclopedia for neuroscience that links brain research concepts to data, models, and the literature that support them. Further it aims to serve as a framework where large-scale neuroscience projects can expose their data to the neuroscience community-at-large. KS is a framework that combines general descriptions of neuroscience concepts found in wikipedia with more detailed content from InterLex. It then integrates the content from those two sources with the latest neuroscience citations found in PubMed and data found in some of the world’s leading neuroscience repositories. KS is a joint development between the Human Brain Project (HBP), the International Neuroinformatics Coordinating Facility (INCF), and the Neuroscience Information Framework (NIF).
Neural Activity Resource
The Neural Activity Resource provides a simplified interface to data and metadata from the KG about neural activity recordings.
Provenance API
The Provenance API provides a simplified interface to computational provenance information in the KG.
Brain atlases
Image service
The Image Service was designed to allow users to process imaging data in order to be used with interactive HBP tools. These tools often need special formats and data descriptors to work, and the Image Service's goal is to provide streamlined workflows with which datasets can be made available to these tools with the simplest possible input, on-demand, using resources allocated in the FENIX Research Infrastructure.
siibra
The siibra toolsuite provides both interactive and programmatic user interfaces for working with “multilevel” brain atlases, that is, brain atlases composed of multiple reference spaces, parcellation maps, and data modalities. siibra-API is a RESTful API service exposing the core functionalities for integration with other applications.
Data analysis
Neo-Viewer
Neo Viewer provides web-based visualisation of electrophysiology data, with support for most of the widely-used file formats in neurophysiology, including community standards such as NIX and NWB. It consists of a REST API for transforming electrophysiology data files into JSON format and a Javascript component that can be embedded in any web page.
Simulation
Model Validation service
The Model Validation Service provides web-based tools for working with computational models, and the validation of such models against experimental data. It consists of a REST web service and two clients: the Model Catalog collaboratory app and a Python client. Underlying metadata are stored in the Knowledge Graph. The service allows users (i) to create, edit, search and view metadata about models and validation tests, (ii) to register, search, view and compare the results of validation tests.
The Virtual Brain
REST API for TVB.
MoDEL-CNS
Molecular Dynamics Extended Library: Central Nervous System (MoDEL-CNS) is a platform designed to provide web-access to atomistic-MD trajectories for relevant signal transduction proteins.
Cellular Level Simulation
Web applications that allow running simulations in different scales (single cell, multiple cells, regions).
Neurorobotics
NRP Frontend-Backend comms
NRP-core
The neurorobotics platform core (referred throughout this document as NRP-core) is the mechanism through which NRP users can implement simulations whereby multiple pieces of simulation software can coexist, synchronize their execution and exchange data in tightly ordered fashion. In previous versions of the NRP, NRP-core was referred to as the "Closed Loop Engine" (CLE), the task of which was to orchestrate the dialogue between the Gazebo robotic simulator and brain models implemented in NEST, Nengo, etc. For those of our users familiar with the CLE, NRP-core is a generalization of the latter, with new generic mechanisms provided to users who want to integrate new simulation engines into their NRP simulations. NRP-core is still built on the so-called Transfer Function framework, although the latter was adapted and renamed Transceiver Functions framework. This renaming is not only cosmetic: users familiar with the NRP up to v3.2 should indeed remain aware of some limited but meaningful evolutions between these two frameworks.
Medical data analytics
No API documentation for this service category is available at the present time.
Neuromorphic computing
Job Queue service
REST API for submitting jobs to the BrainScaleS and SpiNNaker platforms, and for retrieving job results.
Quotas service
REST API for requesting and managing compute quotas for the BrainScaleS and SpiNNaker platforms.
High-performance computing
UNICORE
UNICORE (UNiform Interface to COmputing REsources) provides tools and services for making high-performance computing and data resources accessible in a seamless and secure way for a wide variety of applications.
UNICORE offers RESTful APIs for job submission, job management, data access, data movement and workflows, and is already integrated with the HBP AAI and the user/project management at the HPC sites. UNICORE can help solve many integration issues, provide the necessary building blocks and APIs for creating cross-site workflows and it provides added value such as site-to-site data movement (between POSIX filesystems), access to external data, or sharing of HPC data sets.
Supercomputing Proxy
Supercomputing proxy provides services which run on supercomputers a means of running a job on behalf of an EBRAINS user without requesting that the user have an HPAC account. The job is launched using a service account in the name of the service provider. The service is limited to running jobs which use pre-determined executables. The end-user cannot use the supercomputing resources for purposes not intended by the service provider.
Cloud computing
OpenStack
Red Hat OpenStack Platform provides the foundation to build a private or public Infrastructure-as-a-Service (IaaS) cloud on top of Red Hat Enterprise Linux. It offers a highly scalable, fault-tolerant platform for the development of cloud-enabled workloads.
OpenShift
OpenShift is a family of containerization software products developed by Red Hat.
Developer tools
Gitlab
EBRAINS hosts a self-managed instance of GitLab for source code management and CI/CD.
Docker registry (Harbor)
The EBRAINS Docker registry uses Harbor, an an open source trusted cloud native registry project that stores, signs, and scans content.
Headless Jupyter Notebook Testing service
The EBRAINS Headless Jupyter Notebook Testing service periodically executes automatic browser tests by running notebook cells one-by one to assess/evaluate their successful execution.
Logging/monitoring APIs
TO DO
Administration
PLUS
PLUS is a project management tool for the Human Brain Project.
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