Changes for page API Catalogue

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2 2  
3 3  This page catalogues the [[web API>>https://en.wikipedia.org/wiki/Web_API]]s available for users and developers of [[EBRAINS tools and services>>https://ebrains.eu]].
4 4  
5 -Please note this is a work in progress.[[image:Collabs.technical-coordination.Working Group APIs (EA-WG).API Catalogue.WebHome@1635154142156-729.png]]
5 +Please note this is a work in progress.
6 6  
7 7  ----
8 8  
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10 10  
11 11  === Authentication / Authorization (IAM) ===
12 12  
13 -[[[[image:1635154142156-729.png]]>>https://www.keycloak.org/documentation.html||rel="noopener noreferrer" target="_blank"]]
13 +[[[[image:documentation-icon.png]]>>https://www.keycloak.org/documentation.html||rel="noopener noreferrer" target="_blank"]]
14 14  
15 15  IAM is the EBRAINS **I**dentity and **A**ccess **M**anagement service which is delivered by the Collaboratory and manages user identification and permission management for all EBRAINS users and services.
16 16  
17 17  === Collaboratory wiki ===
18 18  
19 -[[[[image:1635154142156-729.png]]>>https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/XWikiRESTfulAPI||rel="noopener noreferrer" target="_blank"]]
19 +[[[[image:documentation-icon.png]]>>https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/XWikiRESTfulAPI||rel="noopener noreferrer" target="_blank"]]
20 20  
21 21  The [[Wiki service>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Getting%20Started/#HWikipages]] 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.
22 22  
23 23  === Drive ===
24 24  
25 -[[[[image:1635154142156-729.png]]>>https://download.seafile.com/published/web-api/home.md||rel="noopener noreferrer" target="_blank"]]
25 +[[[[image:documentation-icon.png]]>>https://download.seafile.com/published/web-api/home.md||rel="noopener noreferrer" target="_blank"]]
26 26  
27 27  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>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Bucket/]] offers a better solution.
28 28  
29 29  === Bucket (Data Proxy) ===
30 30  
31 -[[[[image:1635154142156-729.png]]>>https://data-proxy-ppd.ebrains.eu/api/docs||rel="noopener noreferrer" target="_blank"]]
31 +[[[[image:documentation-icon.png]]>>https://data-proxy-ppd.ebrains.eu/api/docs||rel="noopener noreferrer" target="_blank"]]
32 32  
33 33  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>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Bucket/]] offers a better solution.
34 34  
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38 38  
39 39  === Knowledge Graph core ===
40 40  
41 -[[[[image:1635154142156-729.png]]>>https://core.kg.ebrains.eu/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config||rel="noopener noreferrer" target="_blank"]]
41 +[[[[image:documentation-icon.png]]>>https://core.kg.ebrains.eu/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config||rel="noopener noreferrer" target="_blank"]]
42 42  
43 43  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.
44 44  
45 45  === Knowledge Space ===
46 46  
47 -[[[[image:1635154142156-729.png]]>>https://api.knowledge-space.org/docs||rel="noopener noreferrer" target="_blank"]]
47 +[[[[image:documentation-icon.png]]>>https://api.knowledge-space.org/docs||rel="noopener noreferrer" target="_blank"]]
48 48  
49 49  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).
50 50  
51 51  === Neural Activity Resource ===
52 52  
53 -[[[[image:1635154142156-729.png]]>>https://neural-activity-resource.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
53 +[[[[image:documentation-icon.png]]>>https://neural-activity-resource.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
54 54  
55 55  The Neural Activity Resource provides a simplified interface to data and metadata from the KG about neural activity recordings.
56 56  
57 57  === Provenance API ===
58 58  
59 -[[[[image:1635154142156-729.png]]>>https://prov.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
59 +[[[[image:documentation-icon.png]]>>https://prov.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
60 60  
61 61  The Provenance API provides a simplified interface to computational provenance information in the KG.
62 62  
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66 66  
67 67  === Image service ===
68 68  
69 -[[[[image:1635154142156-729.png]]>>https://img-svc.apps.hbp.eu/api-docs||rel="noopener noreferrer" target="_blank"]]
69 +[[[[image:documentation-icon.png]]>>https://img-svc.apps.hbp.eu/api-docs||rel="noopener noreferrer" target="_blank"]]
70 70  
71 71  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.
72 72  
73 73  === siibra ===
74 74  
75 -[[[[image:1635154142156-729.png]]>>https://siibra-api.readthedocs.io||rel="noopener noreferrer" target="_blank"]]
75 +[[[[image:documentation-icon.png]]>>https://siibra-api.readthedocs.io||rel="noopener noreferrer" target="_blank"]]
76 76  
77 77  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.
78 78  
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82 82  
83 83  === Neo-Viewer ===
84 84  
85 -[[[[image:1635154142156-729.png]]>>https://neo-viewer.brainsimulation.eu/||rel="noopener noreferrer" target="_blank"]]
85 +[[[[image:documentation-icon.png]]>>https://neo-viewer.brainsimulation.eu/||rel="noopener noreferrer" target="_blank"]]
86 86  
87 87  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.
88 88  
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92 92  
93 93  === Model Validation service ===
94 94  
95 -[[[[image:1635154142156-729.png]]>>https://validation-v2.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
95 +[[[[image:documentation-icon.png]]>>https://validation-v2.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
96 96  
97 97  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.
98 98  
99 99  === The Virtual Brain ===
100 100  
101 -[[[[image:1635154142156-729.png]]>>https://thevirtualbrain-rest.apps.hbp.eu/doc||rel="noopener noreferrer" target="_blank"]]
101 +[[[[image:documentation-icon.png]]>>https://thevirtualbrain-rest.apps.hbp.eu/doc||rel="noopener noreferrer" target="_blank"]]
102 102  
103 103  REST API for TVB.
104 104  
105 105  === MoDEL-CNS ===
106 106  
107 -[[[[image:1635154142156-729.png]]>>https://mmb.irbbarcelona.org/MoDEL-CNS/api/rest/docs/||rel="noopener noreferrer" target="_blank"]]
107 +[[[[image:documentation-icon.png]]>>https://mmb.irbbarcelona.org/MoDEL-CNS/api/rest/docs/||rel="noopener noreferrer" target="_blank"]]
108 108  
109 109  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**.
110 110  
111 111  === Cellular Level Simulation ===
112 112  
113 -[[[[image:1635154142156-729.png]]>>https://humanbrainproject.github.io/hbp-bsp-service-account/introduction/introduction.html||rel="noopener noreferrer" target="_blank"]]
113 +[[[[image:documentation-icon.png]]>>https://humanbrainproject.github.io/hbp-bsp-service-account/introduction/introduction.html||rel="noopener noreferrer" target="_blank"]]
114 114  
115 115  Web applications that allow running simulations in different scales (single cell, multiple cells, regions).
116 116  
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120 120  
121 121  === NRP Frontend-Backend comms ===
122 122  
123 -[[[[image:1635154142156-729.png]]>>https://neurorobotics.net/Documentation/nrp/developer_manual/ExDbackend/index.html||rel="noopener noreferrer" target="_blank"]]
123 +[[[[image:documentation-icon.png]]>>https://neurorobotics.net/Documentation/nrp/developer_manual/ExDbackend/index.html||rel="noopener noreferrer" target="_blank"]]
124 124  
125 125  === NRP-core ===
126 126  
127 -[[[[image:1635154142156-729.png]]>>https://hbpneurorobotics.bitbucket.io/index.html||rel="noopener noreferrer" target="_blank"]]
127 +[[[[image:documentation-icon.png]]>>https://hbpneurorobotics.bitbucket.io/index.html||rel="noopener noreferrer" target="_blank"]]
128 128  
129 129  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>>url:https://hbpneurorobotics.bitbucket.io/transceiver_function.html]] 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.
130 130  
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140 140  
141 141  === Job Queue service ===
142 142  
143 -[[[[image:1635154142156-729.png]]>>https://nmpi.hbpneuromorphic.eu/api/v2/||rel="noopener noreferrer" target="_blank"]]
143 +[[[[image:documentation-icon.png]]>>https://nmpi.hbpneuromorphic.eu/api/v2/||rel="noopener noreferrer" target="_blank"]]
144 144  REST API for submitting jobs to the BrainScaleS and SpiNNaker platforms, and for retrieving job results.
145 145  
146 146  === Quotas service ===
147 147  
148 -[[[[image:1635154142156-729.png]]>>]]
148 +[[[[image:documentation-icon.png]]>>]]
149 149  REST API for requesting and managing compute quotas for the BrainScaleS and SpiNNaker platforms.
150 150  
151 151  ----
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154 154  
155 155  === UNICORE ===
156 156  
157 -[[[[image:1635154142156-729.png]]>>https://sourceforge.net/p/unicore/wiki/REST_API/||rel="noopener noreferrer" target="_blank"]]
157 +[[[[image:documentation-icon.png]]>>https://sourceforge.net/p/unicore/wiki/REST_API/||rel="noopener noreferrer" target="_blank"]]
158 158  
159 159  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.
160 160  
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162 162  
163 163  === Supercomputing Proxy ===
164 164  
165 -[[[[image:1635154142156-729.png]]>>https://unicore-job-proxy.apps.hbp.eu/docs||rel="noopener noreferrer" target="_blank"]]
165 +[[[[image:documentation-icon.png]]>>https://unicore-job-proxy.apps.hbp.eu/docs||rel="noopener noreferrer" target="_blank"]]
166 166  
167 167  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.
168 168  
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172 172  
173 173  === OpenStack ===
174 174  
175 -[[[[image:1635154142156-729.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/openstack/||rel="noopener noreferrer" target="_blank"]]
175 +[[[[image:documentation-icon.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/openstack/||rel="noopener noreferrer" target="_blank"]]
176 176  
177 177  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.
178 178  
179 179  === OpenShift ===
180 180  
181 -[[[[image:1635154142156-729.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/kubernetes/openshift/||rel="noopener noreferrer" target="_blank"]]
181 +[[[[image:documentation-icon.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/kubernetes/openshift/||rel="noopener noreferrer" target="_blank"]]
182 182  
183 183  OpenShift is a family of containerization software products developed by Red Hat.
184 184  
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188 188  
189 189  === Gitlab ===
190 190  
191 -[[[[image:1635154142156-729.png]]>>https://docs.gitlab.com/ee/api/||rel="noopener noreferrer" target="_blank"]]
191 +[[[[image:documentation-icon.png]]>>https://docs.gitlab.com/ee/api/||rel="noopener noreferrer" target="_blank"]]
192 192  
193 193  EBRAINS hosts a self-managed instance of GitLab for source code management and CI/CD.
194 194  
195 195  === Docker registry (Harbor) ===
196 196  
197 -[[[[image:1635154142156-729.png]]>>https://docker-registry.ebrains.eu/devcenter-api-2.0||rel="noopener noreferrer" target="_blank"]]
197 +[[[[image:documentation-icon.png]]>>https://docker-registry.ebrains.eu/devcenter-api-2.0||rel="noopener noreferrer" target="_blank"]]
198 198  
199 199  The EBRAINS Docker registry uses Harbor, an an open source trusted cloud native registry project that stores, signs, and scans content.
200 200  
201 201  === Logging/monitoring APIs ===
202 202  
203 -[[[[image:1635154142156-729.png]]>>]]
203 +[[[[image:documentation-icon.png]]>>]]
204 204  
205 205  TO DO
206 206  
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210 210  
211 211  === PLUS ===
212 212  
213 -[[[[image:1635154142156-729.png]]>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/drive/Shared%20with%20all/PLUS-LAB/PLUS%20KPI-PrI%20API.ipynb||rel="noopener noreferrer" target="_blank"]]
213 +[[[[image:documentation-icon.png]]>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/drive/Shared%20with%20all/PLUS-LAB/PLUS%20KPI-PrI%20API.ipynb||rel="noopener noreferrer" target="_blank"]]
214 214  
215 215  PLUS is a project management tool for the Human Brain Project.
216 216  
Public

API Catalogue