Changes for page API Catalogue

Last modified by lupascu on 2022/05/23 22:36
From version 14.1
edited by adavison
on 2021/12/17 13:41
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To version 10.1
edited by adavison
on 2021/12/17 13:34
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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 -(% class="box warningmessage" %)
6 -(((
7 7  Please note this is a work in progress.
8 -)))
9 9  
10 10  ----
11 11  
12 -{{toc/}}
13 -
14 -----
15 -
16 16  == Core services / Collaboratory ==
17 17  
18 18  === Authentication / Authorization (IAM) ===
19 19  
20 -[[[[image:documentation-icon.png]]>>https://www.keycloak.org/documentation.html||rel="noopener noreferrer" target="_blank"]]
13 +[[[[image:1635154142156-729.png]]>>https://www.keycloak.org/documentation.html||rel="noopener noreferrer" target="_blank"]][[image:documentation-icon.png]]
21 21  
22 22  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.
23 23  
24 24  === Collaboratory wiki ===
25 25  
26 -[[[[image:documentation-icon.png]]>>https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/XWikiRESTfulAPI||rel="noopener noreferrer" target="_blank"]]
19 +[[[[image:1635154142156-729.png]]>>https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/XWikiRESTfulAPI||rel="noopener noreferrer" target="_blank"]]
27 27  
28 28  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.
29 29  
30 30  === Drive ===
31 31  
32 -[[[[image:documentation-icon.png]]>>https://download.seafile.com/published/web-api/home.md||rel="noopener noreferrer" target="_blank"]]
25 +[[[[image:1635154142156-729.png]]>>https://download.seafile.com/published/web-api/home.md||rel="noopener noreferrer" target="_blank"]]
33 33  
34 34  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.
35 35  
36 36  === Bucket (Data Proxy) ===
37 37  
38 -[[[[image:documentation-icon.png]]>>https://data-proxy-ppd.ebrains.eu/api/docs||rel="noopener noreferrer" target="_blank"]]
31 +[[[[image:1635154142156-729.png]]>>https://data-proxy-ppd.ebrains.eu/api/docs||rel="noopener noreferrer" target="_blank"]]
39 39  
40 40  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.
41 41  
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45 45  
46 46  === Knowledge Graph core ===
47 47  
48 -[[[[image:documentation-icon.png]]>>https://core.kg.ebrains.eu/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config||rel="noopener noreferrer" target="_blank"]]
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"]]
49 49  
50 50  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.
51 51  
52 52  === Knowledge Space ===
53 53  
54 -[[[[image:documentation-icon.png]]>>https://api.knowledge-space.org/docs||rel="noopener noreferrer" target="_blank"]]
47 +[[[[image:1635154142156-729.png]]>>https://api.knowledge-space.org/docs||rel="noopener noreferrer" target="_blank"]]
55 55  
56 56  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).
57 57  
58 58  === Neural Activity Resource ===
59 59  
60 -[[[[image:documentation-icon.png]]>>https://neural-activity-resource.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
53 +[[[[image:1635154142156-729.png]]>>https://neural-activity-resource.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
61 61  
62 62  The Neural Activity Resource provides a simplified interface to data and metadata from the KG about neural activity recordings.
63 63  
64 64  === Provenance API ===
65 65  
66 -[[[[image:documentation-icon.png]]>>https://prov.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
59 +[[[[image:1635154142156-729.png]]>>https://prov.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
67 67  
68 68  The Provenance API provides a simplified interface to computational provenance information in the KG.
69 69  
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73 73  
74 74  === Image service ===
75 75  
76 -[[[[image:documentation-icon.png]]>>https://img-svc.apps.hbp.eu/api-docs||rel="noopener noreferrer" target="_blank"]]
69 +[[[[image:1635154142156-729.png]]>>https://img-svc.apps.hbp.eu/api-docs||rel="noopener noreferrer" target="_blank"]]
77 77  
78 78  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.
79 79  
80 80  === siibra ===
81 81  
82 -[[[[image:documentation-icon.png]]>>https://siibra-api.readthedocs.io||rel="noopener noreferrer" target="_blank"]]
75 +[[[[image:1635154142156-729.png]]>>https://siibra-api.readthedocs.io||rel="noopener noreferrer" target="_blank"]]
83 83  
84 84  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.
85 85  
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89 89  
90 90  === Neo-Viewer ===
91 91  
92 -[[[[image:documentation-icon.png]]>>https://neo-viewer.brainsimulation.eu/||rel="noopener noreferrer" target="_blank"]]
85 +[[[[image:1635154142156-729.png]]>>https://neo-viewer.brainsimulation.eu/||rel="noopener noreferrer" target="_blank"]]
93 93  
94 94  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.
95 95  
... ... @@ -99,25 +99,25 @@
99 99  
100 100  === Model Validation service ===
101 101  
102 -[[[[image:documentation-icon.png]]>>https://validation-v2.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
95 +[[[[image:1635154142156-729.png]]>>https://validation-v2.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
103 103  
104 104  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.
105 105  
106 106  === The Virtual Brain ===
107 107  
108 -[[[[image:documentation-icon.png]]>>https://thevirtualbrain-rest.apps.hbp.eu/doc||rel="noopener noreferrer" target="_blank"]]
101 +[[[[image:1635154142156-729.png]]>>https://thevirtualbrain-rest.apps.hbp.eu/doc||rel="noopener noreferrer" target="_blank"]]
109 109  
110 110  REST API for TVB.
111 111  
112 112  === MoDEL-CNS ===
113 113  
114 -[[[[image:documentation-icon.png]]>>https://mmb.irbbarcelona.org/MoDEL-CNS/api/rest/docs/||rel="noopener noreferrer" target="_blank"]]
107 +[[[[image:1635154142156-729.png]]>>https://mmb.irbbarcelona.org/MoDEL-CNS/api/rest/docs/||rel="noopener noreferrer" target="_blank"]]
115 115  
116 116  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**.
117 117  
118 118  === Cellular Level Simulation ===
119 119  
120 -[[[[image:documentation-icon.png]]>>https://humanbrainproject.github.io/hbp-bsp-service-account/introduction/introduction.html||rel="noopener noreferrer" target="_blank"]]
113 +[[[[image:1635154142156-729.png]]>>https://humanbrainproject.github.io/hbp-bsp-service-account/introduction/introduction.html||rel="noopener noreferrer" target="_blank"]]
121 121  
122 122  Web applications that allow running simulations in different scales (single cell, multiple cells, regions).
123 123  
... ... @@ -127,11 +127,11 @@
127 127  
128 128  === NRP Frontend-Backend comms ===
129 129  
130 -[[[[image:documentation-icon.png]]>>https://neurorobotics.net/Documentation/nrp/developer_manual/ExDbackend/index.html||rel="noopener noreferrer" target="_blank"]]
123 +[[[[image:1635154142156-729.png]]>>https://neurorobotics.net/Documentation/nrp/developer_manual/ExDbackend/index.html||rel="noopener noreferrer" target="_blank"]]
131 131  
132 132  === NRP-core ===
133 133  
134 -[[[[image:documentation-icon.png]]>>https://hbpneurorobotics.bitbucket.io/index.html||rel="noopener noreferrer" target="_blank"]]
127 +[[[[image:1635154142156-729.png]]>>https://hbpneurorobotics.bitbucket.io/index.html||rel="noopener noreferrer" target="_blank"]]
135 135  
136 136  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.
137 137  
... ... @@ -147,12 +147,12 @@
147 147  
148 148  === Job Queue service ===
149 149  
150 -[[[[image:documentation-icon.png]]>>https://nmpi.hbpneuromorphic.eu/api/v2/||rel="noopener noreferrer" target="_blank"]]
143 +[[[[image:1635154142156-729.png]]>>https://nmpi.hbpneuromorphic.eu/api/v2/||rel="noopener noreferrer" target="_blank"]]
151 151  REST API for submitting jobs to the BrainScaleS and SpiNNaker platforms, and for retrieving job results.
152 152  
153 153  === Quotas service ===
154 154  
155 -[[[[image:documentation-icon.png]]>>]]
148 +[[[[image:1635154142156-729.png]]>>]]
156 156  REST API for requesting and managing compute quotas for the BrainScaleS and SpiNNaker platforms.
157 157  
158 158  ----
... ... @@ -161,7 +161,7 @@
161 161  
162 162  === UNICORE ===
163 163  
164 -[[[[image:documentation-icon.png]]>>https://sourceforge.net/p/unicore/wiki/REST_API/||rel="noopener noreferrer" target="_blank"]]
157 +[[[[image:1635154142156-729.png]]>>https://sourceforge.net/p/unicore/wiki/REST_API/||rel="noopener noreferrer" target="_blank"]]
165 165  
166 166  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.
167 167  
... ... @@ -169,7 +169,7 @@
169 169  
170 170  === Supercomputing Proxy ===
171 171  
172 -[[[[image:documentation-icon.png]]>>https://unicore-job-proxy.apps.hbp.eu/docs||rel="noopener noreferrer" target="_blank"]]
165 +[[[[image:1635154142156-729.png]]>>https://unicore-job-proxy.apps.hbp.eu/docs||rel="noopener noreferrer" target="_blank"]]
173 173  
174 174  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.
175 175  
... ... @@ -179,13 +179,13 @@
179 179  
180 180  === OpenStack ===
181 181  
182 -[[[[image:documentation-icon.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/openstack/||rel="noopener noreferrer" target="_blank"]]
175 +[[[[image:1635154142156-729.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/openstack/||rel="noopener noreferrer" target="_blank"]]
183 183  
184 184  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.
185 185  
186 186  === OpenShift ===
187 187  
188 -[[[[image:documentation-icon.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/kubernetes/openshift/||rel="noopener noreferrer" target="_blank"]]
181 +[[[[image:1635154142156-729.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/kubernetes/openshift/||rel="noopener noreferrer" target="_blank"]]
189 189  
190 190  OpenShift is a family of containerization software products developed by Red Hat.
191 191  
... ... @@ -195,19 +195,19 @@
195 195  
196 196  === Gitlab ===
197 197  
198 -[[[[image:documentation-icon.png]]>>https://docs.gitlab.com/ee/api/||rel="noopener noreferrer" target="_blank"]]
191 +[[[[image:1635154142156-729.png]]>>https://docs.gitlab.com/ee/api/||rel="noopener noreferrer" target="_blank"]]
199 199  
200 200  EBRAINS hosts a self-managed instance of GitLab for source code management and CI/CD.
201 201  
202 202  === Docker registry (Harbor) ===
203 203  
204 -[[[[image:documentation-icon.png]]>>https://docker-registry.ebrains.eu/devcenter-api-2.0||rel="noopener noreferrer" target="_blank"]]
197 +[[[[image:1635154142156-729.png]]>>https://docker-registry.ebrains.eu/devcenter-api-2.0||rel="noopener noreferrer" target="_blank"]]
205 205  
206 206  The EBRAINS Docker registry uses Harbor, an an open source trusted cloud native registry project that stores, signs, and scans content.
207 207  
208 208  === Logging/monitoring APIs ===
209 209  
210 -[[[[image:documentation-icon.png]]>>]]
203 +[[[[image:1635154142156-729.png]]>>]]
211 211  
212 212  TO DO
213 213  
... ... @@ -217,7 +217,7 @@
217 217  
218 218  === PLUS ===
219 219  
220 -[[[[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"]]
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"]]
221 221  
222 222  PLUS is a project management tool for the Human Brain Project.
223 223  
Public

API Catalogue