Changes for page API Catalogue

Last modified by lupascu on 2022/05/23 22:36
From version 12.1
edited by adavison
on 2021/12/17 13:38
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To version 7.1
edited by adavison
on 2021/12/17 13:28
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1 +This page catalogues the [[web API>>https://en.wikipedia.org/wiki/Web_API||rel="noopener noreferrer" target="_blank"]]s available for users and developers of [[EBRAINS tools and services>>https://ebrains.eu||rel="noopener noreferrer" target="_blank"]].
2 2  
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]].
3 +Please note this is a work in progress. Further information is available in [[this spreadsheet>>https://drive.ebrains.eu/lib/c11f95c0-59fd-428f-b02e-2238566c8499/file/EA-WG/list_of_APIs.xlsx]].
4 4  
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6 -(((
7 -Please note this is a work in progress.
8 -)))
9 -
10 10  ----
11 11  
12 12  == Core services / Collaboratory ==
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13 13  
14 14  === Authentication / Authorization (IAM) ===
15 15  
16 -[[[[image:documentation-icon.png]]>>https://www.keycloak.org/documentation.html||rel="noopener noreferrer" target="_blank"]]
11 +[[[[image:1635154142156-729.png]]>>https://www.keycloak.org/documentation.html||rel="noopener noreferrer" target="_blank"]]
17 17  
18 -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.
13 +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.
19 19  
20 20  === Collaboratory wiki ===
21 21  
22 -[[[[image:documentation-icon.png]]>>https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/XWikiRESTfulAPI||rel="noopener noreferrer" target="_blank"]]
17 +[[[[image:1635154142156-729.png]]>>https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/XWikiRESTfulAPI||rel="noopener noreferrer" target="_blank"]]
23 23  
24 -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.
19 +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.
25 25  
26 26  === Drive ===
27 27  
28 -[[[[image:documentation-icon.png]]>>https://download.seafile.com/published/web-api/home.md||rel="noopener noreferrer" target="_blank"]]
23 +[[[[image:1635154142156-729.png]]>>https://download.seafile.com/published/web-api/home.md||rel="noopener noreferrer" target="_blank"]]
29 29  
30 30  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.
31 31  
32 32  === Bucket (Data Proxy) ===
33 33  
34 -[[[[image:documentation-icon.png]]>>https://data-proxy-ppd.ebrains.eu/api/docs||rel="noopener noreferrer" target="_blank"]]
29 +[[[[image:1635154142156-729.png]]>>https://data-proxy-ppd.ebrains.eu/api/docs||rel="noopener noreferrer" target="_blank"]]
35 35  
36 36  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.
37 37  
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41 41  
42 42  === Knowledge Graph core ===
43 43  
44 -[[[[image:documentation-icon.png]]>>https://core.kg.ebrains.eu/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config||rel="noopener noreferrer" target="_blank"]]
39 +[[[[image:1635154142156-729.png]]>>https://core.kg.ebrains.eu/swagger-ui/index.html?configUrl=/v3/api-docs/swagger-config||rel="noopener noreferrer" target="_blank"]]
45 45  
46 46  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.
47 47  
48 48  === Knowledge Space ===
49 49  
50 -[[[[image:documentation-icon.png]]>>https://api.knowledge-space.org/docs||rel="noopener noreferrer" target="_blank"]]
45 +[[[[image:1635154142156-729.png]]>>https://api.knowledge-space.org/docs||rel="noopener noreferrer" target="_blank"]]
51 51  
52 52  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).
53 53  
54 54  === Neural Activity Resource ===
55 55  
56 -[[[[image:documentation-icon.png]]>>https://neural-activity-resource.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
51 +[[[[image:1635154142156-729.png]]>>https://neural-activity-resource.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
57 57  
58 58  The Neural Activity Resource provides a simplified interface to data and metadata from the KG about neural activity recordings.
59 59  
60 60  === Provenance API ===
61 61  
62 -[[[[image:documentation-icon.png]]>>https://prov.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
57 +[[[[image:1635154142156-729.png]]>>https://prov.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
63 63  
64 64  The Provenance API provides a simplified interface to computational provenance information in the KG.
65 65  
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69 69  
70 70  === Image service ===
71 71  
72 -[[[[image:documentation-icon.png]]>>https://img-svc.apps.hbp.eu/api-docs||rel="noopener noreferrer" target="_blank"]]
67 +[[[[image:1635154142156-729.png]]>>https://img-svc.apps.hbp.eu/api-docs||rel="noopener noreferrer" target="_blank"]]
73 73  
74 -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.
69 +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.
75 75  
76 76  === siibra ===
77 77  
78 -[[[[image:documentation-icon.png]]>>https://siibra-api.readthedocs.io||rel="noopener noreferrer" target="_blank"]]
73 +[[[[image:1635154142156-729.png]]>>https://siibra-api.readthedocs.io||rel="noopener noreferrer" target="_blank"]]
79 79  
80 80  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.
81 81  
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85 85  
86 86  === Neo-Viewer ===
87 87  
88 -[[[[image:documentation-icon.png]]>>https://neo-viewer.brainsimulation.eu/||rel="noopener noreferrer" target="_blank"]]
83 +[[[[image:1635154142156-729.png]]>>https://neo-viewer.brainsimulation.eu/||rel="noopener noreferrer" target="_blank"]]
89 89  
90 90  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.
91 91  
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95 95  
96 96  === Model Validation service ===
97 97  
98 -[[[[image:documentation-icon.png]]>>https://validation-v2.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
93 +[[[[image:1635154142156-729.png]]>>https://validation-v2.brainsimulation.eu/docs||rel="noopener noreferrer" target="_blank"]]
99 99  
100 -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.
95 +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.
101 101  
102 102  === The Virtual Brain ===
103 103  
104 -[[[[image:documentation-icon.png]]>>https://thevirtualbrain-rest.apps.hbp.eu/doc||rel="noopener noreferrer" target="_blank"]]
99 +[[[[image:1635154142156-729.png]]>>https://thevirtualbrain-rest.apps.hbp.eu/doc||rel="noopener noreferrer" target="_blank"]]
105 105  
106 106  REST API for TVB.
107 107  
108 108  === MoDEL-CNS ===
109 109  
110 -[[[[image:documentation-icon.png]]>>https://mmb.irbbarcelona.org/MoDEL-CNS/api/rest/docs/||rel="noopener noreferrer" target="_blank"]]
105 +[[[[image:1635154142156-729.png]]>>https://mmb.irbbarcelona.org/MoDEL-CNS/api/rest/docs/||rel="noopener noreferrer" target="_blank"]]
111 111  
112 112  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**.
113 113  
114 114  === Cellular Level Simulation ===
115 115  
116 -[[[[image:documentation-icon.png]]>>https://humanbrainproject.github.io/hbp-bsp-service-account/introduction/introduction.html||rel="noopener noreferrer" target="_blank"]]
111 +[[[[image:1635154142156-729.png]]>>https://humanbrainproject.github.io/hbp-bsp-service-account/introduction/introduction.html||rel="noopener noreferrer" target="_blank"]]
117 117  
118 118  Web applications that allow running simulations in different scales (single cell, multiple cells, regions).
119 119  
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123 123  
124 124  === NRP Frontend-Backend comms ===
125 125  
126 -[[[[image:documentation-icon.png]]>>https://neurorobotics.net/Documentation/nrp/developer_manual/ExDbackend/index.html||rel="noopener noreferrer" target="_blank"]]
121 +[[[[image:1635154142156-729.png]]>>https://neurorobotics.net/Documentation/nrp/developer_manual/ExDbackend/index.html||rel="noopener noreferrer" target="_blank"]]
127 127  
128 128  === NRP-core ===
129 129  
130 -[[[[image:documentation-icon.png]]>>https://hbpneurorobotics.bitbucket.io/index.html||rel="noopener noreferrer" target="_blank"]]
125 +[[[[image:1635154142156-729.png]]>>https://hbpneurorobotics.bitbucket.io/index.html||rel="noopener noreferrer" target="_blank"]]
131 131  
132 132  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.
133 133  
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143 143  
144 144  === Job Queue service ===
145 145  
146 -[[[[image:documentation-icon.png]]>>https://nmpi.hbpneuromorphic.eu/api/v2/||rel="noopener noreferrer" target="_blank"]]
141 +[[[[image:1635154142156-729.png]]>>https://nmpi.hbpneuromorphic.eu/api/v2/||rel="noopener noreferrer" target="_blank"]]
147 147  REST API for submitting jobs to the BrainScaleS and SpiNNaker platforms, and for retrieving job results.
148 148  
149 149  === Quotas service ===
150 150  
151 -[[[[image:documentation-icon.png]]>>]]
146 +[[[[image:1635154142156-729.png]]>>]]
152 152  REST API for requesting and managing compute quotas for the BrainScaleS and SpiNNaker platforms.
153 153  
154 154  ----
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157 157  
158 158  === UNICORE ===
159 159  
160 -[[[[image:documentation-icon.png]]>>https://sourceforge.net/p/unicore/wiki/REST_API/||rel="noopener noreferrer" target="_blank"]]
155 +[[[[image:1635154142156-729.png]]>>https://sourceforge.net/p/unicore/wiki/REST_API/||rel="noopener noreferrer" target="_blank"]]
161 161  
162 162  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.
163 163  
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165 165  
166 166  === Supercomputing Proxy ===
167 167  
168 -[[[[image:documentation-icon.png]]>>https://unicore-job-proxy.apps.hbp.eu/docs||rel="noopener noreferrer" target="_blank"]]
163 +[[[[image:1635154142156-729.png]]>>https://unicore-job-proxy.apps.hbp.eu/docs||rel="noopener noreferrer" target="_blank"]]
169 169  
170 170  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.
171 171  
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175 175  
176 176  === OpenStack ===
177 177  
178 -[[[[image:documentation-icon.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/openstack/||rel="noopener noreferrer" target="_blank"]]
173 +[[[[image:1635154142156-729.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/openstack/||rel="noopener noreferrer" target="_blank"]]
179 179  
180 180  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.
181 181  
182 182  === OpenShift ===
183 183  
184 -[[[[image:documentation-icon.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/kubernetes/openshift/||rel="noopener noreferrer" target="_blank"]]
179 +[[[[image:1635154142156-729.png]]>>https://wiki.ebrains.eu/bin/view/Collabs/kubernetes/openshift/||rel="noopener noreferrer" target="_blank"]]
185 185  
186 186  OpenShift is a family of containerization software products developed by Red Hat.
187 187  
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191 191  
192 192  === Gitlab ===
193 193  
194 -[[[[image:documentation-icon.png]]>>https://docs.gitlab.com/ee/api/||rel="noopener noreferrer" target="_blank"]]
189 +[[[[image:1635154142156-729.png]]>>https://docs.gitlab.com/ee/api/||rel="noopener noreferrer" target="_blank"]]
195 195  
196 196  EBRAINS hosts a self-managed instance of GitLab for source code management and CI/CD.
197 197  
198 198  === Docker registry (Harbor) ===
199 199  
200 -[[[[image:documentation-icon.png]]>>https://docker-registry.ebrains.eu/devcenter-api-2.0||rel="noopener noreferrer" target="_blank"]]
195 +[[[[image:1635154142156-729.png]]>>https://docker-registry.ebrains.eu/devcenter-api-2.0||rel="noopener noreferrer" target="_blank"]]
201 201  
197 +(% class="wikigeneratedid" %)
202 202  The EBRAINS Docker registry uses Harbor, an an open source trusted cloud native registry project that stores, signs, and scans content.
203 203  
204 204  === Logging/monitoring APIs ===
205 205  
206 -[[[[image:documentation-icon.png]]>>]]
202 +[[[[image:1635154142156-729.png]]>>]]
207 207  
208 208  TO DO
209 209  
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213 213  
214 214  === PLUS ===
215 215  
216 -[[[[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"]]
212 +[[[[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"]]
217 217  
218 218  PLUS is a project management tool for the Human Brain Project.
219 219  
220 220  ----
221 221  
222 -The book icon used on this page is from a [[set of icons by Boca Tutor>>https://www.iconfinder.com/iconsets/tutor-icon-set]] and is licensed under the [[Creative Commons>>https://en.wikipedia.org/wiki/en:Creative_Commons]] [[Attribution-Share Alike 3.0 Unported>>https://creativecommons.org/licenses/by-sa/3.0/deed.en]] license.
218 +(% class="box infomessage" %)
219 +(((
220 +The book icon used on this page is from a [[set of icons by Boca Tutor>>https://www.iconfinder.com/iconsets/tutor-icon-set||rel="noopener noreferrer" target="_blank"]] and is licensed under the [[Creative Commons>>https://en.wikipedia.org/wiki/en:Creative_Commons||rel="noopener noreferrer" target="_blank"]] [[Attribution-Share Alike 3.0 Unported>>https://creativecommons.org/licenses/by-sa/3.0/deed.en||rel="noopener noreferrer" target="_blank"]] license.
221 +)))
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API Catalogue