Changes for page API Catalogue

Last modified by lupascu on 2022/05/23 22:36
From version 13.1
edited by adavison
on 2021/12/17 13:40
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To version 8.1
edited by adavison
on 2021/12/17 13:29
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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 -Please note this is a work in progress.
8 -)))
5 +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]].
9 9  
10 10  ----
11 11  
12 -{{toc/}}
13 -
14 14  == Core services / Collaboratory ==
15 15  
16 16  === Authentication / Authorization (IAM) ===
17 17  
18 -[[[[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"]]
19 19  
20 20  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.
21 21  
22 22  === Collaboratory wiki ===
23 23  
24 -[[[[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"]]
25 25  
26 26  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.
27 27  
28 28  === Drive ===
29 29  
30 -[[[[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"]]
31 31  
32 32  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.
33 33  
34 34  === Bucket (Data Proxy) ===
35 35  
36 -[[[[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"]]
37 37  
38 38  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.
39 39  
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43 43  
44 44  === Knowledge Graph core ===
45 45  
46 -[[[[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"]]
47 47  
48 48  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.
49 49  
50 50  === Knowledge Space ===
51 51  
52 -[[[[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"]]
53 53  
54 54  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).
55 55  
56 56  === Neural Activity Resource ===
57 57  
58 -[[[[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"]]
59 59  
60 60  The Neural Activity Resource provides a simplified interface to data and metadata from the KG about neural activity recordings.
61 61  
62 62  === Provenance API ===
63 63  
64 -[[[[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"]]
65 65  
66 66  The Provenance API provides a simplified interface to computational provenance information in the KG.
67 67  
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71 71  
72 72  === Image service ===
73 73  
74 -[[[[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"]]
75 75  
76 76  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.
77 77  
78 78  === siibra ===
79 79  
80 -[[[[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"]]
81 81  
82 82  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.
83 83  
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87 87  
88 88  === Neo-Viewer ===
89 89  
90 -[[[[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"]]
91 91  
92 92  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.
93 93  
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97 97  
98 98  === Model Validation service ===
99 99  
100 -[[[[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"]]
101 101  
102 102  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.
103 103  
104 104  === The Virtual Brain ===
105 105  
106 -[[[[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"]]
107 107  
108 108  REST API for TVB.
109 109  
110 110  === MoDEL-CNS ===
111 111  
112 -[[[[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"]]
113 113  
114 114  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**.
115 115  
116 116  === Cellular Level Simulation ===
117 117  
118 -[[[[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"]]
119 119  
120 120  Web applications that allow running simulations in different scales (single cell, multiple cells, regions).
121 121  
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125 125  
126 126  === NRP Frontend-Backend comms ===
127 127  
128 -[[[[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"]]
129 129  
130 130  === NRP-core ===
131 131  
132 -[[[[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"]]
133 133  
134 134  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.
135 135  
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145 145  
146 146  === Job Queue service ===
147 147  
148 -[[[[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"]]
149 149  REST API for submitting jobs to the BrainScaleS and SpiNNaker platforms, and for retrieving job results.
150 150  
151 151  === Quotas service ===
152 152  
153 -[[[[image:documentation-icon.png]]>>]]
148 +[[[[image:1635154142156-729.png]]>>]]
154 154  REST API for requesting and managing compute quotas for the BrainScaleS and SpiNNaker platforms.
155 155  
156 156  ----
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159 159  
160 160  === UNICORE ===
161 161  
162 -[[[[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"]]
163 163  
164 164  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.
165 165  
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167 167  
168 168  === Supercomputing Proxy ===
169 169  
170 -[[[[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"]]
171 171  
172 172  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.
173 173  
... ... @@ -177,13 +177,13 @@
177 177  
178 178  === OpenStack ===
179 179  
180 -[[[[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"]]
181 181  
182 182  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.
183 183  
184 184  === OpenShift ===
185 185  
186 -[[[[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"]]
187 187  
188 188  OpenShift is a family of containerization software products developed by Red Hat.
189 189  
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193 193  
194 194  === Gitlab ===
195 195  
196 -[[[[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"]]
197 197  
198 198  EBRAINS hosts a self-managed instance of GitLab for source code management and CI/CD.
199 199  
200 200  === Docker registry (Harbor) ===
201 201  
202 -[[[[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"]]
203 203  
204 204  The EBRAINS Docker registry uses Harbor, an an open source trusted cloud native registry project that stores, signs, and scans content.
205 205  
206 206  === Logging/monitoring APIs ===
207 207  
208 -[[[[image:documentation-icon.png]]>>]]
203 +[[[[image:1635154142156-729.png]]>>]]
209 209  
210 210  TO DO
211 211  
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215 215  
216 216  === PLUS ===
217 217  
218 -[[[[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"]]
219 219  
220 220  PLUS is a project management tool for the Human Brain Project.
221 221  
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API Catalogue