Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -2,38 +2,33 @@
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	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"]][[image:documentation-icon.png]]
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
...	...	@@ -43,25 +43,25 @@
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
...	...	@@ -71,13 +71,13 @@
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
...	...	@@ -87,7 +87,7 @@
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
...	...	@@ -97,25 +97,25 @@
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
...	...	@@ -125,11 +125,11 @@
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
...	...	@@ -145,12 +145,12 @@
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	----
...	...	@@ -159,7 +159,7 @@
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
...	...	@@ -167,7 +167,7 @@
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
...	...	@@ -193,19 +193,19 @@
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
...	...	@@ -215,7 +215,7 @@
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