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  • EBRAINS-Share-Software.pdf
  • My project.jpg
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1		-XWiki.ingrreit
	1	+XWiki.spieschnik

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1	1	== Publishing neuroscience data, models and software via EBRAINS ==
2	2
	3	+The aim of this collab is to provide you with all the information you need to publish your experimental data, simulations, computational models, and software via EBRAINS. Have you already published your data somewhere else? You can increase the exposure and impact of your shared dataset by also listing it on EBRAINS.
3	3
4		-(% class="wikigeneratedid" %)
5		-The aim of this collab is to provide you with detailed information about publishing experimental data, simulations, computational models, and software via EBRAINS. If you want a quick overview of the sharing process, see [[https:~~/~~/ebrains.eu/service/share-data>>https://ebrains.eu/service/share-data]].
6		-
7	7	{{box title="**Contents**"}}
8	8	{{toc depth="3" start="2"/}}
9	9	{{/box}}
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101	101
102	102	==== **Sharing human data ** ====
103	103
	102	+We must ensure data shared on EBRAINS comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
	103	+
104	104	(% class="box floatinginfobox" %)
105	105	(((
106	106	For **Human subject data**, the data must be //either//
107	107
108	108	- Post-mortem data
	109	+
109	109	- Aggregated data
	111	+
110	110	- Pseudonymized subject data with a legal basis for sharing (e.g. Informed Consent)
111	111
112	112	(% class="small" %)//If you have human data that do not classify as any of the above, please get in touch and we will clarify the available options. //
113	113	)))
114	114
115		-We must ensure data shared on EBRAINS comply with [[GDPR >>https://gdpr-info.eu/]]and [[EU directives>>https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex%3A32010L0063]]. The information we need to assess this is collected via our [[Ethics and Regulatory Compliance Survey>>https://nettskjema.no/a/224765]].
	117	+Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
116	116
117		-Post-mortem and aggregated human data can be shared openly. Pseudonymized data is shared via the Human Data Gateway (HDG) due to GDPR regulations. The HDG adds an authentication layer to the data.
118		-
119	119	**Data users** must request access to the data (via their EBRAINS account) and will receive access provided they actively accept the [[EBRAINS Access Policy>>https://ebrains.eu/terms#access-policy]], the [[EBRAINS General Terms of Use>>https://ebrains.eu/terms#general-terms-of-use]], and the [[EBRAINS Data Use Agreement>>https://ebrains.eu/terms#data-use-agreement]]. The account holder also have to accept that information about their request and access to specific data under HDG is being tracked and stored.
120	120	\\**Data owners** must be aware that sharing under the HDG affects the legal responsibilities for the data. They must agree to joint control of the data (see the [[Data Provision Protocol v1>>url:https://strapi-prod.sos-ch-dk-2.exo.io/EBRAINS_Data_Provision_Protocol_dfe0dcb104.pdf]], section 1.4 - 1.5) and the Data Protection Officers of the responsible institutions must have accepted that the data can be shared under HDG.
121	121	\\The Human Data Gateway (HDG) was introduced in February 2021 and developed across multiple teams in the HBP. The initiative to create the service and the initial design originated from EBRAINS Curation in close collaboration with the Data compliance team and the HBP Data Governance Working Group. HDG is a response to the needs of multiple data providers who are bringing data of human origin to EBRAINS. HDG covers the sharing of a limited range of data of human origin, i.e., data without direct identifiers and with very few indirect identifiers (strongly pseudonymized, de-identified). It is an extension of the existing services and does not replace the future EBRAINS Service for sensitive data (planned for 2024) which is outside the domain of the current EBRAINS Data and Knowledge services.
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125	125
126	126	=== Step by Step - Models ===
127	127
128		-(% style="color:#e74c3c" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-1rb0hn"/}}
129		-
130	130	[place-holder-process-diagram]
131	131
132	132	==== **1. model step 1 ** ====
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143	143
144	144	=== Step by Step - Code ===
145	145
146		-[[[[image:swc-flow-no-header.png||alt="swc-flow.png"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
	144	+[place-holder-process-diagram]
147	147
148		-1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]].[[[[image:Thumb.png||alt="EBRAINS-Share-Software.pdf" height="377" style="float:right" width="257"]]>>attach:EBRAINS-Share-Software.pdf]]
149		-1. One of our creators will then open a ticket and contact you with futher instructions. In these instructions you will find the links to your software and software version entries in the Knowledge Graph.
150		-1. In the next step you need to enter the metadata of your software in the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided in the ticket. The links will lead you to the space in the KG, which was created especially for you. You can start directly with the editing of your software. Please provide the metadata for your software as complete as possible. This makes it easier for users to find and use your software. If you have questions feel free to contact the curation support.
151		-1. After you have finished editing your entries, please let the curators know by replying to your ticket. We curate your metadata and get back to you, if necessary.
152		-1. After a quality check, we integrate and publish the information to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
	146	+==== **1. code step 1 ** ====
153	153
154		-If you want to add a new version to an already curated software, please write to [[curation-support@humanbrainproject.eu>>path:mailto:curation-support@humanbrainproject.eu]] or open a ticket at [[https:~~/~~/support.humanbrainproject.eu/.>>url:https://support.humanbrainproject.eu/]]
155		-For more information, visit our [[guide>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]].
	148	+Text
156	156
	150	+
	151	+==== **2. code step 2** ====
	152	+
	153	+Text
	154	+
157	157	----
158	158
159	159	=== Webservices and metadata models ===
160	160
161	161	(% class="wikigeneratedid" id="HContact...." %)
162		-(% style="color:#e74c3c; font-size:16px" %){{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-np253c"/}}(% style="color:#4a5568; font-size:16px" %)
	160	+(% style="color:#e74c3c; font-size:16px" %)Contact....(% style="color:#4a5568; font-size:16px" %)
163	163
164	164	----
165	165
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167	167
168	168	**Located in Norway:**
169	169
	168	+
170	170	|(% style="width:303px" %)(((
171	171	[[image:My project2.jpg||height="209" width="167"]]
172	172
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174	174
175	175	(% class="small" %)Curation Scientist
176	176	Neuroscience (PhD)(%%)
177		-(% class="small" style="color:#4a5568" %)**Behavioral neuroscience and microscopy**
	176	+(% style="color:#4a5568" class="small" %)**Behavioral neuroscience and microscopy**
178	178	)))|(% style="width:303px" %)(((
179		-[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
	178	+[[image:My project1.jpg||height="209" width="167"]]
180	180
181		-**Camilla H. Blixhavn**
	180	+**Sophia Pieschnik**
182	182
183		-(% class="small" %)Curation Scientist,
184		-Phd Student
185		-Neuroscience (M. Sc.)(%%)
186		-(% class="small" style="color:#4a5568" %)**Neuroanatomy and data integration**
	182	+(% class="small" %)Curation Scientist
	183	+Neurocognitive Psychology (M. Sc.)(%%)
	184	+(% style="color:#4a5568" class="small" %)**Neuroimaging **
187	187	)))|(% style="width:303px" %)(((
188	188	[[image:My project (1).jpg||height="209" width="167"]]
189	189
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192	192	(% class="small" %)Curation Scientist,
193	193	Phd Student
194	194	Neuroscience (M. Sc.)(%%)
195		-(% class="small" style="color:#4a5568" %)**Neuroanatomy and structural connectivity**
	193	+(% style="color:#4a5568" class="small" %)**Neuroanatomy and structural connectivity**
196	196	)))|(% style="width:303px" %)(((
197		-[[image:My project1.jpg||height="209" width="167"]]
198		-
199		-**Sophia Pieschnik**
200		-
201		-(% class="small" %)Curation Scientist
202		-Neurocognitive Psychology (M. Sc.)(%%)
203		-(% class="small" style="color:#4a5568" %)**Neuroimaging **
204		-)))
205		-
206		-|(% style="width:303px" %)(((
207	207	[[image:My project.jpg||height="209" width="167"]]
208	208
209		-**Heidi Kleven**
	197	+**Camilla H. Blixhavn**
210	210
211	211	(% class="small" %)Curation Scientist,
212	212	Phd Student
213	213	Neuroscience (M. Sc.)(%%)
214		-(% class="small" style="color:#4a5568" %)**Neuroanatomy and brain atlases**
215		-)))| | |
	202	+(% class="small" %)(% style="color:#4a5568" %)**Neuroanatomy and data integration**
	203	+)))
216	216
217		-
218		-\\**Located in Germany:**
	205	+
	206	+
	207	+
	208	+**Located in Germany:**
219	219
220		-|(% style="width:303px" %)(((
221	221	[[image:My project (2).jpg||height="209" width="167"]]
222	222
223	223	**Jan Gündling**
224	224
225		-(% class="small" %)Curation Scientist,
226		-Phd Student
	214	+(% class="small" %)Curation Scientist
227	227	Sensors and Cognitive Psychology (M. Sc.)(%%)
228		-(% class="small" style="color:#4a5568" %)**Human-Computer Interaction**
229		-)))|(% style="width:303px" %)(((
230		-
	216	+(% class="small" %)(% style="color:#000000" %)Human-Computer Interaction
231	231
232		-
233		-
234		-
235		-
236		-
237		-
238		-
239		-
240		-
241		-
242		-**Lyuba Zehl**
243		-
244		-(% class="small" %)Knowledge Systems Engineer
245		-Dr. rer. nat. (Systems Neuroscience)(%%)
246		-(% class="small" style="color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
247		-)))|(% style="width:303px" %) |
248		-
249	249	----
250	250
251	251	== **Information and resources for researchers looking to share data** ==
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256	256
257	257	=== **Improve your research product ** ===
258	258
259		-(% class="wikigeneratedid" %)
260		-**{{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-fkdv6h"/}}**
261		-
262	262	==== **Add a tutorial or learning resource to your research product ** ====
263	263
264	264	==== (% style="color:#e74c3c" %)- Learning resource [information](%%) ====
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276	276
277	277	* Integrate image data with //the Mio viewer//: EBRAINS Multi-Image OpenSeadragon viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[Mio viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example. MioViewer user manual is found [[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].
278	278	* Integrate atlas-registered 2D image data with //the LocaliZoom viewer//: The EBRAINS LocaliZoom serial section viewer displays series of registered 2D section images with atlas overlay, allowing the users to zoom into high-resolution images and have information about the brain regions. See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example. LocaliZoom user manual is found [[here>>https://localizoom.readthedocs.io/en/latest/index.html]].
279		-* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description] {{mention reference="XWiki.adavison" style="FULL_NAME" anchor="XWiki-adavison-62mbgl"/}}
	245	+* Add your data, models or software to a// Live paper//: (% style="color:#e74c3c" %)[description]
280	280	* Integrate your data to //the Siibra//-explorer: The siibra-explorer is used for visualizing volumetric brain data in all the brain atlases provided by EBRAINS (Human, Monkey, Rat and Mouse). The siibra-explorer viewer uses siibra-api to enable navigation of brain region hierarchies, maps in different coordinate spaces, and linked regional data features. Furthermore, it is connected with the siibra toolsuite providing several analytical workflows. To learn more about how to integrate your data to atlases, check out the [[Atlas services>>https://ebrains.eu/services/atlases#Integratedatatoanatlas]] on ebrains.eu.
281	281
282	282	----
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364	364
365	365	{{putFootnotes/}}
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