2024-05-29 MAY
Journal Club
09:30 AM (5 minutes tolerance): Meeting starts
09:35 AM - Presentation of the EOSC-ENTRUST project by Peter Maccallum (ELIXIR)
10:05 AM - Overview of STRIDES by Nick Weber (NIH/CIT)
The total session will last 1 hour with questions. The main idea is to discuss how Europe is defining and developing Trusted Research Environments and how they are being made available for large pan-European initiatives for the management and analysis of sensitive data (genomic), comparing it with the vision of large initiatives like STRIDES in the US and how researchers are using this infrastructure to deal with sensitive data.
We would also like to inform the community here, the ELIXIR and the BRIDGE staff-exchange team tomorrow.
Ancillary material
EOSC - European Open ScienceConsortium https://eosc.eu/eosc-about
Elixir - https://pubmed.ncbi.nlm.nih.gov/34175941
Observing Elixir and EOSC: https://observablehq.com/@episphere/elixir
Data Commons
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Bob: https://pubmed.ncbi.nlm.nih.gov/36878917
Sci Data 2023 Mar 6;10(1):120. doi: 10.1038/s41597-023-02029-x.
Ten lessons for data sharing with a data commons
Robert L Grossman
Recall reference implementation: https://gen3.org
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CRDC: https://pubmed.ncbi.nlm.nih.gov/38488510
Review Cancer Res 2024 May 2;84(9):1404-1409. doi: 10.1158/0008-5472.CAN-23-2730.
NCI Cancer Research Data Commons: Lessons Learned and Future State
Erika Kim # 1, Tanja Davidsen # 1, Brandi N Davis-Dusenbery 2, Alexander Baumann 3, Angela Maggio 4, Zhaoyi Chen 1 5, Daoud Meerzaman 1, Esmeralda Casas-Silva 1, David Pot 6, Todd Pihl 7, John Otridge 7, Eve Shalley 8; CRDC Program; Jill S Barnholtz-Sloan # 1 9, Anthony R Kerlavage # 1
Hackathon
EOSC data: https://open-science-cloud.ec.europa.eu/resources/data
Question - preferentially (exclusively) backed by Zenodo?
...
Fetching EOSC and Elixir
https://observablehq.com/@episphere/elixir
...
Notes from Presentation
how do you manage disclosure control in STR... by Carole GobleCarole Goble (External)10:17 AM
how do you manage disclosure control in STRIDES?
there are 50 people in HICs where TREEHOOSE... by Carole GobleCarole Goble (External)10:20 AM
there are 50 people in HICs where TREEHOOSE is based
Link https://dareuk.org.uk/driver-project-s... by Carole GobleCarole Goble (External)10:20 AM
https://dareuk.org.uk/driver-project-sacro/
SACRO: Semi-Automated Checking of Research Outputs - DARE UK
dareuk.org.uk Link TELEPORT: Connecting researchers to bi... by Simon Thompson (Unverified)Simon Thompson (Unverified)10:22 AM
TELEPORT: Connecting researchers to big data at light speed - DARE UK
Link TRE-FX: Delivering a federated network... by Simon Thompson (Unverified)Simon Thompson (Unverified)10:22 AM
the Federated Analytics programme of HDR UK... by Carole GobleCarole Goble (External)10:24 AM
the Federated Analytics programme of HDR UK is combining TELEPORT and TRE-FX into a federated architecture. This is where the Five Safes RO-Crate comes from
an example where the code only engages the ... by De Almeida, Jonas (NIH/NCI) [E]10:25 AMDe Almeida, Jonas (NIH/NCI) [E]
an example where the code only engages the data where its "owner" already has it: https://episphere.github.io/prs
Link https://pubmed.ncbi.nlm.nih.gov/378683... by De Almeida, Jonas (NIH/NCI) [E]10:26 AMDe Almeida, Jonas (NIH/NCI) [E]
https://pubmed.ncbi.nlm.nih.gov/37868335
pubmed.ncbi.nlm.nih.gov Download PDF Link PDF Current controversy ... by Carole GobleCarole Goble (External)10:30 AM
Current controversy
Trust and the Goldacre Review: why trusted research environments are not about trust
http://orcid.org/0000-0001-6870-1370Mackenzie Graham1,
Paige Fitzsimmons4,
Correspondence to Dr Mackenzie Graham, Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK; mackenzie.graham@philosophy.ox.ac.uk
https://doi.org/10.1136/jme-2022-108435
This is the approach taken by SATRE - to ex... by Carole GobleCarole Goble (External)10:31 AM
This is the approach taken by SATRE - to explicitly state the properties and functions rather than the name
Begin Reference, how do you manage disclosu... by Weber, Nick (NIH/CIT) [E]Weber, Nick (NIH/CIT) [E]10:33 AM
Carole Goble5/29/2024, 10:17 AMhow do you manage disclosure control in STRIDES? for better or worse, we defer this... the disclosure responsibility is on the data repository / data resource that is leveraging the STRIDES agreements
1 Like reaction.1 zero-install ("zero footprint", "in-browser... by De Almeida, Jonas (NIH/NCI) [E]10:34 AMEditedDe Almeida, Jonas (NIH/NCI) [E]
zero-install ("zero footprint", "in-browser", etc) is our research goal at DCEG
we don't have that luxury by Carole GobleCarole Goble (External)10:35 AM
we don't have that luxury
Link https://www.fedramp.gov/ by Carole GobleCarole Goble (External)10:36 AM
How to Become FedRAMP Authorized | FedRAMP.gov
www.fedramp.gov here's an example of a biomedical research ... by Weber, Nick (NIH/CIT) [E]Weber, Nick (NIH/CIT) [E]10:38 AM
here's an example of a biomedical research platform that has been authorized at the FedRAMP level:
This project tried to deliver federated non... by Peter MaccallumPeter Maccallum (External)10:39 AM
This project tried to deliver federated non-disclosing learning for small molecules - https://www.melloddy.eu/ - with mixed results
MELLODDYwww.melloddy.eu recognising that "sensitive" data is a scal... by Simon Thompson (Unverified)Simon Thompson (Unverified)10:39 AM
recognising that "sensitive" data is a scale of sensativity. So an zero-install/browser in the uk for health data would not be allowed, but interesting idea for other data
RDA 2024 Plenary.... Costa Rica in November... by Weber, Nick (NIH/CIT) [E]Weber, Nick (NIH/CIT) [E]10:41 AM
RDA 2024 Plenary.... Costa Rica in November
Thank you! by Bhawsar, Praphulla (NIH/NCI) [F]Bhawsar, Praphulla (NIH/NCI) [F]10:43 AM
Thank you!
what does that mean to liaise with EOSC? by Carole GobleCarole Goble (External)10:44 AM
what does that mean to liaise with EOSC?
there is an EOSC EU node by Carole GobleCarole Goble (External)10:44 AM
there is an EOSC EU node
the EOSC Portal is not the EOSC by the way! by Carole GobleCarole Goble (External)10:45 AM
the EOSC Portal is not the EOSC by the way!
Link https://www.openaire.eu/ by Peter MaccallumPeter Maccallum (External)10:48 AM
www.openaire.eu Zenodo is just a GREI by Carole GobleCarole Goble (External)10:49 AM
Zenodo is just a GREI
Zenodo is a backend for openAIRE by Carole GobleCarole Goble (External)10:49 AM
Zenodo is a backend for openAIRE
Gaia-X is a similar initiative as EOSC but ... by Mark van de SandenMark van de Sanden (External)10:49 AM
Gaia-X is a similar initiative as EOSC but has a focus on commercial providers. A mechanism to share resources and data from commercial providers to each other.
Gaia-X is a procurement consortium by Carole GobleCarole Goble (External)10:50 AM
Gaia-X is a procurement consortium
Also not really a cloud, but a mechanism to... by Mark van de SandenMark van de Sanden (External)10:50 AM
Also not really a cloud, but a mechanism to share cloud and storage resources across providers and customers.
qinling is no longer maintained by Simon Thompson (Unverified)Simon Thompson (Unverified)10:53 AM
qinling is no longer maintained
Link qinling/README.rst at master - qinling... by Simon Thompson (Unverified)Simon Thompson (Unverified)10:53 AM
qinling/README.rst at master - qinling - OpenDev: Free Software Needs Free Tools
Opensource framework for serverless would b... by Simon Thompson (Unverified)Simon Thompson (Unverified)10:54 AM
Opensource framework for serverless would be better so no dependencies on underlined implementation
thanks Simon for this by Carole GobleCarole Goble (External)10:55 AM
thanks Simon for this
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