GA4GH Discovery News and Updates¶
Discovery Co-Lead Appointed
GA4GH Discovery Work Stream welcomes new Co-Lead Nara Sobreira of Johns Hopkins Medicine
Nara Lygia De Macena Sobreira, associate professor of genetic medicine at Johns Hopkins University School of Medicine, joins the GA4GH Standards Steering Committee as Discovery Work Stream Co-Lead.
Continue readingDiscovery Co-Lead Nominations
Opening for a new work stream co-lead
With the announcement of Marc Fiume's retreat from his Discovery leadership role there is now an opportunity for a person with experience in "-omics" data in biomedical settings as well as a strong interest to shape the future of GA4GH and genommic data exchange in general to step up to the challenge of a workstream leadership position!
Continue readingBeacon v2 standard highlighted during the GA4GH April Connect 2023
Last month Beacon was present at the GA4GH Connect 2023, the working meeting to advance the GA4GH Roadmap and gather feedback on product development and needs.
Beacon v2 at the International Congress of Human Genetics
Hands-on sessions on genomic data discovery
These Hands-on workshops will take place on February the 26th and 27th, in the framework of the International Congress of Human Genetics (ICHG), that is being held in Cape Town from February 22 – 26.
Continue readingBeacon training course: How to make COVID-19 sensitive data discoverable using Beacons
The online workshop BEACON - How to make sensitive data discoverable will take place on November 2 and 3. The European Genome-phenome Archive (EGA) Beacon Team will provide a special hands-on training session for the BY-COVID partners for "Beaconising" the datasets.
Progenetix & BeaconPlus - An open cancer genomics resource on a stack of Beacon code...
ELIXIR All Hands Amsterdam 2022
Michael Baudis¶
Here Michael provides some overview of the multi-year trajectory of the Beacon API development, and how BeaconPlus & Progenetix have been utilized for "implementation driven design".
Continue readingBeacon implementations: Beaconize your genomics data
Beacon v2 Workshop at ELIXIR All Hands
Hosts: Lauren Fromont, Michael Baudis & Jordi Rambla¶
Amsterdam, 7th June 2022 Link to webpage¶
One of the main bottlenecks in human genomics research is the lack of tools for federated discovery of identifiable genomics data that requires tight privacy controls. This problem needs even more attention since genomics data sees an ever greater application in clinical settings, such as for medical diagnostic or prognostic purposes, in rare diseases or cancer. Continue reading
Beacon v2 submitted to GA4GH
Beacon v2 was submitted to the Global Alliance for Genomics and Health and is now available for public review! Our specification is available on Github and several implementations are already available!
The GA4GH Beacon Protocol at BC2
Michael Baudis presenting Beacon in the session Federating computational analyses with GA4GH standards
BC2 Basel 2021¶
During the "Federating computational analyses with GA4GH standards" workshop at
BC2 2021 Michael presented history and the current status of the Beacon
project, as well as its integration with specific data resources and analysis initiatives.
Progenetix, Beacon and GA4GH at RDA
ELIXIR Beacon Project - Concepts | Status | History | Outlook
Michael Baudis¶
Research Data Alliance - RDA Virtual Plenary 17¶
This seminar gives an overview of current state of the Progenetix Beacon project and the overall connection to the Global Alliance for Genomics and Health (GA4GH).
Continue readingELIXIR Beacon Project - Networking Resources Across and Beyond ELIXIR Human Data Communities
ELIXIR Open Day 2020 - Wellcome Trust Genome Campus Hinxton
Michael Baudis¶
In this presentation I introduce the Beacon project and provide my opinions about its future trajectory, and especially its role in driving the alignment of ELIXIR and GA4GH projects in related to (human) genome data sharing.
Links¶
Continue readingDNAstack Launches Clinical Evidence Beacons
DNAstack Launches Clinical Evidence Beacons to Drive Crowdsourcing for Genetic Disease Discovery
TORONTO, Ont. (Oct. 15, 2019) — DNAstack today announced the launch of "Clinical Evidence Beacons" on the Beacon Network, a real-time search engine for finding genetic mutations across a global network of genomic datasets. These additions will enable medical laboratories to crowdsource the interpretation of variants through a secure social network.
Continue readingFederated discovery and sharing of genomic data using Beacons
Beacon publication at Nature Biotechnology
Marc Fiume, Miroslav Cupak, Stephen Keenan, Jordi Rambla, Sabela de la Torre, Stephanie O. M. Dyke, Anthony J. Brookes, Knox Carey, David Lloyd, Peter Goodhand, Maximilian Haeussler, Michael Baudis, Heinz Stockinger, Lena Dolman, Ilkka Lappalainen, Juha Törnroos, Mikael Linden, J. Dylan Spalding, Saif Ur-Rehman, Angela Page, Paul Flicek, Stephen Sherry, David Haussler, Susheel Varma, Gary Saunders and Serena Scollen¶
Today, Nature Biotechnology published the Beacon manuscript "Federated discovery and sharing of genomic data using Beacons". This was accompanied by a GA4GH press release. Enjoy!
Continue readingPress Release: GA4GH and ELIXIR Release Beacon API v1...
GA4GH and ELIXIR Release Beacon API v1 with increased security measures
ELIXIR and the Global Alliance for Genomics and Health (GA4GH) have announced the release of the first genomic data interoperability standard from the GA4GH 2018 Strategic Roadmap.
Continue readingGA4GH Beacon v1.0
Release of the first official GA4GH Beacon product
The official Beacon API v1.0.0 has been approved through the GA4GH Product Approval Process.
Continue readingGlobal network of Beacons - Beacon v0.4
Global network of Beacons lighting up the world of genomic data
The Beacon Project has released new Beacon API v0.4 specifications to provide greater search functions and richer search results.
These API specifications are available through the new Beacon website which will provide up-to-date support and regular updates on the project developments. v0.4 of Beacon has been developed with support from ELIXIR and constitutes the basis for the upcoming GA4GH approval process towards a "v1".
Continue reading