1

nf-core/proteinfold: a bioinformatics best-practice pipeline for protein 3D structure prediction

Authors: Athanasios Baltzis [1]; Jose Espinosa-Carrasco [1]; Luisa Santus [1]; Martin Steinegger [3,4]; Harshil Patel [5]; Cedric Notredame [1,2]

Authors’ Affiliation:
[1] Centre for Genomic Regulation (CRG), Barcelona, Spain.
[2] Universitat Pompeu Fabra (UPF), Barcelona, Spain.
[3] School of Biological Sciences, Seoul National University, Seoul, South Korea.
[4] Artificial Intelligence Institute, Seoul National University, Seoul, South Korea.
[5] Seqera Labs, Barcelona, Spain

2

A novel reference architecture for multi-party federation: enabling joint analysis of large-scale clinical-genomic data across distributed Trusted Research Environments

Craig Davison1, Ingrid Knarston1, Bruno Vieira1, Ismael Peral1, Sangram Keshari Sahu1, Rafael Zochling1, Eleni Kyriakou1, Thorben Seeger1, Nate Raine1, Maria Alvarellos1, Rosanna Fennessy2, Chiara Bacchelli1, Parker Moss3, Maria Chatzou Dunford1, Pablo Prieto Barja1, Mark Avery4,5 and Serena Nik-Zainal2,6.

1 Lifebit Biotech Limited, London, UK
2 University of Cambridge, Cambridge, UK
3 Genomics England, London, UK
4 Eastern Academic Health Science Network, Cambridge, UK
5 Cambridge University Health Partners, Cambridge, UK
6 NIHR Cambridge Biomedical Research Centre, Cambridge, UK

3

Accessing UK Biobank-derived statistics through the AZ PheWAS portal, with reassigned phenotypic ICD10 codes. 

K. Mégy1, A. O’Neill1, Q. Wang2, K. Carss1, R. S. Dhindsa2, A. Harper1, G. Alamgir1, S. Das1, A. Nag1, I. Tachmazidou1, D. Vitsios1, S. Deevi1, J. Okae1, S. Wasilewski1, E. Wheeler1, J. Harrow1, K. R. Smith1, S. Petrovski1, AstraZeneca Genomics Initiative.
1) Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
2) Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA, USA.

4

African Data and Biospecimen Exchange (ADBEx) – a platform to facilitate equitable and ethical sharing of African data and biospecimens

Tsaone Tamuhla1,2, Eddie Lulamba1, Abiola Babajide1, Nicki Tiffin1
1South African National Bioinformatics Institute, University of the Western Cape, South Africa
2Division of Computational Biology, Integrative Biomedical Sciences Department, Faculty of Health Sciences, University of Cape Town, South Africa

5

Elsa Data - Practical Data Release for Human Genomics

Andrew Patterson (UMCCR)
Oliver Hofmann (UMCCR)

6

nf-core as the standard for BovReg reference pipelines

Authors:
Jose Espinosa-Carrasco (1,2), Björn E. Langer (1,2), Philip A. Ewels (4), Harshil Patel (4), Peter Harrison (3), Cedric Notredame (1,2)

Affiliation:
(1) Centre for Genomic Regulation (CRG), Barcelona, Spain.
(2) Universitat Pompeu Fabra (UPF), Barcelona, Spain.
(3) European Molecular Biology Laboratory-European Bioinformatics Institute, United Kingdom.
(4) Seqera Labs, Barcelona, Spain.

7

How FAIR is my data: the FAIRe(nough) benchmark at AstraZeneca

Jon Ison, Ben Gardner, Pablo Porras, John Berrisford, Mathew Woodwark - Astrazeneca

8

Guiding European genomics infrastructure advancement along a pathway paved with standards

Giselle Kerry (ELIXIR Hub), Dylan Spalding (CSC Finland), Arshiya Merchant (ELIXIR Hub), Anamika Chatterjee (ELIXIR Hub), Serena Scollen (ELIXIR Hub), Juan Arenas, (ELIXIR Hub)

9

Ensuring Equity, Diversity and Inclusion at GA4GH

Shakuntala Baichoo (University of Mauritius), Andy Yates (EMBL-EBI), Melissa Konopko (ELIXIR Hub), Laura Paglione (Spherical Cow Group), Neerjah Skantharajah (GA4GH, OICR)

Special thanks to all GA4GH EDI Advisory Group and REWS Diversity members.

10

Digital Use Conditions

Francis Jeanson, Datadex
Alexander Bernier, McGill University
Spencer Gibson, University of Leicester
Anthony Brookes, University of Leicester
Pinar Alper, University of Luxembourg
Nancy Mah, Berlin Institute of Health, Charité
Petr Holub, BBMRI
Ann K Novakowski, Sage Bionetworks
Esther van Enckevort, University of Groningen
Annalisa Landi, Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus
Regina Becker, University of Luxembourg
Stephanie Dyke, McGill University
Daniel Mietchen, Berlin Institute of Health, Charité
Mark Wilkinson, Universidad Politecnica de Madrid
Oussama Benhamed, Universidad Politecnica de Madrid
Georg Philip Krog, Signatu
Megan Doerr, Sage Bionetworks
Morris Swertz, University of Groningen
Adrian Thorogood, University of Luxembourg
Alessandro Sulis, CRS4 Sardegna
Francesca Frexia, CRS4 Sardegna
Chisato Yamasaki, Osaka University
Christina Kyriakopoulou, European Commission
David Zaccagnini, Lynkeus Europe
Dylan Spalding, EBI
Fabian Prasser, Berlin Institute of Health, Charité
Franz Schaefer, University of Heidelberg
Gary Saunders, ELIXIR Europe
Helen Parkinson, EBI
Ibrahim Bashefarah, EDDRP UK
Joe M Saul, University of Michigan
Johanna Bleckman, University of Michigan
Maggie Levenstein, University of Michigan
Jo Roach, Accelerating Detection of Disease UK
Jonathan Lawson, Broad Institute
Katy Wolstencroft, Leiden University
Mary Wang, Telethon Italy
Melanie Courtot, Ontario Institute for Cancer Research
Melissa Haendel, Monarch Initiative
Michele Mattioni, Seven Bridges
Pio Szamel, Seven Brdiges
Olga Tzortzatou, Bioacademy Athens
Pim Kamerling, Radboudumc
Rebecca Boyles, RTI International
Saskia Sanderson, Accelerating Detection of Disease UK
Soichi Ogishima, Tohoku Megabank
Susan Wallace, University of Leicester
Vandan Juvekar, University of Michigan
Vanessa Unkeless-Perez, University of Michigan

11

The X-omics FAIR Data Cube, architecture, implementation and demonstration

Anna Niehues (1,2) , Martin Brandt (3) , Cenna Doornbos (1) , Tom Ederveen (1) , Junda Huang (1) , Purva Kulkarni (1,2) , Joeri van der Velde (4) , Casper de Visser (1) , Michael van Vliet (5) and Peter-Bram ’t Hoen (1)

1. Center for Molecular and Biomolecular Informatics, Radboud university medical center, Nijmegen, The Netherlands
2. Translational Metabolic Laboratory, Radboud university medical center, Nijmegen, The Netherlands
3. SURF, Amsterdam, The Netherlands
4. Genomics Coordination Center and Department of Genetics, University of Groningen and UMCG, The Netherlands
5. Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands

12

Deployment of GA4GH standards at the European Genome-phenome Archive

Lauren A. Fromont[1], Ana Alonso Ayuso[1], Amy J. Curwin[1], Csaba Halmagyi[2], Coline Thomas[2], Mallory Ann Freeberg[2], Thomas Keane[2], Jordi Rambla[1]

Affiliations: [1] CRG, [2] EMBL-EBI

13

Quality Control of Whole Genome Sequencing

HEBRARD Maxime(1), HOFMANN Oliver(2), BERTIN Nicolas(1), SMITH Lindsay(3), on behalf of GHIF QC for WGS Workgroup
1. Precision Health Research Singapore (PRECISE), Genome Institute of Singapore (GIS), Singapore
2. Australian Genomics, Melbourne, Australia
3. Global Alliance for Genomics and Health (GA4GH), Ontario Institute for Cancer Research (OICR), Canada

14

Federating National Health Research Data - CanDIG in 2022

Shaikh Farhan Rashid - CanDIG (UHN), Karen Kranston - CanDIG (UHN), Guillaume Bourque - C3G (McGill), Michael Brudno - UHN (UofT)

15

Beacon v2 - Feature-rich implementation of the Genomic Data Discovery Protocol

Michael Baudis, Rahel Paloots, Hangjia Zhao, Ziying Yang and members of the Beacon developer community

16

The GA4GH Regulatory and Ethics Work Stream

Maili Raven-Adams, Lindsay Smith, Beatrice Kaiser, Yann Joly and Dianne Nicol

17

Facilitating data sharing in H3Africa

Mamana Mbiyavanga, Nicola Mulder, on behalf of the H3Africa consortium

H3ABioNet/H3Africa, Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, South Africa

18

Keycloak server as a GA4GH Passport broker: Leveraging GA4GH Passport for handling data permissions among different data repositories in the scope of the iPC project.

Dmitry Repchevsky [Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center (BSC)], Alejandro J. Canosa Valls [Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center (BSC)], Salvador Capella-Gutierrez [Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center (BSC)], Josep L. Gelpí [Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center (BSC), Universitat de Barcelona (UB)], Oscar Martinez Llobet [Barcelona Supercomputing Center (BSC)]

19

iPC (individualizedPaediatricCure) platform: A cloud-based architecture for the visualization, sharing, and analysis of paediatric cancer data aligned to the GA4GH standards.

Authors:

Alejandro J. Canosa Valls(1,2), Dmitry Repchevsky(1,2), Frédéric Haziza(1,3), Roberto Ariosa(1,3), Laura-Rodríguez-Navas(1,2), José M. Fernández(1,2), Laia Codo(1,2), Jolanda Modic(5), Josep-L. Gelpí(1,2, 4), Salvador Capella-Gutierrez(1,2)

Affiliations:

1 Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
2 Barcelona Supercomputing Center (BSC), Barcelona, Spain
3 Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
4 Dept Biochemistry and Molecular Biomedicine, University of Barcelona (UB)
5 XLAB d.o.o, Pot za Brdom 100, SI-1000 Ljubljana, Slovenia

20

WESkit: Flexible Workflow Execution for HTC and Cloud

Alexander Kanitz (University of Basel & Swiss Institute of Bioinformatics), Cibin Sadasivan Baby (Wellcome Sanger Institute), Ivo Buchhalter (DKFZ), Matthieu Muffato (Wellcome Sanger Institute), Philip R. Kensche (DKFZ), Valentin Schneider-Lunitz (Berlin Institute of Health at Charité), Sven Twardziok (Berlin Institute of Health at Charité)

21

Genxt Confidential Computing Network for privacy-by-design collaborative genomic data analysis

Pavel Nikonorov (Genxt), Mariam Makhmutova (Genxt), Ruslan Vakhitov (Genxt), Stanislav Nikolskiy (Genxt)

22

The eLwazi Open Data Science Platform for African Biomedical Scientists

Gerrit Botha, Nicola Mulder on behalf of the eLwazi consortium

23

ELIXIR Beacon Network goes v2.

Author: Dmitry Repchevsky¹², Sergi Aguiló-Castillo¹², Michael Baudis³⁴, Jordi Rambla de Argila¹⁵, Babita Singh¹⁵, Salvador Capella-Gutierrez¹², J. Dylan Spalding⁶⁷, Teemu Kataja⁶⁷, Ville Muilu⁶⁷, Juha Törmroos⁶⁷, Josep Ll. Gelpí¹²⁸, Lauren A Fromont¹⁵

¹ Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
² Barcelona Supercomputing Center (BSC)
³ Department of Molecular Life Sciences, University of Zurich
⁴ SIB | Swiss Institute of Bioinformatics
⁵ Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
⁶ CSC-IT Center for Science Ltd.
⁷ ELIXIR Finland
⁸ Dept. Biochemistry and Molecular Biomedicine, University of Barcelona (UB)

24

The ELIXIR: GA4GH Cloud

Alexander Kanitz (University of Basel, Switzerland & Swiss Institute of Bioinformatics), Justin Clark-Casey (EMBL-EBI, European Molecular Biology Institute, European Bioinformatics Institute), Michael Crusoe (Vrije Universiteit Amsterdam, Amsterdam, The Netherlands), Thanasis Vergoulis (“Athena” Research Center, Athens, Greece), Jonathan Tedds (ELIXIR Hub), Álvaro González (CSC, Finnish IT Center for Science, Espoo, Finland), and the ELIXIR Cloud & AAI Driver Project

25

Secured and annotated execution of workflows with WfExS-backend

José M. Fernández 1,2, Laura Rodríguez-Navas 1,2, Salvador Capella-Gutierrez 1,2

1 Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
2 Barcelona Supercomputing Center (BSC)

26

Manifest-based DRS import: A practical solution for cross-DCC dataset analysis to empower translational discovery using Kids First and GTEx data

Authors:
Surya Saha 1, Michele Mattioni 1, Milos Trboljevac 1, Eric Wenger 2, Allison Heath 2, Yuankun Zhu 2, Robert Carter 3, Michelle Giglio 3, Suvvi Nadendla 3, C. Titus Brown 4, Bailey K Farrow 2, Daniel J. B. Clarke 5, Adam Kraya 2, Kristin Ardlie 6, Jared Nedzel 6, Lan Nguyen 5, Avi Ma’ayan 4, Owen White 3, Jack DiGiovanna 1, Adam Resnick 2

Affiliations:
1Seven Bridges Inc., Charlestown, MA 02129, USA
2 Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
3 Institute for Genome Sciences, University of Maryland, Baltimore, MD 21201, USA
4 School of Veterinary Medicine, University of California, Davis, CA 95616, USA
5 The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
6 Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA

27

Genxt Confidential Computing Network for privacy-by-design collaborative genomic data analysis

Andrew Ponomarev, Ruslan Vakhitov, Mariam Makhmutova, Stas Nikolskiy, Pavel Nikonorov

28

sagetasks: a Python package for data and workflow orchestration in the cloud

Bruno M. Grande, Tess M. Thyer, James A. Eddy, Thomas V. Yu, Brian D. O’Connor

Sage Bionetworks, Seattle, WA, USA

29

DRS and FHIR: integrating different standards to power complex scientific research in the INCLUDE DCC Project

Michele Mattioni (1), Surya Saha (1), Nevena Vukojicic(1), Milos Trboljevac(1), Jack DiGiovanna(1), Jeremy Costanza(2), Jean-Philippe Thibert(2), Vincent Ferretti(2), Brian O’Connor(3), Joaquin Espinosa(4), Robert J Carroll(5), Bailey Farrow(6), Allison P. Heath(6), Adam Resnick(6)

1.Seven Bridges
2. Research Centre of the Sainte-Justine University Hospital
3. Sage Bionetworks, Seattle, WA
4. Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus
5. Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
6. Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia

30

Aligning 3,500 NIH studies to the Data Use Ontology

Jonathan M Lawson1, Elena Ghanaim2, Jinyoung Baek1, Harin Lee1, Pamela Bretscher1
1Broad Institute, Data Science Platform, Cambridge, MA, 2National Human Genome Research Institute, Office of Genomic Data Science, Rockville, MD

31

The Spanish node of Federated EGA

Hornos Albert(1,2), Codó Laia(1,2), Fernandez Jose María(1,2), Canosa Alejandro(1,2), Haziza Frederic(1,3), Jene Aina(1,3), Curwin Amy(1,3), Fromont Lauren(1,3), Rambla Jordi(1,3), Navarro Arcadi(1,5,6), Valencia Alfonso(1,2,6), Gelpí Josep Lluís(1,2,4) and Capella-Gutierrez Salvador(1,2)
 
1 Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
2 Barcelona Supercomputing Center (BSC)
3 Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
4 Dept Biochemistry and Molecular Biomedicine, University of Barcelona (UB)
5 Universitat Pompeu Fabra (UPF)
6 Catalan Institution for Research and Advanced Studies (ICREA)

32

Manifest-based DRS import: A practical solution for cross-DCC dataset analysis to empower translational discovery using Kids First and GTEx data

Surya Saha 1, Michele Mattioni1, Milos Trboljevac 1 ,Eric Wenger2, Allison Heath2, Yuankun Zhu2, Robert Carter3, Michelle Giglio3, Suvarna Nadendla3, C. Titus Brown4, Bailey K Farrow2, Daniel J. B. Clarke5, Adam Kraya2, Kristin Ardlie6, Jared Nedzel6, Lan Nguyen5, Avi Ma’ayan4, Owen White3, Jack DiGiovanna 1, Adam Resnick2

Affiliations:
1 Seven Bridges Inc., Charlestown, MA 02129, USA
2 Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
3 Institute for Genome Sciences, University of Maryland, Baltimore, MD 21201, USA
4 School of Veterinary Medicine, University of California, Davis, CA 95616, USA
5 The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
6 Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA

33

Proposing a {GW/Ex/Ph/++}AS Format 

Yossi Farjoun / Lady Davis Institute,
James Hayhurst / EBI, Laura Harris / EBI

34

What happened at GA4GH this year? A snapshot from GA4GH Communications

Stephanie Li (GA4GH), Connor Graham (GA4GH), Julia Ostmann (GA4GH)