Peer Review Report For: Community-driven ELIXIR activities in single-cell omics [version 1; peer review: 2 approved with reservations]

Abstract

Single-cell omics (SCO) has revolutionized the way and the level of resolution by which life science research is conducted, not only impacting our understanding of fundamental cell biology but also providing novel solutions in cutting-edge medical research. The rapid development of single-cell technologies has been accompanied by the active development of data analysis methods, resulting in a plethora of new analysis tools and strategies every year. Such a rapid development of SCO methods and tools poses several challenges in standardization, benchmarking, computational resources and training. These challenges are in line with the activities of ELIXIR, the European coordinated infrastructure for life science data. Here, we describe the current landscape of and the main challenges in SCO data, and propose the creation of the ELIXIR SCO Community, to coordinate the efforts in order to best serve SCO researchers in Europe and beyond. The Community will build on top of national experiences and pave the way towards integrated long-term solutions for SCO research.

Authors 27

1. Paulo Czarnewski corresponding

   Stockholm University · Science for Life Laboratory · National Bioinformatics Infrastructure Sweden

   Affiliation as printed

   Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Solna

2. Ahmed Essam Mahfouz Aachen Department of Human Genetics Netherlands & Delft Bioinformatics Lab

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Department of Human Genetics, The Netherlands & Delft Bioinformatics Lab, Leiden University Medical Center, Delft University of Technology, Leiden, Delft

3. Raffaele Calogero

   University of Turin

   Affiliation as printed

   Bioinformatics and Genomics unit, Dept. Molecular Biotechnology and Health Science, University of Torino, Torino

4. Patricia M. Palagi

   SIB Swiss Institute of Bioinformatics

   Affiliation as printed

   SIB Swiss Institute of Bioinformatics, Lausanne

5. Laura Portell-Silva

   Barcelona Supercomputing Center

   Affiliation as printed

   Barcelona Supercomputing Center, Barcelona

6. Asier Gonzalez‐Uriarte

   Barcelona Supercomputing Center

   Affiliation as printed

   Barcelona Supercomputing Center, Barcelona

7. Charlotte Soneson

   SIB Swiss Institute of Bioinformatics · Friedrich Miescher Institute

   Affiliation as printed

   Friedrich Miescher Institute for Biomedical Research, Basel

   SIB Swiss Institute of Bioinformatics, Lausanne

8. Tony Burdett

   European Bioinformatics Institute

   Affiliation as printed

   European Bioinformatics Institute, Hinxton

9. Barbara Szomolay

   Cardiff University

   Affiliation as printed

   Division of Infection and Immunity, School of Medicine, Cardiff University, Wales

10. Pavankumar Videm

    University of Freiburg

    Affiliation as printed

    Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg

11. Hans-Rudolf Hotz

    Friedrich Miescher Institute

    Affiliation as printed

    Friedrich Miescher Institute for Biomedical Research, Basel

12. Irene Papatheodorou

    European Bioinformatics Institute

    Affiliation as printed

    European Bioinformatics Institute, Hinxton

13. John M. Hancock

    University of Ljubljana

    Affiliation as printed

    Institute of Biochemistry and Molecular Genetics, Faculty of Medicine,, University of Ljubljana, Ljubljana

14. B Grüning

    University of Freiburg

    Affiliation as printed

    Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg

15. Wilfried Haerty

    Earlham Institute

    Affiliation as printed

    Earlham Institute, Norwich

16. Roland Krause

    University of Luxembourg · Luxembourg Centre for Systems Biomedicine

    Affiliation as printed

    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg

17. Salvador Capella-Gutierrez

    Barcelona Supercomputing Center

    Affiliation as printed

    Barcelona Supercomputing Center, Barcelona

18. Brane L. Leskošek

    University of Ljubljana

    Affiliation as printed

    Institute of Biochemistry and Molecular Genetics, Faculty of Medicine,, University of Ljubljana, Ljubljana

19. Luca Alessandrì

    University of Turin

    Affiliation as printed

    Bioinformatics and Genomics unit, Dept. Molecular Biotechnology and Health Science, University of Torino, Torino

20. Maddalena Arigoni

    University of Turin

    Affiliation as printed

    Bioinformatics and Genomics unit, Dept. Molecular Biotechnology and Health Science, University of Torino, Torino

21. Tadeja Režen

    University of Ljubljana

    Affiliation as printed

    Institute of Biochemistry and Molecular Genetics, Faculty of Medicine,, University of Ljubljana, Ljubljana

22. Alexander Botzki

    Vlaams Instituut voor Biotechnologie

    Affiliation as printed

    VIB Bioinformatics Core, Ghent

23. Polonca Ferk

    University of Ljubljana

    Affiliation as printed

    Institute of Biochemistry and Molecular Genetics, Faculty of Medicine,, University of Ljubljana, Ljubljana

24. Jessica Lindvall

    Stockholm University · Science for Life Laboratory · National Bioinformatics Infrastructure Sweden

    Affiliation as printed

    Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Solna

25. Katharina F. Heil

    ELIXIR

    Affiliation as printed

    ELIXIR Hub, Wellcome Genome Campus, Hinxton

26. Naveed Ishaque

    Berlin Institute of Health at Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Digital Health Center, Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin

27. Eija Korpelainen

    CSC - IT Center for Science (Finland)

    Affiliation as printed

    CSC – IT center for science, Espoo