All Stories

  1. BioHackEU24 report: Integrating Bioconductor packages with the ELIXIR Research Software Ecosystem using EDAM

    Article • April 2025, Center for Open Science

    Matúš Kalaš

  2. An assessment of Croissant ML metadata descriptors for AI-ready datasets

    Article • April 2025, Center for Open Science

    Matúš Kalaš

  3. Development of FAIR image analysis workflows and training in Galaxy

    Article • March 2025, Center for Open Science

    Matúš Kalaš

  4. Correlated multimodal imaging in life sciences: lessons learnt

    Article • Frontiers in Biomaterials Science, July 2024, Frontiers

    Matúš Kalaš

  5. The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity

    Article • F1000Research, May 2024, Faculty of 1000, Ltd.

    Matúš Kalaš

  6. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

    Article • Nucleic Acids Research, May 2024, Oxford University Press (OUP)

    Krzysztof Poterlowicz, Matúš Kalaš, Björn Grüning

  7. How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources

    Article • April 2024, Center for Open Science

    Matúš Kalaš

  8. Enhancing the image analysis community in Galaxy

    Article • April 2024, Center for Open Science

    Matúš Kalaš, Björn Grüning

  9. Synergising ELIXIR resources for training in systems biology

    Article • April 2024, Center for Open Science

    Matúš Kalaš

  10. How to increase the findability, visibility, and impact of Galaxy tools for your scientific community

    Article • April 2024, Center for Open Science

    Matúš Kalaš, Dr Ove J R Gustafsson

  11. Infrastructure for synthetic health data

    Article • July 2023, Center for Open Science

    Matúš Kalaš

  12. The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity

    Article • F1000Research, May 2023, Faculty of 1000, Ltd.

    Matúš Kalaš

  13. An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems

    Article • February 2023, Center for Open Science

    Matúš Kalaš, Dr Ove J R Gustafsson

  14. The future of food and nutrition in ELIXIR

    Article • F1000Research, August 2022, Faculty of 1000, Ltd.

    Matúš Kalaš, Dr John M Hancock

  15. BioSimulators: a central registry of simulation engines and services for recommending specific tools

    Article • Nucleic Acids Research, May 2022, Oxford University Press (OUP)

    Matúš Kalaš

  16. Galaxy: A Decade of Realising CWFR Concepts

    Article • Data Intelligence, January 2022, The MIT Press

    Matúš Kalaš

  17. Perspectives on automated composition of workflows in the life sciences

    Article • F1000Research, September 2021, Faculty of 1000, Ltd.

    Matúš Kalaš

  18. Bioimage analysis workflows: community resources to navigate through a complex ecosystem

    Article • F1000Research, April 2021, Faculty of 1000, Ltd.

    Matúš Kalaš

  19. biotoolsSchema: a formalized schema for bioinformatics software description

    Article • GigaScience, January 2021, Oxford University Press (OUP)

    Matúš Kalaš

  20. EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020)

    Article • March 2020, Faculty of 1000, Ltd.

    Matúš Kalaš

  21. Community curation of bioinformatics software and data resources

    Article • Briefings in Bioinformatics, October 2019, Oxford University Press (OUP)

    Dr John M Hancock, Matúš Kalaš

  22. The bio.tools registry of software tools and data resources for the life sciences

    Article • August 2019, Springer Science + Business Media

    Mr Rafael C Jimenez, Matúš Kalaš

  23. EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (2019 update)

    Article • February 2019, Faculty of 1000, Ltd.

    Matúš Kalaš

  24. Norwegian e-Infrastructure for Life Sciences (NeLS)

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Erik Hjerde, Prof Nils Peder Willassen, Matúš Kalaš

  25. BioXSD | BioJSON | BioYAML – towards unified formats for sequences, alignments, features, and annotations

    Article • June 2018, Faculty of 1000, Ltd.

    Matúš Kalaš

  26. The GTrack ecosystem - expressive file formats for analysis of genomic track data

    Article • March 2018, Faculty of 1000, Ltd.

    Matúš Kalaš

  27. Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

    Article • Data Science and Engineering, September 2017, Springer Science + Business Media

    Matúš Kalaš

  28. Workflow-ready bioinformatics packages and Debian’s infrastructure for low-friction reproducible research

    Article • July 2017, Faculty of 1000, Ltd.

    Matúš Kalaš

  29. BioXSD, BioJSON, BioYAML – towards unified formats for sequences, alignments, features, and annotations

    Article • July 2017, Faculty of 1000, Ltd.

    Matúš Kalaš

  30. The EDAM ontology and its integration into Galaxy

    Article • June 2017, Faculty of 1000, Ltd.

    Matúš Kalaš

  31. ReGaTE: Registration of Galaxy Tools in Elixir

    Article • GigaScience, April 2017, Oxford University Press (OUP)

    Björn Grüning, Matúš Kalaš

  32. BioXSD | BioJSON | BioYAML – Towards unified formats for sequences, alignments, features, and annotations

    Article • September 2016, Faculty of 1000, Ltd.

    Matúš Kalaš

  33. The EDAM ontology

    Article • September 2016, Faculty of 1000, Ltd.

    Matúš Kalaš

  34. Tools and data services registry: a community effort to document bioinformatics resources

    Article • Nucleic Acids Research, November 2015, Oxford University Press (OUP)

    Mr Rafael C Jimenez, Björn Grüning, Dr Tunca Dogan, Matúš Kalaš

  35. BioXSD — a data model for sequences, alignments, features, measured and inferred values<br /> 

    Article • July 2015, Faculty of 1000, Ltd.

    Matúš Kalaš

  36. Using registries to integrate bioinformatics tools and services into workbench environments

    Article • International Journal on Software Tools for Technology Transfer, July 2015, Springer Science + Business Media

    Matúš Kalaš

  37. The EDAM Ontology

    Article • July 2015, Faculty of 1000, Ltd.

    Matúš Kalaš

  38. The EDAM Ontology

    Article • July 2015, Faculty of 1000, Ltd.

    Matúš Kalaš

  39. Community-driven development for computational biology at Sprints, Hackathons and Codefests

    Article • BMC Bioinformatics, November 2014, Springer Science + Business Media

    Matúš Kalaš

  40. FreeContact: fast and free software for protein contact prediction from residue co-evolution

    Article • BMC Bioinformatics, March 2014, Springer Science + Business Media

    Matúš Kalaš

  41. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

    Article • Journal of Biomedical Semantics, January 2014, Springer Science + Business Media

    Matúš Kalaš, Yosuke Nishimura

  42. Sprints, Hackathons and Codefests as community gluons in computational biology

    Article • EMBnet journal, October 2013, EMBnet Stichting

    Matúš Kalaš

  43. The Genomic HyperBrowser: an analysis web server for genome-scale data

    Article • Nucleic Acids Research, April 2013, Oxford University Press (OUP)

    Matúš Kalaš

  44. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

    Article • Bioinformatics, March 2013, Oxford University Press (OUP)

    Matúš Kalaš

  45. Workshop on laboratory protocol standards for the molecular methods database

    Article • New Biotechnology, January 2013, Elsevier

    Matúš Kalaš

  46. Identifying elemental genomic track types and representing them uniformly

    Article • BMC Bioinformatics, December 2011, Springer Science + Business Media

    Matúš Kalaš

  47. Interoperable Semantic Web services (Tutorials)

    Article • Nature Photonics, January 2011, Springer Science + Business Media

    Matúš Kalaš

  48. Interoperable Semantic Web services (Tutorials)

    Article • Nature Photonics, January 2011, Springer Science + Business Media

    Matúš Kalaš

  49. BioXSD: the common data-exchange format for everyday bioinformatics web services

    Article • Bioinformatics, September 2010, Oxford University Press (OUP)

    Matúš Kalaš

  50. The EMBRACE web service collection

    Article • Nucleic Acids Research, May 2010, Oxford University Press (OUP)

    Matúš Kalaš