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University of Bergen
Matus Kalas's picture

Matus Kalas

Senior Engineer
Department of Informatics
  • E-mailMatus.Kalas@uib.no
  • Visitor Address
    HIB - Thormøhlens gate 55
    5006 Bergen
  • Postal Address
    Postboks 7803
    5020 Bergen

Open source|science|society

Interoperable, efficient, accessible, reliable scientific computing, especially bioinformatics

ORCiD: 0000-0002-1509-4981

https://twitter.com/matuskalas

https://github.com/matuskalas

 

Selected projects:

 

Teaching: The Carpentries, especially Software Carpentry, Bergen Open Source community, and other ...

 

Publications, see:

Academic article
  • Show author(s) (2024). The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity [version 1; peer review: 1 approved with reservations, 1 not approved]. F1000 Research.
  • Show author(s) (2024). How to increase the findability, visibility, and impact of Galaxy tools for your scientific community. OSF Preprints.
  • Show author(s) (2024). Enhancing the image analysis community in Galaxy. OSF Preprints.
  • Show author(s) (2023). The future of food and nutrition in ELIXIR [version 1; peer review: 2 approved with reservations]. F1000 Research. 978.
  • Show author(s) (2023). Infrastructure for synthetic health data. OSF Preprints.
  • Show author(s) (2023). An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems. OSF Preprints.
  • Show author(s) (2022). Galaxy: A Decade of Realising CWFR Concepts. Data Intelligence. 358-371.
  • Show author(s) (2022). BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research (NAR). W108-W114.
  • Show author(s) (2021). biotoolsSchema: a formalized schema for bioinformatics software description. GigaScience. 19 pages.
  • Show author(s) (2021). Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved] . F1000 Research. 897.
  • Show author(s) (2021). Bioimage analysis workflows: community resources to navigate through a complex ecosystem [version 1; peer review: 2 approved]. F1000 Research. 320.
  • Show author(s) (2019). The bio.tools registry of software tools and data resources for the life sciences. Genome Biology. 4 pages.
  • Show author(s) (2019). Community curation of bioinformatics software and data resources. Briefings in Bioinformatics. 1697-1705.
  • Show author(s) (2018). Norwegian e-Infrastructure for Life Sciences (NeLS). F1000 Research. 15 pages.
  • Show author(s) (2017). Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis. Data Science and Engineering. 232-244.
  • Show author(s) (2016). Using registries to integrate bioinformatics tools and services into workbench environments. International Journal on Software Tools for Technology Transfer (STTT). 581-586.
  • Show author(s) (2016). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research (NAR). D38-D47.
  • Show author(s) (2014). FreeContact: Fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics.
  • Show author(s) (2014). Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics.
  • Show author(s) (2014). BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics. 5.
  • Show author(s) (2013). Workshop on laboratory protocol standards for the molecular methods database. New Biotechnology. 109-113.
  • Show author(s) (2013). The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research (NAR). W133-W141.
  • Show author(s) (2013). Sprints, Hackathons and Codefests as community gluons in computational biology. EMBnet.journal. 40-42.
  • Show author(s) (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics. 1325-1332.
  • Show author(s) (2011). Identifying elemental genomic track types and representing them uniformly. BMC Bioinformatics.
  • Show author(s) (2010). The EMBRACE web service collection. Nucleic Acids Research (NAR). W683-W688.
  • Show author(s) (2010). BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics. i540-i546.
Report
  • Show author(s) (2024). D3.4 (M18) - Report on developments and operations of the FAIRtracks ecosystem (an ELIXIR Norway ELIXIR3 deliverable). .
  • Show author(s) (2023). D3.3 (M18) - Report on curation in core ELIXIR registries (an ELIXIR Norway ELIXIR3 deliverable). .
Academic lecture
  • Show author(s) (2022). WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software.
  • Show author(s) (2022). EDAM - The data analysis and management ontology (update 2022).
  • Show author(s) (2021). Bio.tools, EDAM, Galaxy, et al. - Infrastructure for accessible computational tools not only for biosciences.
Short communication
  • Show author(s) (2022). EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]. F1000 Research. 1.
  • Show author(s) (2020). EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. F1000 Research. 563.
  • Show author(s) (2020). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. F1000 Research. 162.
  • Show author(s) (2017). ReGaTE: Registration of galaxy tools in Elixir. GigaScience. 1-4.
Software
  • Show author(s) (2021). EDAM Browser 2.0.0: Browsing multiple version of EDAM.
  • Show author(s) (2020). EDAM Bioimaging: The ontology of (bio-)image informatics and machine learning (Version alpha06).
Doctoral dissertation
  • Show author(s) (2015). Efforts towards accessible and reliable bioinformatics.
Abstract
  • Show author(s) (2023). The ELIXIR research software ecosystem: an open software metadata commons (BOSC track) [version 1; not peer reviewed]. F1000 Research. 1044.
  • Show author(s) (2023). The ELIXIR research software ecosystem [version 1; not peer reviewed]. F1000 Research. 1026.
Poster
  • Show author(s) (2022). EDAM, life sciences ontology for data analysis and management.
  • Show author(s) (2021). EDAM: the bioscientific data analysis ontology (update 2021).
  • Show author(s) (2021). EDAM Browser: visualization of EDAM and annotated bioinformatics resources.
  • Show author(s) (2020). EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020).
  • Show author(s) (2020). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020).
Multimedia product
  • Show author(s) (2022). bio.tools and EDAM - making it easier to find, understand and cite biological tools and software.
  • Show author(s) (2022). EDAM - The data analysis and management ontology (update 2022).
  • Show author(s) (2021). EDAM ontology - introduction (2 mins) Narrated by Dr. Melissa Black, written by Dr. Melissa Black and Matúš Kalaš.

More information in national current research information system (CRIStin)