Matus Kalas

Senior Engineer

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

ORCiD: 0000-0002-1509-4981

Selected projects:

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

Publications, see:

Academic article

Show author(s) (2023). The future of food and nutrition in ELIXIR [version 1; peer review: 1 approved with reservations]. F1000 Research. 978.
Show author(s) (2023). An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems. Journal of Open Source Software (JOSS).

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.

Academic lecture

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) (2020). EDAM Bioimaging: The ontology of (bio-)image informatics and machine learning (Version alpha06).

Doctoral dissertation

Poster

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) (2021). EDAM ontology - introduction (2 mins) Narrated by Dr. Melissa Black, written by Dr. Melissa Black and Matúš Kalaš.