Work
Open source|science|society
Interoperable, efficient, accessible, reliable scientific computing, especially bioinformatics
ORCiD: 0000-0002-1509-4981
https://twitter.com/matuskalas
Selected projects:
- EDAM ontology, for bioinformatics and bioimage informatics
- Bio.tools registry of computational tools for life sciences
- ELIXIR Europe & ELIXIR Norway
- BioXSD|GTrack family of data formats
Teaching: The Carpentries, especially Software Carpentry, Bergen Open Source community, and other ...
Publications, see:
Publications
Academic article
- Zierep, Paul; Batut, Bérénice; Soranzo, Nicola et al. (2024). How to increase the findability, visibility, and impact of Galaxy tools for your scientific community. (external link)
- Rioualen, Claire; Bacall, Finn; Furlan, Cristina et al. (2024). Synergising ELIXIR resources for training in systems biology. (external link)
- Batut, Berenice; Bernt, Matthias; Hojat Ansari, Mina et al. (2024). How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources. (external link)
- Kostrykin, Leonid; Woller, Tatiana; Kalaš, Matúš et al. (2024). Enhancing the image analysis community in Galaxy. (external link)
- Rudraiah, Pavitra Sokke; Camacho, Rafael; Fernandez-Rodriguez, Julia et al. (2024). Correlated multimodal imaging in life sciences: lessons learnt. (external link)
- Waterhouse, Robert M.; Adam-Blondon, Anne-Françoise; Balech, Bachir et al. (2024). The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity. (external link)
- Zhang, Chong; Gaignard, Alban; Kalas, Matus et al. (2023). Bio-Image Informatics Index BIII: A unique database of image analysis tools and workflows for and by the bioimaging community. (external link)
- Balech, Bachir; Brennan, Lorraine; Carillo de Santa Pau, Enrique et al. (2023). The future of food and nutrition in ELIXIR [version 1; peer review: 2 approved with reservations]. (external link)
- Lamothe, Lucie; Rugaard Bregndahl Jensen, Jennifer; Ienasescu, Hans et al. (2023). An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems. (external link)
- Queralt Rosinach, Núria; Alshaikhdeeb, Basel; Bolzani, Luca et al. (2023). Infrastructure for synthetic health data. (external link)
- Shaikh, Bilal; Smith, Lucian P; Vasilescu, Dan et al. (2022). BioSimulators: a central registry of simulation engines and services for recommending specific tools. (external link)
- Serrano-Solano, Beatriz; Fouilloux, Anne Claire Mireille; Eguinoa, Ignacio et al. (2022). Galaxy: A Decade of Realising CWFR Concepts. (external link)
- Lamprecht, Anna-Lena; Palmblad, Magnus; Ison, Jon et al. (2021). Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved] . (external link)
- Paul-Gilloteaux, Perrine; Tosi, Sébastien; Hériche, Jean-Karim et al. (2021). Bioimage analysis workflows: community resources to navigate through a complex ecosystem [version 1; peer review: 2 approved]. (external link)
- Ison, Jon; Ienasescu, Hans; Rydza, Emil et al. (2021). biotoolsSchema: a formalized schema for bioinformatics software description. (external link)
- Ison, Jon; Ménager, Hervé; Brancotte, Bryan et al. (2019). Community curation of bioinformatics software and data resources. (external link)
- Ison, Jon; Ienasescu, Hans; Chmura, Piotr et al. (2019). The bio.tools registry of software tools and data resources for the life sciences. (external link)
- Tekle, Kidane M; Gundersen, Sveinung; Klepper, Kjetil et al. (2018). Norwegian e-Infrastructure for Life Sciences (NeLS). (external link)
- Möller, Steffen; Prescott, Stuart W.; Wirzenius, Lars et al. (2017). Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis. (external link)
- Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer et al. (2016). Using registries to integrate bioinformatics tools and services into workbench environments. (external link)
- Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé et al. (2016). Tools and data services registry: a community effort to document bioinformatics resources. (external link)
- Kaján, László; Hopf, Thomas A.; Kalaš, Matúš et al. (2014). FreeContact: Fast and free software for protein contact prediction from residue co-evolution. (external link)
- Katayama, Toshiaki; Wilkinson, Mark; ..., ... et al. (2014). BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. (external link)
- Möller, Steffen; Afgan, Enis; Banck, Michael et al. (2014). Community-driven development for computational biology at Sprints, Hackathons and Codefests. (external link)
- Möller, Steffen; Afgan, Enis; Banck, Michael et al. (2013). Sprints, Hackathons and Codefests as community gluons in computational biology. (external link)
- Ison, Jon; Kalaš, Matúš; Jonassen, Inge et al. (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. (external link)
- Klingström, Tomas; Soldatova, Larissa; Stevens, Robert et al. (2013). Workshop on laboratory protocol standards for the molecular methods database. (external link)
- Sandve, Geir Kjetil; Gundersen, Sveinung; Johansen, Morten et al. (2013). The Genomic HyperBrowser: an analysis web server for genome-scale data. (external link)
- Gundersen, Sveinung; Kalaš, Matúš; Abul, Osman et al. (2011). Identifying elemental genomic track types and representing them uniformly. (external link)
- Pettifer, Steve; Ison, Jon; Kalaš, Matúš et al. (2010). The EMBRACE web service collection. (external link)
- Kalas, Matus; Puntervoll, Pål; Joseph, Alexandre et al. (2010). BioXSD: the common data-exchange format for everyday bioinformatics web services. (external link)
Report
- Gundersen, Sveinung; Bianchini, Federico; Vázquez, Pável et al. (2024). D3.4 (M18) - Report on developments and operations of the FAIRtracks ecosystem (an ELIXIR Norway ELIXIR3 deliverable). (external link)
- Calhoun, Erin Elizabeth; Kalaš, Matúš; Bösl, Korbinian Michael et al. (2023). D3.3 (M18) - Report on curation in core ELIXIR registries (an ELIXIR Norway ELIXIR3 deliverable). (external link)
Abstract
- Ienasescu, Hans; Capella-Gutiérrez, Salvador; Coppens, Frederik et al. (2023). The ELIXIR research software ecosystem: an open software metadata commons (BOSC track) [version 1; not peer reviewed]. (external link)
- Ienasescu, Hans; Capella-Gutiérrez, Salvador; Coppens, Frederik et al. (2023). The ELIXIR research software ecosystem [version 1; not peer reviewed]. (external link)
Short communication
- Black, Melissa; Lamothe, Lucie; Eldakroury, Hager et al. (2022). EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]. (external link)
- Kalaš, Matúš; Ménager, Hervé; Gaignard, Alban et al. (2020). EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. (external link)
- Kalaš, Matúš; Plantard, Laure; Lindblad, Joakim et al. (2020). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. (external link)
- Doppelt-Azeroual, Olivia; Mareuil, Fabien; Deveaud, Eric et al. (2017). ReGaTE: Registration of galaxy tools in Elixir. (external link)
Multimedia product
- Burke, Melissa; Kalaš, Matúš; Ienasescu, Hans (2022). bio.tools and EDAM - making it easier to find, understand and cite biological tools and software. (external link)
- Lamothe, Lucie; Ménager, Hervé; Kalaš, Matúš (2022). EDAM - The data analysis and management ontology (update 2022). (external link)
- Black, Melissa; Kalaš, Matúš (2021). EDAM ontology - introduction (2 mins) Narrated by Dr. Melissa Black, written by Dr. Melissa Black and Matúš Kalaš. (external link)
Academic lecture
- Ienasescu, Hans; Kalaš, Matúš (2022). WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software. (external link)
- Lamothe, Lucie; Kierkegaard, Mads; Black, Melissa et al. (2022). EDAM - The data analysis and management ontology (update 2022). (external link)
- Kalaš, Matúš (2021). Bio.tools, EDAM, Galaxy, et al. - Infrastructure for accessible computational tools not only for biosciences. (external link)
Poster
- Lamothe, Lucie; Gaignard, Alban; Kierkegaard, Mads et al. (2022). EDAM, life sciences ontology for data analysis and management. (external link)
- Eldakroury, Hager; Dhamija, Sakshi; Rathi, Rashika et al. (2021). EDAM Browser: visualization of EDAM and annotated bioinformatics resources. (external link)
- Black, Melissa; Lamothe, Lucie; Eldakroury, Hager et al. (2021). EDAM: the bioscientific data analysis ontology (update 2021). (external link)
- Kalaš, Matúš; Plantard, Laure; Lindblad, Joakim et al. (2020). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020). (external link)
- Kalaš, Matúš; Ménager, Hervé; Gaignard, Alban et al. (2020). EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020). (external link)
Software
- Eldakroury, Hager; Dhamija, Sakshi; Rathi, Rashika et al. (2021). EDAM Browser 2.0.0: Browsing multiple version of EDAM. (external link)
- Lindblad, Joakim; Plantard, Laure; Jones, Martin et al. (2020). EDAM Bioimaging: The ontology of (bio-)image informatics and machine learning (Version alpha06). (external link)