Have a personal or library account? Click to login
KadiStudio: FAIR Modelling of Scientific Research Processes Cover

KadiStudio: FAIR Modelling of Scientific Research Processes

Open Access
|Sep 2022

References

  1. 1Afgan, E, et al. 2018. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic acids research, 46(W1): W537W544. DOI: 10.1093/nar/gky379
  2. 2Berthold, MR, et al. 2009. KNIME-the Konstanz information miner: version 2.0 and beyond. AcM SIGKDD explorations Newsletter, 11(1): 2631. DOI: 10.1145/1656274.1656280
  3. 3Brandt, N, et al. 2021. Kadi4Mat: A Research Data Infrastructure for Materials Science. Data Science Journal 20.1. DOI: 10.5334/dsj-2021-008
  4. 4Crusoe, MR, et al. 2021. Methods included: standardizing computational reuse and portability with the common workflow language. arXiv preprint arXiv, 2105.07028. DOI: 10.1145/3486897
  5. 5Crusoe, MR, et al. May 2022. Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. Commun. ACM, 65(6): 5463. DOI: 10.1145/3486897
  6. 6Demšar, J, et al. 2013. Orange: Data Mining Toolbox in Python. Journal of Machine Learning Research, 14: 23492353.
  7. 7Di Tommaso, P, et al. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4): 316319. DOI: 10.1038/nbt.3820
  8. 8Dmitry, PEA. 2017. Qt5 Node Editor. https://github.com/paceholder/nodeeditor.
  9. 9Draxl, C and Scheffler, M. 2020. Big data-driven materials science and its FAIR data infrastructure. Handbook of Materials Modeling: Methods: Theory and Modeling, 4973. DOI: 10.1007/978-3-319-44677-6_104
  10. 10Frazer, S, et al. 2012. Workflow Description Language – Specification and Implementations. https://libraries.io/github/openwdl/wdl.
  11. 11Goel, A. 2010. Computer fundamentals. Pearson Education India.
  12. 12Hey, AJ, Tansley, S, Tolle, KM, et al. 2009. The fourth paradigm: data-intensive scientific discovery. Vol. 1. WA: Microsoft research Redmond.
  13. 13Jain, A, et al. 2015. FireWorks: A dynamic workflow system designed for high-throughput applications. Concurrency and Computation: Practice and Experience, 27(17): 50375059. DOI: 10.1002/cpe.3505
  14. 14Kadi4Mat Team and Contributors. June 2022a. IAM-CMS/kadi-apy: Kadi4Mat API Library. Version 0.23.0. DOI: 10.5281/zenodo.6623518
  15. 15Kadi4Mat Team and Contributors. June 2022b. IAM-CMS/kadi: Kadi4Mat. Version 0.25.1. DOI: 10.5281/zenodo.6623521
  16. 16Kadi4Mat Team and Contributors. July 2022c. IAM-CMS/workflow-nodes. Version 0.15.0. DOI: 10.5281/zenodo.6806747
  17. 17Kadi4Mat Team and Contributors. February 2022d. IAM-CMS/xmlhelpy. Version 0.9.2. DOI: 10.5281/zenodo.5971732
  18. 18Kadi4Mat Team and Contributors. July 2022e. kadistudio: 0.1.0.alpha1. Version 0.1.0.alpha1. DOI: 10.5281/zenodo.6810891
  19. 19Kluyver, T, et al. 2016. Jupyter Notebooks? A publishing format for reproducible computational workflows. In: Loizides, F and Scmidt, B (eds.), Positioning and Power in Academic Publishing: Players, Agents and Agendas. IOS Press. pp. 8790. DOI: 10.3233/978-1-61499-649-1-87
  20. 20Mölder, F, et al. 2021. Sustainable data analysis with Snakemake. F1000 Research, 10. DOI: 10.12688/f1000research.29032.1
  21. 21Pizzi, G, et al. 2016. AiiDA: automated interactive infrastructure and database for computational science. Computational Materials Science, 111: 218230. DOI: 10.1016/j.commatsci.2015.09.013
  22. 22The Pallets Projects. 2014. Click – The Pallets Projects. https://palletsprojects.com/p/click/.
  23. 23Wilkinson, MD, et al. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific data, 3(1): 19. DOI: 10.1038/sdata.2016.18
  24. 24Zelle, JM. 2004. Python programming: an introduction to computer science. Franklin: Beedle & Associates, Inc.
  25. 25Zschumme, P, Schoof, E, et al. July 2022. IAM-CMS/process-engine. Version 0.5.0. DOI: 10.5281/zenodo.6806707
  26. 26Zschumme, P, Steinhülb, J and Brandt, N. February 2022. IAM-CMS/process-manager. Version 0.2.0. DOI: 10.5281/zenodo.5972885
Language: English
Submitted on: Jul 8, 2022
Accepted on: Sep 6, 2022
Published on: Sep 23, 2022
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2022 Lars Griem, Philipp Zschumme, Matthieu Laqua, Nico Brandt, Ephraim Schoof, Patrick Altschuh, Michael Selzer, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.