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Ir. Jonathan de Bruin

Ontwikkelaar ICT 
Universitaire Bestuursdienst
Directie Information and Technology Services
Cluster Applications
Research and Data Management Services
Research and Data Management Services
Bestuursgebouw
Heidelberglaan 8
3584 CS Utrecht

Ir. Jonathan de Bruin

Ontwikkelaar ICT
Research and Data Management Services
j.debruin1@uu.nl
Profiel Publicaties Activiteiten Prijzen In de media Contact
Profiel Publicaties Activiteiten Prijzen In de media Contact
Expertises
Vaardigheden

Most of my work is published on GitHub https://github.com/j535d165. 

 

Featured software

Python Record Linkage Toolkit

The Python Record Linkage Toolkit is a Python module to perform data linkage and deduplication using quasi-identifying variables. The toolkit provides an intuitive API with extensive documentation. The toolkit has more than 150k installations a month (Januari 2022).

 

CBS Open Data in Python

CBSOData is a tool to retrieve data from the open data interface of Statistics Netherlands (Centraal Bureau voor de Statistiek) with Python. The data is identical in content to the tables which can be retrieved and downloaded from StatLine. CBS datasets are accessed via the CBS open data portal. More info can be found at the website of CBS: https://www.cbs.nl/en-gb/corporate/2019/36/an-easy-quick-start-guide-to-cbs-open-data. CBSOData has around 3500 installations a month (Januari 2022). 

 

Sleutelpublicaties

Schoot, R. V. D., Bruin, J. D., Schram, R., Zahedi, P., Boer, J. D., Weijdema, F., Kramer, B., Huijts, M., Hoogerwerf, M., Ferdinands, G., Harkema, A., Willemsen, J., Ma, Y., Fang, Q., Hindriks, S., Tummers, L., & Oberski, D. (2021). An open source machine learning framework for efficient and transparent systematic reviews. Nature Machine Intelligence, 3(2), 125-133. https://doi.org/10.1038/s42256-020-00287-7
https://dspace.library.uu.nl/bitstream/handle/1874/411488/s42256_020_00287_7.pdf?sequence=1
de Bruin, J. (2019). Python Record Linkage Toolkit: A toolkit for record linkage and duplicate detection in Python. Software https://doi.org/10.5281/ZENODO.3559042

Publicaties

2024

Wetenschappelijke publicaties

Harmsen, W., de Groot, J., Harkema, A., van Dusseldorp, I., de Bruin, J., van den Brand, S., & van de Schoot, R. (2024). Machine learning to optimize literature screening in medical guideline development. Systematic Reviews , 13(1), Article 177. https://doi.org/10.1186/s13643-024-02590-5
https://research-portal.uu.nl/ws/files/233528740/s13643-024-02590-5.pdf
Byrne, F., Hofstee, L., Teijema, J., De Bruin, J., & van de Schoot, R. (2024). Impact of Active learning model and prior knowledge on discovery time of elusive relevant papers: a simulation study. Systematic Reviews , 13(1), Article 175. https://doi.org/10.1186/s13643-024-02587-0
https://research-portal.uu.nl/ws/files/233528480/s13643-024-02587-0.pdf
Romanov, S., Siqueira, A. S., Bruin, J. D., Teijema, J., Hofstee, L., & Schoot, R. V. D. (2024). Optimizing ASReview simulations: A generic multiprocessing solution for ‘light-data’ and ‘heavy-data’ users. Data Intelligence, 6(2), 320-343. https://doi.org/10.1162/dint_a_00244
https://research-portal.uu.nl/ws/files/233811641/dint_a_00244.pdf
Bruin, J. D. (2024). PyAlex. Software, Zenodo. https://doi.org/10.5281/zenodo.7423916
Bruin, J. D. (2024). Datahugger - One downloader for many scientific repositories. Software, Zenodo. https://doi.org/10.5281/zenodo.8370403
Teijema, J. J., van de Schoot, R., Ferdinands, G., Lombaers, P., & de Bruin, J. (2024). Makita-A workflow generator for large-scale and reproducible simulation studies mimicking text labeling. Software Impacts, 21, Article 100663. https://doi.org/10.1016/j.simpa.2024.100663
https://research-portal.uu.nl/ws/files/229497782/PIIS2665963824000514.pdf
Lombaers, P., de Bruin, J., & van de Schoot, R. (2024). Reproducibility and Data Storage for Active Learning-Aided Systematic Reviews. Applied Sciences, 14(9), Article 3842. https://doi.org/10.3390/app14093842
https://dspace.library.uu.nl/bitstream/handle/1874/452798/applsci-14-03842-v2.pdf?sequence=1

Vakpublicaties

Bengel, L., Dong, A., Flores-Dourojeanni, J. P., Quené, H., & de Bruin, J. (2024, Jun 30). SPSS, MATLAB, and Mathematica Usage at Utrecht University: A Trend Analysis and Survey. Utrecht University. https://doi.org/10.5281/zenodo.12606474

2023

Wetenschappelijke publicaties

Teijema, J. J., Hofstee, L., Brouwer, M., de Bruin, J., Ferdinands, G., de Boer, J., Vizan, P., van den Brand, S., Bockting, C., van de Schoot, R., & Bagheri, A. (2023). Active learning-based systematic reviewing using switching classification models: the case of the onset, maintenance, and relapse of depressive disorders. Frontiers in Research Metrics and Analytics, 8, Article 1178181. https://doi.org/10.3389/frma.2023.1178181
https://dspace.library.uu.nl/bitstream/handle/1874/435312/frma-08-1178181.pdf?sequence=1
Ferdinands, G., Schram, R., de Bruin, J., Bagheri, A., Oberski, D. L., Tummers, L., Teijema, J. J., & van de Schoot, R. (2023). Performance of active learning models for screening prioritization in systematic reviews: a simulation study into the Average Time to Discover relevant records. Systematic Reviews , 12(1), Article 100. https://doi.org/10.1186/s13643-023-02257-7
https://dspace.library.uu.nl/bitstream/handle/1874/434228/s13643-023-02257-7.pdf?sequence=1

2022

Wetenschappelijke publicaties

Brouwer, M., Hofstee, L., Brand, S. A. G. E. V. D., Teijema, J., Ferdinands, G., Boer, J. D., Weijdema, F., Kramer, B., Wiers, R., Bockting, C., Bruin, J. D., & Schoot, R. V. D. (2022). AI-aided Systematic Review to Create a Database with Potentially Relevant Papers on Depression, Anxiety, and Addiction. PsyArXiv. https://doi.org/10.31234/osf.io/j6nqz
https://research-portal.uu.nl/ws/files/231887774/Mega-Meta_data-paper_pre-print.pdf
ASReview LAB developers (2022). ASReview systematic review datasets. Data set/Database https://github.com/asreview/systematic-review-datasets
ASReview LAB developers (2022). ASReview artwork. Digital or Visual Products https://github.com/asreview/asreview-artwork
ASReview LAB developers (2022). ASReview Makita [version 0.6]. Software https://github.com/asreview/asreview-makita
ASReview LAB developers (2022). ASReview Wordcloud [version 1.0]. Software https://doi.org/10.5281/zenodo.6625855
ASReview LAB developers (2022). ASReview Insights [version 1.0]. Software https://doi.org/10.5281/zenodo.6626070
ASReview LAB developers (2022). ASReview LAB - A tool for AI-assisted systematic reviews [version 1.0]. Software https://doi.org/10.5281/zenodo.6625304
Schram, R., Garcia Bernardo, J., van Kesteren, E.-J., de Bruin, J., & Stamkou, E. (2022). ArtScraper: A Python library to scrape online artworks. Software http://zenodo.org/record/7129975
Teijema, J., Hofstee, L., Brouwer, M., Bruin, J. D., Ferdinands, G., Boer, J. D., Siso, P. V., Brand, S. A. G. E. V. D., Bockting, C., Schoot, R. V. D., & Bagheri, A. (2022). Active learning-based Systematic reviewing using switching classification models: the case of the onset, maintenance, and relapse of depressive disorders. PsyArXiv. https://doi.org/10.31234/osf.io/t7bpd
https://dspace.library.uu.nl/bitstream/handle/1874/437239/Mega-Meta_paper_1_-_Depression_Simulation_Paper_-_2202-07-15.pdf?sequence=1
Bruin, J. D. (2022). Scisort - Sort files in science projects. Software, Zenodo. https://doi.org/10.5281/ZENODO.7265751

2021

Wetenschappelijke publicaties

Teijema, J., de Bruin, J., van de Schoot, R., Hofstee, L., & Bagheri, A. (2021). ASReview wide doc2vec plugin. Software, Zenodo. https://doi.org/10.5281/zenodo.5084877
Ferdinands, G., Gipmans, S., van den Brand, S., de Bruin, J., Cheung, K.-C., & van de Schoot, R. (2021). Results for Simulations of Risk Analysis Documents Medicine Information Centre from the Royal Dutch Pharmacists Association. Data set/Database https://doi.org/10.17605/OSF.IO/KCQHZ
Ferdinands, G., De Bruin, J., van den Brand, S., Cheung, K.-C., Gipmans, S., & Van de Schoot, R. (2021). Scripts for simulation report on risk analyses of the KNMP. Software, Zenodo. https://doi.org/10.5281/zenodo.5771612
Vizán Siso, P., de Bruin, J., van de Schoot, R., Hofstee, L., & Bagheri, A. (2021). Code repository for: "Evaluation of the performance of neural network models and classical models in the context of Active Learning for Systematic Reviewing". Software https://doi.org/10.5281/ZENODO.5161100
Verberg, G., de Bruin, J., van de Schoot, R., Hofstee, L., & Bagheri, A. (2021). Scripts for a simulation on the effect of dataset size on neural network performance for active learning applied to systematic reviewing. Software, Zenodo. https://doi.org/10.5281/zenodo.5112498
Teijema, J., de Bruin, J., van de Schoot, R., Hofstee, L., & Bagheri, A. (2021). ASReview model switcher plugin. Software, Zenodo. https://doi.org/10.5281/zenodo.5084863
Ma, Y., Van de Schoot, R., & De Bruin, J. (2021). Wordclouds: A tool to create a visual impression of the verbal content within a systematic review dataset. Software, Zenodo. https://doi.org/10.5281/zenodo.4672242
Harmsen, W., de Groot, J., Harkema, A., van Dusseldorp, I., De Bruin, J., Van den Brand, S., & Van de Schoot, R. (2021). Scripts for paper on Towards up-to-date medical guidelines. Software, Zenodo. https://doi.org/10.5281/zenodo.5031390
Harmsen, W., de Groot, J., Harkema, A., van Dusseldorp, I., De Bruin, J., Van den Brand, S., & Van de Schoot, R. (2021). Artificial intelligence supports literature screening in medical guideline development: towards up-to-date medical guidelines. (pp. 1-18). Zenodo. https://doi.org/10.5281/ZENODO.5031907
https://dspace.library.uu.nl/bitstream/handle/1874/415177/Artificial_intelligence_supports_literature_screening_in_medical_guideline_development.pdf?sequence=1
Ferdinands, G., Smid, S., van den Brand, S., de Bruin, J., & van de Schoot, R. (2021). Preprocessing systematic review data of Smid et al. (2019) for use in ASReview. Software https://doi.org/10.17605/OSF.IO/PUQ7X
Brouwer, M., Ferdinands, G., van den Brand, S., de Boer, J., de Bruin, J., Schulte-Frankenfeld, P., van de Schoot, R., & Bockting, C. (2021). Systematic review data from “Psychological theories of depressive relapse and recurrence” (Brouwer et al., 2019). Data set/Database https://osf.io/r45yz/
Steegmans, J., & de Bruin, J. (2021). Online housing search dataset: Information flows of real estate platform users. Data in Brief, 38, 1-9. Article 107327. https://doi.org/10.1016/j.dib.2021.107327
https://dspace.library.uu.nl/bitstream/handle/1874/413267/1_s2.0_S2352340921006119_main.pdf?sequence=1
Steegmans, J., & de Bruin, J. (2021). Online housing search: A gravity model approach. PLoS One, 16(3), 1-31. Article e0247712. https://doi.org/10.1371/journal.pone.0247712
https://dspace.library.uu.nl/bitstream/handle/1874/411768/journal.pone.0247712.pdf?sequence=1
van Kesteren, E.-J., Vida, L. J., de Bruin, J., & Oberski, D. (2021). osmenrich - Enrich sf Data with Geographic Features from OpenStreetMaps. Software https://doi.org/10.5281/ZENODO.4548774
Schoot, R. V. D., Bruin, J. D., Schram, R., Zahedi, P., Boer, J. D., Weijdema, F., Kramer, B., Huijts, M., Hoogerwerf, M., Ferdinands, G., Harkema, A., Willemsen, J., Ma, Y., Fang, Q., Hindriks, S., Tummers, L., & Oberski, D. (2021). An open source machine learning framework for efficient and transparent systematic reviews. Nature Machine Intelligence, 3(2), 125-133. https://doi.org/10.1038/s42256-020-00287-7
https://dspace.library.uu.nl/bitstream/handle/1874/411488/s42256_020_00287_7.pdf?sequence=1
de Bruin, J., Ferdinands, G., Harkema, A., de Boer, J., van den Brand, S., Ma, Y., & van de Schoot, R. (2021). ASReview Software Documentation.. Software, Zenodo. https://doi.org/10.5281/zenodo.4287119

2020

Wetenschappelijke publicaties

Ferdinands, G., Schram, R., Van de Schoot, R., & De Bruin, J. (2020). Scripts for 'ASReview: Open Source Software for Efficient and Transparent Active Learning for Systematic Reviews'. Software, Zenodo. https://doi.org/10.5281/zenodo.4024122
Hagenzieker, M. P., Van Der Kint, S., Vissers, L., Van Schagen, I. N. L. G., De Bruin, J., Van Gent, P., & Commandeur, J. J. F. (2020). Interactions between cyclists and automated vehicles: Results of a photo experiment. Journal of Transportation Safety and Security, 12(1), 94-115. https://doi.org/10.1080/19439962.2019.1591556
https://dspace.library.uu.nl/bitstream/handle/1874/411614/Interactions_between_cyclists_and_automated_vehicles_Results_of_a_photo_experiment.pdf?sequence=1
Piper, A., Bijleveld, C., Dennison, S., & Bruin, J. D. (2020). Female and Male Prisoners in Queensland 1880–1899. In M. van der Heijden, M. Pluskota, & S. Muurling (Eds.), Women's Criminality in Europe, 1600–1914 (pp. 148-170). Cambridge University Press. https://doi.org/10.1017/9781108774543.008
https://research-portal.uu.nl/ws/files/235629712/female-and-male-prisoners-in-queensland-1880-1899.pdf
Ferdinands, G., Schram, R., Bruin, J. D., Bagheri, A., Oberski, D. L., Tummers, L., & Schoot, R. V. D. (2020, Sept 16). Active learning for screening prioritization in systematic reviews - A simulation study. OSFPREPRINTS. https://doi.org/10.31219/osf.io/w6qbg
https://dspace.library.uu.nl/bitstream/handle/1874/415518/manuscript_Ferdinands.pdf?sequence=1
Viola, L., & de Bruin, J. (2020). Visualising changes in the construction of meaning with Word Vector Space. Software https://doi.org/10.5281/ZENODO.4264496
van de Schoot, R., & de Bruin, J. (2020). Researcher-in-the-loop for systematic reviewing of text databases (video). Digital or Visual Products, Zenodo. https://doi.org/10.5281/zenodo.4013207
van de Schoot, R., de Bruin, J., Schram, R., Zahedi, P., de Boer, J., Weijdema, F., Kramer, B., Huijts, M., Ferdinands, G., Harkema, A., Fang, Q., & Oberski, D. L. (2020). Extension for COVID-19 related datasets in ASReview.. Software, Zenodo. https://doi.org/10.5281/zenodo.3764749
van de Schoot, R., de Bruin, J., Schram, R., Zahedi, P., de Boer, J., Weijdema, F., Kramer, B., Huijts, M., Hoogerwerf, M., Ferdinands, G., Harkema, A., Willemsen, J., Ma, Y., Fang, Q., Tummers, L., & Oberski, D. L. (2020). ASReview: Active learning for systematic reviews.. Software https://doi.org/10.5281/zenodo.3345592

2019

Wetenschappelijke publicaties

Viola, L., & de Bruin, J. (2019). The GeoNewsMiner (GNM): An interactive spatial humanities tool to visualize geographical references in historical newspapers. Software https://doi.org/10.5281/ZENODO.3484591
de Bruin, J. (2019). Python Record Linkage Toolkit: A toolkit for record linkage and duplicate detection in Python. Software https://doi.org/10.5281/ZENODO.3559042

2018

Wetenschappelijke publicaties

Vlakveld, W., van Nes, N., de Bruin, J., Vissers, L., & van der Kroft, M. (2018). Situation awareness increases when drivers have more time to take over the wheel in a Level 3 automated car: A simulator study. Transportation Research Part F: Traffic Psychology and Behaviour. https://doi.org/10.1016/j.trf.2018.07.025

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