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A decoupled, modular and scriptable architecture for tools to curate data platforms

Published in Bioinformatics, 2021

cmd-iaso is a decoupled, modular and scriptable curation tool built on top of the existing identifiers.org platform.

Recommended citation: Tyree, J. & Hermjakob, H. & Llinares, M. B. (2021) A decoupled, modular and scriptable architecture for tools to curate data platforms. Bioinformatics. btab233. Available from: doi:10.1093/bioinformatics/btab233.
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Communication-free and Parallel Simulation of Neutral Biodiversity Models

Published in Imperial College London, 2021

necsim-rust implements a novel communication-free algorithm for individual-based probabilistic neutral biodiversity simulations.

Recommended citation: Tyree, J. (2021) Communication-free and Parallel Simulation of Neutral Biodiversity Models. Master’s Thesis. Available from: doi:10.48550/arXiv.2108.05815.
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Prudent Response Surface Models: Exploring a Framework for Approximating Simulations with Confidence and Certainty

Published in University of Helsinki, 2023

The Icarus Response Surface Model architecture combines an out-of-distribution detector, a prediction model, and an uncertainty quantifier.

Recommended citation: Tyree, J. (2023) Prudent Response Surface Models: Exploring a Framework for Approximating Simulations with Confidence and Certainty. Master’s Thesis. Available from: URN:NBN:fi:hulib-202305151941.
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phepy: Visual Benchmarks and Improvements for Out-of-Distribution Detectors

Published in arXiv, 2023

phepy is a benchmark for out-of-distribution detection, which includes three novel and easily-visualisable toy examples.

Recommended citation: Tyree, J., Rupp, A., Clusius, P. S., Boy, M. H. (2023) phepy: Visual Benchmarks and Improvements for Out-of-Distribution Detectors. Preprint. Available from: doi:10.48550/arXiv.2503.05169.
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χiplot: Web-First Visualisation Platform for Multidimensional Data

Published in Lecture Notes in Computer Science, 2023

χiplot is an HTML5-based system for interactive exploration of data and machine learning models.

Recommended citation: Tanaka, A., Tyree, J., Björklund, A., Mäkelä, J., and Puolamäki, K. (2023) χiplot: Web-First Visualisation Platform for Multidimensional Data. In: De Francisci Morales, G., Perlich, C., Ruchansky, N., Kourtellis, N., Baralis, E., Bonchi, F. (eds) Machine Learning and Knowledge Discovery in Databases: Applied Data Science and Demo Track. ECML PKDD 2023. Lecture Notes in Computer Science, 14175. Available from: doi:10.1007/978-3-031-43430-3_26.
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ESiWACE3 Deliverable D3.3 - Report on the online version of the data sets

Published in Zenodo, 2024

This deliverable documents the development of an Online Laboratory for Data Compression in Climate Science and Meteorology and the publication of the data compression datasets that allow the testing of various compression methods for output of both weather and climate models.

Recommended citation: Faghih-Naini, S., Tyree, J., Yepes-Arbós, X., Peters-von Gehlen, K., Dueben, P., Järvinen, H. J. (2024) ESiWACE3 Deliverable D3.3 - Report on the online version of the data sets. Available from: doi:10.5281/zenodo.14622238.
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Can General Circulation Toy Models run with lossy-compressed states?

Published: May 15, 2024

Tyree, J. & Ekblom, M. (15.05.2024) Can General Circulation Toy Models run with lossy-compressed states? 2024 OpenIFS User Meeting. Available from: doi:10.5281/zenodo.14095029.

Online Laboratory for Data Compression in Climate Science and Meteorology

Published: November 20, 2024

Tyree, J., Faghih-Naini, S., Dueben, P., Peters-von Gehlen, K., Järvinen, H. J. (20.11.2024) Online Laboratory for Data Compression in Climate Science and Meteorology. Finnish National Hydrological and Climate Modelling Seminar. Available from: doi:10.5281/zenodo.14191942.

An Online (Compression) Laboratory for Climate Science and Meteorology

Published: February 19, 2025

Tyree, J., Faghih-Naini, S., Dueben, P., Peters-von Gehlen, K., Järvinen, H. J. (19.02.2025) An Online (Compression) Laboratory for Climate Science and Meteorology. CASTIEL2 Code of the Month #14. Available from: doi:10.5281/zenodo.15024552.

2019 PPT Undergraduate Teaching Assistant

Undergraduate course, Imperial College London, Department of Computing, 2019

• 2019/10 - 2020/03
• Weekly tutoring a group of eight first-year Joint-Maths-and-Computing students
• Grading and giving feedback on their Haskell and Java computing lab exercises
• Responsible Teacher: Dr Marek Rei

2023 Sustainable.now Teaching Assistant

Undergraduate course, University of Helsinki, Institute for Atmospheric and Earth System Research, 2023

• 2023/09 - 2023/10
• Weekly feedback on the learning diaries of the >30 students
• Assist in supervising the group projects
• Responsible Teachers:
  • Dr Bernhard R. Reischl, University of Helsinki
  • Joula O. Siponen, University of Helsinki
  • Dr Janne J. Salovaara, University of Helsinki
  • Dr Ivo Neefjes, University of Helsinki
  • Dr Ásványi Katalin, Corvinus University of Budapest

2024 Numerical Meteorology I Teaching Assistant

Graduate course, University of Helsinki, Institute for Atmospheric and Earth System Research, 2024

• 2024/01 - 2024/03
• Weekly exercise sessions
• Grading and feedback for the exercises
• Helped prepare and supervise the exam
• Responsible Teachers:
  • Dr Madeleine Ekblom, University of Helsinki
  • Prof. Heikki J. Järvinen, University of Helsinki

2025 Numerical Meteorology I Co-Teacher

Graduate course, University of Helsinki, Institute for Atmospheric and Earth System Research, 2025

• 2025/01 - 2025/03
• Presented two lectures, on sustainable scientific model software development and boundary conditions in the shallow water model
• Developed new grading rubrics and hints for the exercises
• Weekly exercise sessions
• Grading and feedback for the exercises
• Prepared, supervised, and graded the exam
• Responsible Teachers:
  • Prof. Heikki J. Järvinen, University of Helsinki
  • Juniper Tyree, University of Helsinki

2025 Numerical Meteorology II Teaching Assistant

Graduate course, University of Helsinki, Institute for Atmospheric and Earth System Research, 2025

• 2025/03 - 2025/05
• Weekly exercise sessions
• Grading and feedback for the exercises
• Responsible Teachers:
  • Prof. Heikki J. Järvinen, University of Helsinki