CV
Education
- Doctoral Student in Atmospheric Sciences, University of Helsinki, Finland, 2023-2027 (expected)
- MSc in Theoretical and Computational Methods, University of Helsinki, Finland, 2021-2023
- MEng in Computing, Imperial College London, United Kingdom, 2017-2021
- Allgemeine Hochschulreife, Hans-Sachs Gymnasium Nürnberg, Germany, 2009-2017
Language Skills
- German (native)
- English (C2)
- French (B1+)
Work Experience
- 2023/05-: Doctoral Researcher
- University of Helsinki, Institute for Atmospheric and Earth System Research
- Investigating safe lossy data compression for weather and climate model data
- Supervisors:
- Prof. Heikki J. Järvinen, University of Helsinki
- Dr Milan Klöwer, University of Oxford
- Thesis Committee:
- Prof. Michale Boy, University of Helsinki, LUT University
- Prof. James Rosindell, Imperial College London
- Dr Holger Pirk, Imperial College London
- 2022/09-2023/04: Research Assistant
- University of Helsinki, Institute for Atmospheric and Earth System Research
- Investigated Out-of-Distribution Detection, Uncertainty Quantification, and Response Surface Modelling for a 1D atmospheric transport chemistry and aerosol process model, SOSAA
- Implemented a graphical user interface to configure and run the SOSAA model
- Supervisors:
- Prof. Michael Boy, University of Helsinki, LUT University
- Dr Andreas Rupp, LUT University
- Petri Clusius, University of Helsinki
- 2022/05-2022/09: Research Assistant
- University of Helsinki, Department of Computing
- Investigated dimensionality reduction for eXplainable AI for molecular data
- Implemented a WebAssembly-based serverless data analysis and visualisation platform, xiplot
- Supervisors:
- Prof. Kai Puolamäki, University of Helsinki
- Anton Björklund, University of Helsinki
- 2020/04-2020/09: Industrial Placement
- EMBL-EBI (European Bioinformatics Institute)
- Automated and streamlined the curation process of the identifiers.org platform
- Supervisors:
- Henning Hermjakob, European Bioinformatics Institute
- Manuel Bernal Llinares, European Bioinformatics Institute
- 2019/08-2019/09: Undergraduate Research Opportunity
- Imperial College London, Department of Life Sciences
- Investigated neutral simulations of species richness and extended the analytical description to account for endemic islands and the transition from endemicity to migration
- Co-implemented the Gillespie algorithm as an optimisation to the coalescence simulation
- Supervisors:
- Prof. James Rosindell, Imperial College London
- Dr Lucas D. Fernandes, Imperial College London
- 2017-2021: Group leader in curriculum group projects
- Imperial College London, Department of Computing
- Developed & optimised a scalable peer-to-peer collaborative drawing Web App using conflict-free replicated data types (CRDTs) and WebRTC
- Iteratively designed and user-tested the first prototype for the Octopus science publishing platform, https://www.octopus.ac/
- Developed an optimising compiler with an error recovering frontend for the WACC language in Rust
- Implemented system-level thread scheduling, system calls and virtual memory for PintOS in C
- Created an assembler and emulator for the Raspberry Pi and its GPIO pins in C to develop a game
Teaching Experience
Career Breaks
- Parental Leave, 2023/11-2024/01 (full-time), 2024/01-2025/07 (part-time)
Funding
- 2023-2026: 100% PhD salary, from: ESiWACE3, Center of excellence for weather and climate phase 3. Horizon EuroHPC. Available from: doi:10.3030/101093054.
Publications
Journal Articles
A decoupled, modular and scriptable architecture for tools to curate data platforms
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.
Conference Papers
χiplot: Web-First Visualisation Platform for Multidimensional Data
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.
Theses
Prudent Response Surface Models: Exploring a Framework for Approximating Simulations with Confidence and Certainty
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.
Communication-free and Parallel Simulation of Neutral Biodiversity Models
Tyree, J. (2021) Communication-free and Parallel Simulation of Neutral Biodiversity Models. Master’s Thesis. Available from: doi:10.48550/arXiv.2108.05815.
Technical Reports
ESiWACE3 Deliverable D3.3 - Report on the online version of the data sets
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.
Preprints
phepy: Visual Benchmarks and Improvements for Out-of-Distribution Detectors
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.
Presentations
An Online (Compression) Laboratory for Climate Science and Meteorology
Invited Presentation at CASTIEL2 Code of the Month, Online
Online Laboratory for Data Compression in Climate Science and Meteorology
Conference Presentation at Finnish National Hydrological and Climate Modelling Seminar, Finnish Meteorological Institute, Helsinki, Finland
Can General Circulation Toy Models run with lossy-compressed states?
Conference Presentation at 2024 OpenIFS User Meeting, Online
Professional Contributions
- Convener: Bouvier, C., Co-Conveners: Ray, W., Santoro, M., Tyree, J., Borejko, W., Tinto, O., Faghih-Naini, S. (05/2025). Big Data in Earth System Sciences: The Challenges of Data Compression & Data Spaces in the cloud computing era. EGU25 Session ESSI2.13. Available from: https://meetingorganizer.copernicus.org/EGU25/session/52084 [Accessed: 17th March 2025]
Awards and Honours
- Governor’s MEng Prize in Computing to the final year student with the best overall performance, Imperial College London, 2020-2021
- Dean’s List (Year 4), Imperial College London, 2020-2021
- Aspect Capital Prize for an outstanding final year undergraduate individual projectImperial College London, 2020-2021
- Dean’s List (Year 3), Imperial College London, 2019-2020
- G-Research Prize for academic excellence, Imperial College London, 2019-2020
- David Howarth Group Project Prize for excellence in group projects in the third year, Imperial College London, 2019-2020
- G-Research Prize for academic excellence, Imperial College London, 2018-2019
- Olav Beckmann Project Prize for outstanding 2nd-year laboratory project work, Imperial College London, 2018-2019
- Computing Entrance Scholarship, Imperial College London, 2017-2018