Research and technical projects
This page offers short descriptions of projects I am currently involved in or have previously worked on.
Current research projects
BioDT
Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities
- Funding: Horizon Europe (€11M)
- Period: 2022 - 2025
- Coordinator: CSC - IT Center for Science Ltd
Description
BioDT seeks to develop prototype digital twins to push the current boundaries of our understanding of biodiversity dynamics, leveraging the LUMI supercomputer.
Tasks
- Project Manager / PI
- Work Package member (simulation, modelling and data analytics)
PerMedCoE
HPC / Exascale Centre of Excellence in Personalised Medicine
- Funding: Horizon Europe (€5M)
- Period: 2020 - 2023
- Coordinator: Barcelona Supercomputing Center
Description
PerMedCoE seeks to improve the usability and compatibility of key personalised medicine modelling tools with next-generation exascale supercomputing systems.
Tasks
- Work Package Lead (analytical workflows)
- Organising Committee Member (2023 PerMedCoE Summer School)
LIFEPLAN
- Funding: ERC (€12M)
- Period: 2020 - 2026
- Coordinator: University of Jyväskylä
Description
LIFEPLAN aims to establish the current state of biodiversity across the globe and to use the insights for generating accurate predictions of its future state under future scenarios.
Tasks
- Collaborator (upscaling of data analysis tools for high-performance computing)
Past research projects
Postdoctoral projects
Topics I have worked on as part of postdoctoral positions (2012-2019) include:
- Planetary limits for life and the habitability of multi-extreme environments (funding: STFC)
- Bioinformatics as part of NASA BASALT (Biologic Analog Science Associated with Lava Terrains)
- Metabarcoding as a tool for monitoring ecosystem health (funding: Academy of Finland)
Environment maintenance & design
r-env
R / RStudio container on Puhti supercomputer
Description
r-env is an Apptainer container including R, RStudio Server and TensorFlow. Many of the 1300+ R packages included offer support for parallel computing (including MPI jobs) and geospatial analyses.
Tasks
2019-2022:
- Design, implementation and maintenance on Puhti (Finnish national supercomputing cluster)
- Research support (500+ users) and maintaining technical user documentation
- R environment design for the CSC Sensitive Data Desktop
Chipster microbiome analysis
Semi-automated tools for microbial community metabarcoding analysis
Description
Chipster is a user-friendly analysis software for next-generation sequencing data, such as scRNA-seq, RNA-seq, ChIP-seq and microbial community metabarcoding data.
Tasks
2019-2021:
- Developed a semi-automated toolbox for OTU-based microbial community comparisons