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
- Scientific Coordinator / PI
- Work Package member (simulation, modelling and data analytics)
Past research projects
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)
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