Biomathematics and Statistics Scotland
JCMB, The King's Buildings, Peter Guthrie Tait Road,
EDINBURGH, EH9 3FD, Scotland, UK.
I lead the Process and Systems Modelling team at BioSS as well co-leading the Large Scale and Sectoral Modelling theme on the RESAS strategic research programme. I develop process-based models of biological systems, generally using ordinary or delay differential equations. Since joining BioSS my research has focussed on two main topics - microbial communities and crop pests (see below).
My current research includes two scottish government funded (RESAS) projects (Large-scale and Systems modelling and Biodiversity and Ecosystem Tools) as well as UKRI projects funded by BBSRC (Modelling the impact of cabbage stem flea beetle on oilseed rape crops) and a NERC funded project on Quantifying the impact of anthropogenic nutrient imbalance on carbon flux from freshwater lakes.
I am also the Open Science Champion at BioSS. Sharing my work is others is very important to me and I endeavour to release all of my code in user-friendly packages where possible - please see my software page and my github repo for more info.
Modelling Microbial Communities
I am interested in the dynamic modelling (based on ordinary differential equations) of microbial communities in the human colon. Particularly in modelling the emergent dynamics of these complex systems.
Royal Society Blog post on modelling gut microbes
Microbial case studies: Modelling Gut Bacteria, Diversity maintenance through pH self-regulation
- R package microPop for modelling microbial communities.
- R Shiny App to visualize the microbial networks contained in microPop.
- Kettle H, P Louis, HJ Flint, 2022. Process-based modelling of microbial community dynamics in the human colon. Journal of the Royal Society Interface. 19: 2022048920220489 doi.org/10.1098/rsif.2022.0489
- Kettle H, G Holtrop, P Louis, HJ Flint. 2018. microPop: Modelling microbial populations and communities in R. Methods in Ecology and Evolution, 9 (2), p399-409. doi: 10.1111/2041-210X.12873
- Kettle H, P Louis, G Holtrop, S. Duncan, HJ Flint. 2015. Modelling the Emergent Dynamics and Major Metabolites of the Human Colonic Microbiota. Environmental Microbiology, 17, 1615-1630.
Modelling Crop Pathogens
I have worked on a number of projects involving modelling crop pests, e.g., potato cyst nematodes (PCN), rice pests (LEGATO project) and more recently the cabbage stem flea beetle. These all involve stage-structured populations which I model using time-delay differential equations or integro-differential equations. I have written an R package (stagePop - see below) which solves these type of equations for a wide range of pests and can also include pest-predator-parasitoid interactions.
Software: stagePop: an R-package to model stage-structured populations and any number of interacting populations (e.g. parasitoids and predators).
- Ewing, D.A., V. Blok and Kettle, H.. 2021. A process-based, stage-structured model of potato cyst nematode population dynamics: Effects of temperature and resistance. Journal of Theoretical Biology v 522. DOI: https://doi.org/10.1016/j.jtbi.2021.110701
- Kettle, H., C. Sann and G. Marion. 2019. Quantifying parasitoid and predator controls on rice hopper eggs using a dynamic stage-structured model and field data. Journal of Applied Ecology v 56 (11) p2536-2550. DOI: https://doi.org/10.1111/1365-2664.13473
- Kettle H & D Nutter. 2015. stagePop: Modelling stage-structured populations in R. 2015. Methods in Ecology and Evolution, 6, 1484-1490.