Maths, modelling and quantitative biology

The diverse group of modellers and mathematical biologists in EPI has now reached critical mass with some 15 in-house researchers and students. They direct a range of concepts and tools to questions in systems biology, at scales of organ, individual and community, and in applications as diverse as plant-plant sensing, multi-trophic interactions, ‘industrial’ genotypes and GM coexistence policy.

Modelling and various mathematical approaches now permeate much of the science and some of the applications in EPI. A common and defining feature of the work is the exploration of 'the individual' in 'the system', in which the interactions among individual organisms, organs or cells give rise to emergent properties not predictable from the characteristics of the individuals themselves. Biologists, modellers and software developers combine their skills to address central and essential challenges in modern biology. The examples below are of current work (main funders in parenthesis).

Data mining techniques for analysing complex simulation models

Individual-based models of plant populations and communities can be highly complex, reflecting the underlying dynamics of the natural systems under study. Analysing and understanding model behaviour can be extremely challenging. To address this we are collaborating with researchers from the Department of Knowledge Technologies of the Jožef Stefan Institute, Slovenia on the application of data mining and machine learning techniques to the analysis of the IBMs we have developed.

Model analysis

Machine learning methods are being used to analyse the relationship between simulation outputs with IBM inputs (model parameters) in order to gain insight into the behaviour of the model system. Here we rely on a Monte Carlo approach in which simulations are based on IBM parameter values sampled at random from across a predefined parameter space. By applying machine learning methods, we can generalise over the specific simulations made and derive more general rules concerning the behaviour of the system.

Plant population and community modelling

The objective of plant population and community modelling in the Agroecology group is to understand, and where necessary anticipate, the effects on arable vegetation of technical innovations and global change, and thereby to understand the role of the vegetation in the sustainability of the arable system as a whole.  System-level responses, such as primary production, nutrient retention and biodiversity, emerge over time, often unpredictably, from complex ecological and evolutionary processes. By developing models of plant populations and communities, we are able to assess the response of arable vegetation in a way that can't be addressed by experiment or observation alone.

Our current focus is the influence of the genetic and functional characteristics (life-history traits or their physiological determinants) of plants on system-level properties. A common thread is the definition of populations and communities in terms of the genetic and functional variation of individuals. Using the individual enables intra- and inter-specific variation to be presented on a common scale and both ecological and evolutionary processes to be combined in a single model framework.

Trait characterisation in crops

Photograph of growing-tubes in SCRI glasshousesCrop productivity has increased dramatically in recent decades through a combination of improved arable management and breeding of higher yielding crop genotypes.

Further increases in productivity are needed to cope with growing demands for food. The price, availability and high energy costs (carbon footprint) of inorganic fertiliser mean that food production will need to be achieved with fewer chemical inputs and with greater emphasis on a sustainable approach to arable cropping. 

New crop genotypes that require less chemical fertiliser and pesticide for a given level of yield could be developed by characterising plant traits associated with reduced nutrient requirements and high pest tolerance.

Contact: Alison Karley

Multi-Trophic Interactions

Photograph of a beetle on chicory flowerMulti-trophic Interactions is a new major research topic in Agroecology that combines existing lines of study at both SCRI and the University of Dundee. Trophic (or feeding) interactions drive the cycling of energy and nutrients in farmland. Insects and other invertebrates feed on plants and in turn are fed on by other insects, spiders, various symbionts, pathogens and vertebrates. A very small proportion of the total species in trophic interactions are pests of agriculture. Most mediate processes that are essential to the cropping cycle, such as the breakdown of dead organisms (crops, weeds, wood, animals), the regulation of pests and the pollination of flowers. These trophic interactions are exceedingly complex and are studied using advanced concepts and methods in organism biology, molecular biology and mathematical modelling.  Through gaining basic knowledge, the topic aims to provide a scientific basis for future management of invertebrate populations in farmland.

Plants and plant communities

Photograph of happy field workers sampling plantsResearch in Plants and Plant Communities aims to define those properties of crops and arable plants that would maintain yield and the purity of yield while reducing the environmental footprint of cropping. The work includes basic studies of plant processes such as germination, flowering and nutrition, genetic and physiological variation in model crops and arable plants, the ecology of plant (seedbank) communities, plants as the base of the arable food web and models of geneflow, selection and evolution. The practical output will be combinations of plant traits that can be targeted in crop improvement or encouraged by agronomy. Disciplines and methods include plant physiology, genetics, statistics, modelling, microscopy and field survey.

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