Computational Modelling Group

IfLS

The Institute for Life Sciences represents a University-wide multidisciplinary collaboration drawing together expertise in science and engineering, with a shared goal to apply scientific discovery to the grand challenges of the day. The Institute's mission is to facilitate fusions of expertise in education and research from a range of disciplines, in order to broaden scientific opportunities.

For more information, please visit: http://www.soton.ac.uk/ifls/

For queries about this topic, contact Richard Edwards.

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Projects

A spatially-explicit agent-based model of jaguar population dynamics

Jason Noble, Patrick Doncaster (Investigators), Angela Watkins

A single species spatially-explicit agent-based model has been developed that illustrates the role of simulation modelling, integrated with an adapted least-cost modelling approach and real-world geographical data, in exploring jaguar population dynamics.

Agent-based simulations of jaguar movements through conservation corridors

Jason Noble, Patrick Doncaster (Investigators), Angela Watkins

We present an agent-based model of jaguars (Panthera onca),
scaled for fragmented habitat in Belize where proposals already exist for creating a jaguar corridor. We use a least cost approach to simulate movement paths through alternative possible landscapes.

Image Based Modelling of Fluid Flow through Lymph Nodes

Tiina Roose, Bharathram Ganapathisubramani, Geraldine Clough (Investigators), Laura Cooper

In this project we are using images of mouse lymph nodes to investigate the fluid transport pathways through it. The images of the nodes are taken using selective plane illumination microscopy, and synchrotron micro computed tomography. The fluid flow is modelled using Darcy's law in COMSOL Multiphysics and the models are run on the Iridis cluster.

Integrating least-cost models with agent-based simulations: example hedgehog responses to fragmented landscapes

Jason Noble, Patrick Doncaster (Investigators), Angela Watkins

This study presents a novel analysis of an agent-based model of hedgehog movements integrated with a least-cost model of hedgehog dispersal and validated in landscapes with a varying degree of habitat fragmentation. A comparison of the fitness of individual agents reveals that incorporating a simple rule into
individual agents, to better mimic movement choices by real hedgehogs, dramatically affects the relationship between individual fitness and fragmentation.

Investigations of Lymphatic Fluid Flow

Tiina Roose, Bharathram Ganapathisubramani, Geraldine Clough (Investigators), Laura Cooper

The lymphatic system performs three main roles returns interstitial fluid back into the blood stream to maintain tissue fluid homeostasis. The aim of this project is to increase our understanding of how the lymph flows through the system by creating three dimensional fluid structure interaction models of the secondary lymphatic valves and image based models of lymph nodes.

Tag based transcriptome analysis of gene expression in a promising green algae

Richard Edwards (Investigator), Andreas Johansson

We use SuperSAGE in combination with next-generation sequencing to compare differences in gene expression between selected mutants and the wild type of a green algae. The data in the form of millions of 26 bp tags representing short stretches of expressed genes, will be analysed to find patterns of variation in gene expression under different conditions.

People

Geraldine Clough
Professor, Medicine (FM)
Bharathram Ganapathisubramani
Professor, Engineering Sciences (FEE)
Peter Smith
Professor, Institute for Life Sciences (FHS)
Patrick Doncaster
Reader, Biological Sciences (FNES)
Nicolas Green
Reader, Electronics and Computer Science (FPAS)
Rohan Lewis
Reader, Medicine (FM)
Tiina Roose
Reader, Engineering Sciences (FEE)
Fraser Sturt
Senior Lecturer, Humanities (FH)
Jane Gibson
Lecturer, Biological Sciences (FNES)
Alistair Bailey
Research Fellow, Medicine (FM)
Jason Noble
Research Fellow, Electronics and Computer Science (FPAS)
Laura Cooper
Postgraduate Research Student, Engineering Sciences (FEE)
Andreas Johansson
Postgraduate Research Student, National Oceanography Centre (FNES)
Sonya Ridden
Postgraduate Research Student, Mathematics (FSHS)
Angela Watkins
Postgraduate Research Student, Biological Sciences (FNES)
Matthew Higgins
Undergraduate Research Student, Biological Sciences (FNES)
Richard Edwards
Alumnus, University of New South Wales, Australia