Newcastle University Systems Modelling of Ageing

We will systematically analyse large datasets of multiple types to: (i) identify key components affected by age or experimental perturbation; (ii) establish networks of interaction; (iii) develop dynamic computational models based on these networks; (iv) use model selection methods to discriminate between alternative network topologies and generate predictive models. To characterise the data, we will apply an ensemble of methods, including frameworks in R/Bioconductor and toolboxes connected via ...

This project aims to develop an agent based model using the Netlogo package which can then be used for outreach in schools and the wider community. This model represents cellular senescence in skin with the potential for users to explore the effects of combination treatments in silico.

Web application developed using RStudio-Shiny for outreach. Incorporates information, videos and images, worksheets and simulations surrounding cellular senescence and therapy. Incorporates NetLogo simulation from "Outreach - Simulation of cellular senescence using an agent based modelling approach" project.

Overall, we will measure in-vitro and model in-silico the short-term biochemical network dynamics of extra cellular matrix maintenance (ECM) in populations of young, old and senescent dermal fibroblasts. We have shown in previous work that differences in network dynamics are highly informative and provide a means to identify parts of the network that could be targeted to restore healthy function.

The work will be first carried out in 2D culture of human dermal fibroblasts then extended to a novel ...

MicroRNAs are a recently discovered group of factors that control cell behaviour. There are thousands of microRNAs, but specific ones control the behaviour of cartilage cells and have key roles in osteoarthritis. Changing the level of a single microRNA can alter osteoarthritis, but we know that several microRNAs change during disease. The group has identified four microRNAs which have key roles in cartilage. This programme seeks:

to show that these microRNAs have a role in osteoarthritis in the ...

Small set of values for entering into NetLogo Simulation

Very simple unrealistic values for Metformin kinetics (Km). For use in a simple graphical model.

Very simple unrealistic values for Fisetin kinetics (Km). For use in a simple graphical model.

desktop version of NetLogo model of cellular senescence in dermal layer of skin

fifth worksheet for RStudio-Shiny application, relating to the following pages:

simulation2 concluding question (all pages, simulations, worksheets)

fourth worksheet for RStudio-Shiny application, relating to the following pages:

Therapies and senescence simulation1

third worksheet for RStudio-Shiny application, relating to the following pages:

Senescence in tissue biology

second worksheet for RStudio-Shiny application, relating to the following pages:

Cellular senescence

first worksheet for RStudio-Shiny application, relating to the following pages:

Systems Biology