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Computational and Data Resources

As part of our research at the Kennedy Institute, we have developed high quality data sets, computational models and tools which we make available to the community.

Computational Tools

CXCL13Sim

A hybrid multiscale simulator that captures the migration of B cells in response to the chemokine CXCL13 within a lymph node follicle. 

ARTIMMUS (artificial murine multiple sclerosis simulation)

The ARTIMMUS simulation is an agent-based simulation of experimental autoimmune encephalomyelitis, a T-cell mediated autoimmune disease. 

 

ARTOO (Argumentation Tool)

Within YCIL we have developed a tool to enable the construction of logical arguments to support our simulations. This tool enables you to build and manipulate a graphical structure consisting of text-containing nodes and arrows that represents your argument. Specifically, it uses the syntax of the Goal Structuring Notation. Structures can be saved to file and exported as PNG images.

 

ASPASIA

Calibrating computational models of biological systems, assigning parameter values to ensure the model reflects behaviours observed biologically, can greatly impact the strength of hypotheses the model generates. A calibrated model provides baseline behaviour upon which sensitivity analysis techniques can be used to analyse potential pathways impacting model response. 

 

PPSim (Peyer's Patch Development Simulator)

Adopting an agent-based modelling approach, we have developed a simulator that captures the development of lymphoid organs in the gut: Peyer's Patches. 

 

Spartan

Successful integration of computer simulation with real world experimentation requires the relationship between simulation and the real-world system to be established.