Demonstrations
Demonstrations of the project's developing infrastructure and scientific achievements are given at appropriate conferences such as the annual EPSRC e-Science Programme Meeting in the spring and the e-Science All Hands Meeting in the autumn. Besides providing a good focus for development within the project team, these demonstrations help to disseminate news of the significant scientific progress which use of e-Science technology is achieving in this area to the broader research community in the UK.
Demonstrations given by June 2005 include:
- Job submission, via the prototype Integrative Biology portal, of the Tulane ventricular model to
the NGS node in Oxford using SRB on the NGS node at RAL to store input and output files, an adapted
version of Meshalyser to visualise results and the Integrative Biology visualisation service to make
a movie of the simulation
Episode of shock-induced arrhythmogenesis in the ventricles simulated using the Tulane whole ventricular model running on the NGS with data stored in SRB. This shows the transmembrane potential distribution on the epicardium or in a transmural view of the ventricles at the time of shock delivery, the end of the shock 8ms later and 100ms post-shock. RV and LV refer to right and left ventricles respectively and arrows show the direction of wave propagation.
A screenshot of the IB tools in use showing model visualization with Meshalyser - Job submission and steering of a single simulation for the Cardiac Virtual Tissue model developed by Richard Clayton
at Sheffield. In this case, it is using a Fenton-Karma 4 variable model on a 2D slice of tissue. The simulation executes
remotely, for example on an NGS or White Rose Grid compute node, and the client shows the state of the 4 model variables
using a greyscale image, where the value of the variable is mapped to intensity, white being large. The left hand side
of the figure below shows the steering controls for both starting/stopping the simulation and viewing/altering the simulation
parameters. The client was built in Matlab and the model is coded in C with gViz middleware providing the discovery and
communication. Further research is investigating methods for providing a single visualisation of all the model variables
simultaneously.
- The screenshot below shows the first multiple simulation client for the 2D Cardiac Virtual Tissue model. In this case the
simple Barkley model is used, as written by Simon Scarle at Sheffield, and multiple runs have been spawned onto an NGS compute
node. Each simulation can be paused/continued through this client, and this demonstration simply provides a method of
monitoring and controlling many runs on a remote resource. In this instance all the models are using the same parameters,
but have staggered starting times.
- Job submission using a Matlab interface developed by Integrative Biology based in part on software from the Geodise project to run an Oxford tissue deformation code on the NGS with visualisation of results using a stereo monitor