Visualizing physiological data: you need to see it to believe it

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About Visualizing physiological data: you need to see it to believe it


MSc internship project co-supervised by Dr B.G. Olivier ([1]) and Dr M. Swat ([2]).

How do we make computer models in biology and medicine useful? One answer to this question has been the use of so called whole-body models to try to understand the causes and progression of multi-factorial diseases, e.g. metabolic syndrome, cancer, etc. However, working with such models is complicated by the fact that we cannot easily interpret the data generated by them using traditional methods (multi-plot graphs etc.). Therefore, a new approach is required which takes into consideration that these models consist of multiple compartments (organs) which can contain detailed kinetic descriptions of their function and that all of these are connected by circulatory system.

This then is the main focus of this project: to develop an interactive software module specifically tailored for the visualisation of model data generated by physiological, multi-compartment models. In the process of development the prospective candidate will also be working with an example of such physiological model and will thereby gain exposure to the field of Computational Systems Biology. The general software specification is as follows and should include:

  • a flexible, interactive, graphical user interface that allows for the viewing of data in traditional (i.e. graphs) as well as new forms (e.g. as values on images of the module(s) of interest),
  • be able to load models (and associated images) using a standard input format (to be developed),
  • have the ability to accept data from static data sources such as from text files, SQL database data or live data streams from a network resource e.g. a TCP/IP based interface using an XML data representation (or equivalent).

It is important that this software allow for cross-platform usage and therefore, ideally, should be developed in a language capable of utilising the Qt libraries ([3]) (C++, Java, Python).