IST has played a significant role in developing the software behind Physiomics, the leading edge biosciences company located in the U.K.'s Oxford Science Park. Physiomics developed SystemCell, a modelling and simulation system, to accelerate and improve the development of pharmaceutical products and to solve problems that would otherwise be addressed through more traditional laboratory techniques.

SystemCell is a flexible modelling product that enables scientists to create, enhance and maintain biochemical models. The shape, structure and behaviour of individual components is completely customizable, giving users of the product full control. Modelling components can be turned into templates, simplifying the task of creating new models by enabling fragments of previous models to be reused.

A graphical view of the components in a model showing the interconnection between components as well as their hierarchical structure	A view of the components in a model, as described within SystemCell

Note that clicking on any of the images on this page will display them larger in a new window.

IST became the Physiomics technology partner in 2001. The combination of IST's expertise in the range of areas needed for this project and the cutting edge technology requirements of Physiomics has resulted in some exciting developments in the features of SystemCell.

The majority of the modelling work takes place using the Java-based modelling tool. This platform-independent application can be used on any workstation to create and maintain SystemCell models. Models are constructed visually, using a "drag and drop" style interface in tandem with a set of configuration menus and a powerful scripting language. IST has applied its proven Java and user interface skills to make major improvements to this application.

The back-end of the system is a high performance modelling engine. This verifies the structure of a user's model, executes simulations and generates result sets that can then be analysed and visualized.

IST's C++ and Microsoft skills have enabled the modelling engine to provide additional simulation features to users of SystemCell. An example of this work is the Dynamic Modelling capabilities that IST added to SystemCell, enabling parameters of a model to be altered in real-time while the model is being executed.

IST also added the Visualization tool which gives a 3D view of the state of a mathematical model. The Vizualization tool loads a 3D model specified in XML and then animates the model using information from a data stream read from a file or socket. The screen shots below show an animation of a model using a schematic diagram of a cell, showing genes, promoters and products.

View of the model	Flying into the model	A graph of the model's state

In summary, IST's activities on the Physiomics project have included:

• Determining the scientific requirements and studying how the software package can best be shaped to meet them.
• Project management of a large number of changes.
• Programming new features into the "modelling engine" using C++ and Microsoft Visual Studio.
• Programming new features into the user interface front end using Java on Windows and UNIX.
• Building and applying test models to verify enhancements in conjunction with scientists at Physiomics.

For more information visit the Physiomics web site or contact our Sales Desk (email: sales@ist-inc.com)