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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.
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A graphical view of the components in a model showing the interconnection between components as well as their hierarchical structure
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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.
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| 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)
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