The Interactorium: visualising proteins, complexes and interaction networks in a virtual 3-D cell.

Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The tool has been designed to display very complex networks of up to 40 000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real-time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein "twins" when they occur in multiple locations. Since the Interactorium permits multi-level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net.

AFL and FRL: abstraction and representation for field interchange.

The holy grail of biomedical modelling is an integrated model of the entire human body. To this end, research groups around the world need to interchange experimental data, models and model results. A good interchange will have an efficient representation for storage and sharing and will have tools for modelling, data verification, authoring, data conversions and so on. A field is a spatially varying properly. In this paper we present the abstract field layer (AFL) and the field representation language (FRL). The AFL provides the field abstraction together with a set of common field operations. The FRL provides an efficient means for field representation and storage. We show how fields can be used to interchange information between modelling systems and between modelling and visualisation systems. We are currently developing a software system that composes multiple single cell solvers to create a tissue solver.

A three-dimensional fractal model of tumour vasculature.

We constructed a three-dimensional fractal model of the vascular network in a tumour periphery. We model the highly disorganised structure of the neoplastic vasculature by using a high degree of variation in segment properties such as length, diameter and branching angle. The overall appearance of the vascular tree is subjectively similar to that of the disorganised vascular network which encapsulates tumours. The fractal dimension of the model is within the range of clinically measured values.