Background

The Visible Cell™ project based at the Institute for Molecular Bioscience (IMB) and the ARC Centre of Excellence in Bioinformatics (ACB) at the University of Queensland (UQ) represents a large-scale, cross-disciplinary, multi-institutional and international e-Science initiative that is changing the way we think about mammalian cells.

Aims

The Visible Cell™ project aims to inform advanced in silico studies of cell and molecular organisation in 3D using the mammalian cell as a unitary example of an ordered complex system. This unique initiative is founded on the provision of complete sets of 3D spatio-temporal coordinates for whole mammalian cells at a range of resolutions and the integration of data on gene products, molecular interactions, pathways, networks and processes into the corresponding cellular coordinates. Investigators will interact with the cellular structures, molecules and processes (driven by user-supplied computational models) inside an integrated visualisation environment.

Outcomes

One anticipated outcome of this endeavour is the development the world's first navigable 'Visible Cell™ atlas': a single high-resolution map of the 3D landscape for an entire insulin-secreting pancreatic beta cell, imaged and reconstructed by cellular tomography at ~4-5nm resolution.

This high-resolution atlas will be complemented by a high-throughput cellular tomography pipeline for whole cells at 15-20nm resolution and parts of cells at ~5nm under different physiological conditions or disease states, and will serve as a unique framework for protein and organelle annotation, database integration, 3D visualisation and 4D animations of cells at pseudo-molecular resolution.

Importantly, the Visible Cell™ project will play a key role in scientific educational outreach and e-Research initiatives at both the national and international levels.

During the next 5 years, the Visible Cell™ will emerge as a sophisticated data environment where proteomic, genomic, molecular, cell and developmental biology data from multiple, diverse sources will be integrated. Through the Visible Cell™ interface, researchers will be able to utilise advanced computational simulations to model and predict changes in cellular behaviour at molecular and cellular levels. These simulations will represent a major advance in the ability to understand normal cell function as well as cell dysfunction, especially in the context of chronic diseases such as diabetes and cancer.