SCIENCE & ENGINEERING NEWS
Princeton, N.J. — Physiome Sciences, Inc. and researchers at the University of Auckland announced the launch of a new website that provides a tool to standardize and streamline the creation of computer-based models of cells, organs and tissues. The launch was announced by Warren Hedley of the Bioengineering Research Group at the University of Auckland on Saturday, October 14, at the 2000 Biomedical Engineering Society Annual Fall Meeting, held from October 12-14, 2000 (Seattle, WA). The website, http://www.CellML.org , represents a major step forward in allowing scientists to create and customize computer models that integrate data from a wide variety of sources, including genomic, proteomic, cell and organ studies, and public and private databases. The language will be developed as a common standard that will be available free of charge to all users.
The CellML Language is an XML-based mark-up language designed to represent and exchange computer-based biological models and their components. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. CellML is expected to enable scientists to more effectively manage and interpret gene and protein data and apply it to study diseases, identify potential drug targets and test new drugs “in silico.”
“Up until now, scientists tended to put single data sets into one, inflexible model, so that when the model was published, it wasn’t clear how it was put together,” said Dr. Thomas Colatsky, Executive Vice President and Chief Scientific Officer of Physiome. “CellML allows researchers to describe the components of a model in a highly readable format that makes each component reusable in other models, so that models of greater complexity can be built and understood. For example, if someone models an excitable cell, such as a heart muscle cell, and someone else models the biochemical response to a specific neurotransmitter, these two models can now be easily integrated to develop a more complete working model of the heart.”
The website results from collaboration between Physiome Sciences and the University of Auckland to develop and maintain a standardized computer language for biological modeling. CellML is an Extensible Markup Language (XML) application that provides a single means of integrating biological data in a platform-independent way. The University of Auckland team developed language standards for describing anatomical data and the distribution of biological properties in three dimensions, while Physiome developed XML-based descriptions of cellular and subcellular process, including biochemical pathways.
Dr. Peter Hunter, Professor of Engineering Science at the University of Auckland, said “We and our collaborators at Physiome initiated this project to allow cell models to be submitted in a universal, standardized electronic format. This format allows the individual investigators to manipulate the model using their own data without the introduction of human error involved in non-electronic format. CellML provides a universal language for defining cellular functions so that any biological function can be defined quantitatively.”
“Physiome is taking a leading role in expanding the use of computer models in biological research by promoting technologies that are critical to exchanging, integrating, and simulating biological data. This will help bring modeling into the mainstream of the drug discovery process,” commented Dr. Jeremy Levin, Chairman and Chief Executive Officer of Physiome. “The technologies on the CellML website offer academics and our customers a simple and functional means to exchange critical information. This will aid drug discovery on a global basis.” Dr. Levin continued, “Physiome offers proprietary, sophisticated and data-rich computer models to our customers.”
Physiome Sciences, Inc., a privately held technology company, is a leader in the commercial development of software tools, proprietary databases, and web applications for simulating life processes. This biological operating system can be harnessed to model cells, tissues and organs in a virtual setting, enabling scientists to generate predictive information using their own data. Drug developers, for example, use Physiome’s operating system and models to predict the effects of specific drugs on animals and humans. This greatly speeds the selection of drugs for entry into human trials. The selection process becomes more rational and potentially increases drug quality at an early stage of development.