[October 17, 2000] "The CellML language is an XML-based markup language being developed by Physiome Sciences Inc. in Princeton, New Jersey, in conjunction with the Bioengineering Research Group at the University of Auckland's Department of Engineering Science and affiliated research groups. The purpose of CellML is to store and exchange computer-based biological models. 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 includes information about model structure (how the parts of a model are organizationally related to one another) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). CellML includes mathematics and documentation by leveraging existing languages, including MathML and (X)HTML. In the future, CellML may also use other existing languages to specify data and define simulation and rendering information. The CellML project is closely affiliated with two other XML-based language projects currently underway at the University of Auckland. Combined, these languages will provide a complete vocabulary for describing biological information at a range of resolutions from the subcellular to organism level. (1) AnatML is aimed at exchanging information at the organ level, and has been used at the University of Auckland to store geometric information and documentation that was generated during a skeleton digitization project. (2) FieldML can be used to describe spatially and temporally varying field information using finite elements. It is appropriate for storing geometry information inside AnatML, spatial distribution of parameters inside compartments in CellML, or the spatial distribution of cellular model parameters across an entire organ."
"The first models created with CellML were electrophysiological models of heart cells. Since the early days, however, the language has been generalized. Now CellML can be used to create virtually any type of biological model. CellML has been particularly successful at enabling modeling at the cellular level. Electrophysiological and signal transduction (pathway) models have been created using CellML. Mechanical models (such as those that simulate heart muscle cell contraction) are another area of study. In the future, it will be possible to describe all three types of models with CellML."
"Physiome Sciences, Inc. is a privately held technology company, focused on the development and commercial application of software tools and proprietary databases needed to simulate life processes on the computer. The Company's broad technology base includes a range of integrated components. At its core is the proprietary In Silico Cell system, which links mathematical tools, annotated biological databases and an XML-based modeling language to facilitate the construction and extension of biological models. In Silico Cell interfaces with powerful software tools to create a unique software environment that enables the rapid construction, analysis, and integration of cell models and their components. The Company uses this proprietary platform to build experimentally-detailed computer models of biochemical pathways, cells, organs and systems that accurately predict physiological responses across multiple species, from mouse to man..."
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[October 17, 2000] "Physiome Sciences and the University of Auckland Launch Cell Modeling Website (www.CellML.org) to Provide Users World-Wide with Universal Language for Developing Computer Models of Cells, Tissues, and Organs." - "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."
[July 12, 2000] "Physiome Science Gives Biological Computer Models a Single New Language. Process could speed new drug development." - "Physiome Sciences, Inc. today announced a collaboration with the University of Auckland in New Zealand to establish and maintain a standardized computer language that enables the rapid development and exchange of "virtual" models of living cells, tissues and organs. The announcement was made today at a meeting in London, which was attended by scientists from around the world who gathered to learn about the new technology and its use as a critical tool in the management and interpretation of gene and protein data. The field of computational biology is hampered by the use of different computer languages and data formats that make it difficult for scientists around the world to share information and compare findings. Now, the new Cell Markup Language, or CellML, will enhance and facilitate the exchange and validation of information among laboratories with a speed and accuracy not previously possible. CellML is an Extensible Markup Language (XML) application that provides a single means of integrating biological models, experimental data and text documents in a platform-independent and web-accessible way. The team at the University of Auckland is developing markup language standards for describing anatomic data (Anat ML) and the distribution of biological properties in three dimensions (Field ML), while Physiome Sciences is developing XML-based descriptions of cellular and subcellular process. Together, these new standards will enable biomedical researchers to simulate living cells and organs on the computer. 'For the first time ever, scientists in separate laboratories will be able to share their findings quickly, and easily,' said Dr. Jeremy Levin, Chairman and Chief Executive Officer of Physiome. 'These computer models will allow scientists to study diseases, identify potential drug targets, and pre-test new drugs faster, more confidently, and less expensively than ever before'. Physiome Sciences, Inc., will develop and maintain a website as the primary source of information about CellML and its development. The website will also provide access to cell models in the public domain that can be downloaded, run, modified and updated. Researchers will be invited to learn about Cell ML and to use a wide range of computer models in their research."
