## CellML

** Category** Cross-Omics>Pathway Analysis/Tools

** Abstract** CellML (Cell Markup Language) is an open software standard
based on the Extensible Markup Language (XML).

The purpose of CellML is to store and exchange computer-based mathematical 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 is intended to support the definition of models of cellular and sub-cellular processes.

CellML facilitates the reuse of models and parts of models by using a component-based architecture. Models are split into logical sub-parts called components that are connected together to form a model.

CellML separates the specification of the underlying mathematics of a model from the implementation of the model's solution.

This makes a model independent of a particular operating system or programming language and allows modelers to easily integrate parts of other peoples' models into their own models.

CellML also allows the generation of equations for publishing from the same definition upon which the solution method is based, removing inconsistencies between the model and associated results in academic papers, and allowing others to reliably reproduce these results.

The scope of the CellML language is specifically limited to the definition of model-structure. All other types of information that modelers need or want to include in a model document are incorporated using other languages.

For instance, mathematics is included in CellML documents using the Mathematical Markup Language (MathML).

MathML is intended to facilitate the use and re-use of mathematical and scientific content on the Web, and for other applications such as computer algebra systems, print typesetting, and voice synthesis.

MathML can be used to encode both the presentation of mathematical notation for high-quality visual display, and mathematical content, for applications where the semantics plays more of a key role such as scientific software or voice synthesis.

Metadata may be included using the Resource Description Framework.

The Resource Description Framework (RDF) integrates a variety of applications from library catalogs and world-wide directories to syndication and aggregation of news, software, and content to personal collections of music, photos, and events using XML as interchange syntax.

The RDF specifications provide a lightweight 'ontology system' to support the exchange of knowledge on the Web.

Although CellML was originally intended for the description of biological models, it has a broader application (for an example, the classical 'Mooney-Rivlin Constitutive Material Law', which defines the relationship between eight (8) independent strain components and the stress components).

The CellML project is closely affiliated with another XML-based language project currently underway at the University of Auckland, FieldML.

Combined, these languages will provide a complete vocabulary for describing biological information at a range of resolutions from the sub- cellular to organism level.

FieldML can be used to describe spatially and temporally varying field information.

It is appropriate for storing geometry information and 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. The language has now been generalized with the aim of being able to specify virtually any type of cellular-level model.

CellML has been particularly successful at enabling modeling at the cellular level. Electrophysiological, 'signal transduction', and 'metabolic pathway' models have been created using CellML.

Mechanical models (such as those that simulate heart muscle cell contraction) are another area of study.

CellML Model Repository --

The CellML model repository contains examples of 'single models' which describe more than one process - embedding, for example, 'metabolic pathways' within an electrophysiological system.

At present, CellML is able to describe systems of linear algebra and ordinary differential equations and real numbers.

Repository Models - There are currently ‘367’ unique models in the repository.

CellML Tools -- (see G6G Abstract Number 20294).

Overview of Tools relating to CellML - The CellML team is committed to providing freely available tools for creating, editing, and using CellML models.

Information regarding tools being developed internally is provided and links to external projects developing tools which utilize the CellML format are also provided.

- 1) API Specifications and Implementations;
- 2) Model Databases;
- 3) Complete CellML Environments;
- 4) Other Modeling Environments;
- 5) Validation Tools;
- 6) Simulation Tools; and
- 7) Miscellaneous Utilities.

CellML Tutorials provided --

- 1) Notation - Graphical Notation for CellML Networks.
- 2) XML Guide - A Quick Introduction to XML.
- 3) Electrophysiological - Example CellML Electrophysiological Models.
- 4) Signal Transduction - Example CellML Signal Transduction Models.
- 5) CellML 1.1 - Example CellML 1.1 Models.
- 6) Best Practice - Modeling in CellML - Tips for Writing a CellML Model.
- 7) Curation - An overview of the CellML Model Repository. CellML Model Curation: the Theory, CellML Model Curation: the Practice, etc.

*System Requirements*

Contact manufacturer.

*Manufacturer*

- Auckland Bioengineering Institute
- University of Auckland
- Level 6, 70 Symonds St
- Auckland
- New Zealand

** Manufacturer Web Site** Auckland Bioengineering Institute, CellML

** Price** Contact manufacturer.

** G6G Abstract Number** 20293

** G6G Manufacturer Number** 102852