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another. The encapsulation relationship is special because it is the only relationship that affects the interpretation of the rest of the model. The effect of encapsulation is that components encapsulated beneath other components are private and cannot be accessed except by the component directly above in the encapsulation tree. The modeller is free to use encapsulation as a conceptual tool, and it does not necessarily have any physical interpretation.
123:). However, most CellML processing software will only accept a limited of range of mathematics (for example, some processing software requires equations with a single variable on one side of an equality). The choice of MathML makes CellML particularly suited for describing models containing differential equations. There is no mechanism for the expression of stochastic models or any other form of randomness.
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Science at the University of Auckland. The language was an application of the XML specification developed by the World Wide Web Consortium – the decision to use XML was based on late 1998 recommendations from Warren Hedley and André (David) Nickerson. Existing XML-based languages were leveraged to describe the mathematics (content
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in mind, and hence used primarily to describe models relevant to the field of biology. This is reflected in its name CellML, although this is simply a name, not an abbreviation. CellML is growing in popularity as a portable description format for computational models, and groups throughout the world
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Components can be connected in other components using a connection element, which describes the name of two components to be connected, and the variables in the first component which are mapped to variables in the second component. Such connections are a statement that the variable in one component
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The CellML language grew from a need to share models of cardiac cell dynamics among researchers at a number of sites across the world. The original working group formed in 1998 consisted of David
Bullivant, Warren Hedley, and Poul Nielsen; all three were at that time members of the Department of
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CellML models also allow relationships between components to be expressed. The CellML specification defines two types of relationship, encapsulation and containment, however more can be defined by the user. The containment relationship is used to express that one component is physically within
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A CellML model consists of a number of components, each described in their own component element. A component can be an entirely conceptual entity created for modelling convenience, or it can have some real physical interpretation (for example, it could represent the cell membrane).
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Each component contains a number of variables, which must be declared by placing a variable element inside the component. For example, a component representing a cell membrane may have a variable called V representing the potential difference (voltage) across the cell membrane.
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2001. This first draft was followed by specifications for CellML Metadata and an update to CellML to accommodate structured nesting of models with the addition of the <import> element. Physiome
Sciences Inc. also produced the first CellML capable software. The
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In 2002 the CellML 1.1 specification was written, in which imports were added. Imports provide the ability to incorporate external components into a model, enabling modular modelling. This specification was frozen in early 2006. Work has continued on
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aims to provide a focal point for the CellML community. Members can submit, review, and update models and receive feedback and help from the community. A CellML discussion mailing list can be found at
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introduced the ability to import components and units. In order to fully support this feature, variables in CellML 1.1 accept variable names as initial values.
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is used to annotate models with a variety of information; relevant references, authorship information, the species the model is relevant to, and so on.
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CellML has several metadata specifications, used to annotate models or provide information for running and/or visualizing simulations of models.
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CellML is defined by core specifications as well as additional specifications for metadata, used to annotate models and specify simulations.
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In July 2009 the CellML website was completely revamped, and an initial version of the new CellML repository software (PMR2) was released.
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and to validate the models against standards of unit balance and biophysical constrains such as conservation of mass, charge, energy etc.
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provides information to specify particular visualizations of simulation output, for example to reproduce a particular graph from a paper.
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are using CellML for modelling or developing software tools based on CellML. CellML is similar to
Systems Biology Markup Language
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effort in late 2000, when Warren Hedley attended the 2nd workshop on
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but provides greater scope for model modularity and reuse, and is not specific to descriptions of biochemistry.
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