CellMLEvolution
This section aims to discuss the current issues with the CellML language that have dropped out of developing tools for CellML.
It is probably wise to reconstruct some of the goals and requirements of CellML previous to this tool development work.
Historical goals
This by no means says that they are no longer goals, they are just goals that were around this section was written.
From the "introduction" on the website itself we have
CellML is intended to support the definition of models of cellular and subcellular processes. CellML facilitates the re-use 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 a particular implementation of the model's solution. This makes a model independent of a particular operating system or programming language, and allows modellers 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 modellers need or want to include in a model document are incorporated using other languages. For instance, mathematics is included in CellML documents using Mathematical Markup Language (MathML). Metadata may be included using the Resource Description Framework and the Dublin Core Metadata Element Set.
From the minutes of some meeting in CellML s history we have a "requirements":CellMLLanguageRequirements.pdf document. Some people listed on that document deny it's validity.
Current goals
Our thinking is extending a little more into some of the intensions of the physiome project and model representation in generl. It is probably useful to look at the model representation(ModelRepresentation) discussion and especially the physiome document that is referenced there.
Another important document to read through is some thoughts(RequirementsDiscussion2) I had on CellML as the requirments to satisfy the development of a CellML rendering tool evolved. These should probably appear in a more formal manner as this section gets a structure.
Given this information, what are the starting goals for CellML Evolution itself?
- Integrate ontologies into CellML
- Integrate typing into CellML.
