An overview of the CellML API and its implementation

Abstract

BackgroundCellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and for archival in a model repository. Allowing for the exchange and archival of models in a computer readable form is a key strategic goal in bioinformatics, because of the associated improvements in scientific record accuracy, the faster iterative process of scientific development, and the ability to combine models into large integrative models.However, for CellML models to be useful, tools which can process them correctly are needed. Due to some of the more complex features present in CellML models, such as imports, developing code ab initio to correctly process models can be an onerous task. For this reason, there is a clear and pressing need for an application programming interface (API), and a good implementation of that API, upon which tools can base their support for CellML.ResultsWe developed an API which allows the information in CellML models to be retrieved and/or modified. We also developed a series of optional extension APIs, for tasks such as simplifying the handling of connections between variables, dealing with physical units, validating models, and translating models into different procedural languages.We have also provided a Free/Open Source implementation of this application programming interface, optimised to achieve good performance.ConclusionsTools have been developed using the API which are mature enough for widespread use. The API has the potential to accelerate the development of additional tools capable of processing CellML, and ultimately lead to an increased level of sharing of mathematical model descriptions.

Myokit: A simple interface to cardiac cellular electrophysiology

“…The CellML advanced programming interface (API) defines a number of ways to interact with a model, including translating it to other languages (Miller et al, 2010). An implementation of the API is available on the CellML website and can be used to translate CellML models to C, MATLAB and Python.…”

Standards and tools supporting collaborative development of the virtual physiological human

“…The CellML API is an open-source software library that tool developers are able to use to aid in the use of models encoded in CellML in their software projects [5]. Several tools have been developed which use CellML and a listing of some of them is available (http://www.cellml.org/tools).…”

Code Generation: A Strategy for Neural Network Simulators

“…There are several pure CellML simulators that support code generation (Garny et al 2008). In some cases, these build on the CellML Code Generation Service (CCGS) of the CellML API (Miller et al 2010), which in turn uses the API's MathML Language Expression Service (MaLaES) to convert MathML fragments into expressions in several different programming languages. Many SBML tools also use code generation (http://sbml.org/SBML_Software_ Guide/SBML_Software_Summary), but there are no common code generation tools equivalent to CCGS and MaLaES.…”