CellML: its future, present and past

Abstract

Advances in biotechnology and experimental techniques have lead to the elucidation of vast amounts of biological data. Mathematical models provide a method of analysing this data; however, there are two issues that need to be addressed: (1) the need for standards for defining cell models so they can, for example, be exchanged across the World Wide Web, and also read into simulation software in a consistent format and (2) eliminating the errors which arise with the current method of model publication. CellML has evolved to meet these needs of the modelling community. CellML is a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. In this paper we summarise the structure of CellML, its current applications (including biological pathway and electrophysiological models), and its future development--in particular, the development of toolsets and the integration of ontologies.

Space as the final frontier in stochastic simulations of biological systems

“…While countless numbers of custom-made programs designed for local users used to be the rule, general-purpose software tools, relying on basic computer proficiency of users, are being developed with obvious efforts to adapt to a broader community [18], offering extensive documentation, workspaces that help structure the modeling process, rich graphical user interfaces, links to databases or to the community (Virtual Cell), and standards in model specification languages (open standards like SBML [19] and CellML [20] based on the XML markup language).…”

A mathematical framework simulating nerve fiber physiology

“…These models were encoded using the CellML modelling benchmark (Hedley et al, 2001;Lloyd et al, 2004). Through these electrophysiological models, we were able to calculate the values of membrane potential, ionic currents, conductances, and their respective ordinary ODEs in CellML which resulted in the calculation of the action potential at a single grid point along the 1D SSEM.…”

Chaste: A test-driven approach to software development for biological modelling

“…(3), is solved by a suitable numerical scheme. A typical ODE system, such as Luo-Rudy 1991 [7] can be described in the implementation-independent CellML format [10] (see Section 4.2.1), contains 10 to 50 differential equations (representing the rate of change of ionic concentrations and of the number of open cell-membrane gates) and can be solved using any numerical ODE solver. The exact choice of numerical method for the ODE solution will vary according to the time-and space-resolutions required and according to the stability and convergence properties of particular schemes.…”

“…10 When a developer compiles the code of Chaste, they typically build and test either a single test-suite, a library component or an entire raft of test-suites-known as the continuous test pack. In every case, code is compiled as necessary and executables are constructed corresponding to each test-suite.…”