CellML and associated tools and techniques

Abstract

We have, in the last few years, witnessed the development and availability of an ever increasing number of computer models that describe complex biological structures and processes. The multi-scale and multi-physics nature of these models makes their development particularly challenging, not only from a biological or biophysical viewpoint but also from a mathematical and computational perspective. In addition, the issue of sharing and reusing such models has proved to be particularly problematic, with the published models often lacking information that is required to accurately reproduce the published results.The International Union of Physiological Sciences Physiome Project was launched in 1997 with the aim of tackling the aforementioned issues by providing a framework for the modelling of the human body. As part of this initiative, the specifications of the CellML mark-up language were released in 2001. Now, more than 7 years later, the time has come to assess the situation, in particular with regard to the tools and techniques that are now available to the modelling community. Thus, after introducing CellML, we review and discuss existing editors, validators, online repository, code generators and simulation environments, as well as the CellML Application Program Interface. We also address possible future directions including the need for additional mark-up languages.

Cardiac cell modelling: Observations from the heart of the cardiac physiome project

“…There exist numerous software environments for model simulation, such as COR and PCEnv (Garny et al 2008), some of which incorporate tools for parameter estimation and sensitivity analysis. For example, the JSim package incorporates sophisticated optimisation routines for parameter estimation as well as the ability to automatically calculate sensitivity functions and generate multiple simulations by looping through ranges of parameter values.…”

“…In our experience, many of these issues also relate to the reuse of model components ). Specifically, while markup languages such as CellML (Garny et al 2008) and SBML (Hucka et al 2004) allow models to be reused with fidelity, there is no clear way for the assumptions and data on which individual model components are based to also be inherited. This means there is potential for existing submodels to be embedded in new frameworks which aim to simulate a dynamic range inappropriate for the initial parameterisation of the model component.…”

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

“…CellML is an XML-based language that represents electrophysiological models (amongst others) as a structured document that may be read by both humans and computers. Chaste programs utilise the locally developed open source tool PyCml [41,42] for CellML verification and for automatic generation of efficient C++ code. For details of the current state of CellML, see [42] and the CellML website.…”

“…Chaste programs utilise the locally developed open source tool PyCml [41,42] for CellML verification and for automatic generation of efficient C++ code. For details of the current state of CellML, see [42] and the CellML website. 13 …”

A physiome standards-based model publication paradigm

“…sourceforge.net/cellmlsimulator/)). There are also several specific tools available, addressing the various needs of the community (for a recent review, see Garny et al 2008).…”