Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

Recent advances in biotechnology and the availability of ever more powerful computers have led to the formulation of increasingly complex models at all levels of biology. One of the main aims of systems biology is to couple these together to produce integrated models across multiple spatial scales and physical processes. In this review, we formulate a definition of multi-scale in terms of levels of biological organisation and describe the types of model that are found at each level. Key issues that arise in trying to formulate and solve multi-scale and multi-physics models are considered and examples of how these issues have been addressed are given for two of the more mature fields in computational biology: the molecular dynamics of ion channels and cardiac modelling. As even more complex models are developed over the coming few years, it will be necessary to develop new methods to model them (in particular in coupling across the interface between stochastic and deterministic processes) and new techniques will be required to compute their solutions efficiently on massively parallel computers. We outline how we envisage these developments occurring.

SUMMARYFinite element (FE) cardiac electro-physiology solvers commonly have ionic current determined at mesh nodes but required element interiors. We consider two interpolation approaches: (i) ionic current interpolation (ICI), where nodal ionic currents are linearly interpolated into the element and (ii) state variable interpolation (SVI), where cell model state variables are interpolated instead, from which the ionic current is evaluated. We explain why SVI leads to a method which is massively more computationally demanding than ICI (more than might originally be expected), and then demonstrate that the difference in results can be surprisingly large even on what are generally considered suitably fine meshes. We explain why the conduction velocity in ICI simulations is generally too large, identify how ICI can give 'accidentally' accurate conduction velocities through two particular sources of error balancing, and illustrate how the difference between ICI and SVI can be huge in anisotropic problems. We also characterize the ICI/SVI difference over a range of cell models, in terms of model upstroke-velocity and formulation of the fast sodium current. Finally, we propose and evaluate a hybrid method which provides the accuracy of SVI, while retaining the efficiency of ICI.

A glutamine synthetase (GS) gene, glnA, from Bacteroides fragilis was cloned on a recombinant plasmid pJS139 which enabled Escherichia coli glnA deletion mutants to utilize (NH4)2SO4 as a sole source of nitrogen. DNA homology was not detected between the B. fragilis glnA gene and the E. coli glnA gene. The cloned B fragilis glnA gene was expressed from its own promoter and was subject to nitrogen repression in E. coli, but it was not able to activate histidase activity in an E. coli glnA ntrB ntrC deletion mutant containing the Klebsiella aerogenes hut operon. The GS produced by pJS139 in E. coli was purified; it had an apparent subunit Mr of approximately 75,000, which is larger than that of any other known bacterial GS. There was very slight antigenic cross-reactivity between antibodies to the purified cloned B. fragilis GS and the GS subunit of wild-type E. coli.

The cloned Bacteroides fragilis glutamine synthetase (GS) subunit produced in Escherichia coli had the same apparent M, of approximately 75000 as the GS subunit from B. fragilis cells. The B. fragilis GS enzyme had an apparent M, of approximately 490000 and it is concluded that the GS is a hexamer. The cloned GS did not appear to be regulated by adenylylation and deadenylylation and the cloned enzyme was inactivated by snake venom phosphodiesterase. The pH profiles of the cloned GS, assayed by the y-glutamyl transferase (GGT) assay were similar for NH,+-shocked and unshocked cell extracts and an isoactivity point was not obtained from these curves. The cloned GS was subject to feedback inhibition by amino acids but not by AMP. The GGT activity of the cloned GS in NH,+-shocked and unshocked cell-free extracts was inhibited by Mg2+. Mn2+ stimulated the cloned GS GGT activity of NHI-shocked cell-free extracts. Western blotting indicated that GS production was regulated by nitrogen in B. fragilis cells but cell extracts showed no GGT activity. Cloned B. fragilis GS produced in E. coli was specifically and irreversibly inactivated by B. fragilis cell extracts.