Driven by the availability of experimental data and ability to simulate a biological scale which is of immediate interest, the cellular scale is fast emerging as an ideal candidate for middle-out modelling. As with ‘bottom-up’ simulation approaches, cellular level simulations demand a high degree of computational power, which in large-scale simulations can only be achieved through parallel computing. The flexible large-scale agent modelling environment (FLAME) is a template driven framework for agent-based modelling (ABM) on parallel architectures ideally suited to the simulation of cellular systems. It is available for both high performance computing clusters (www.flame.ac.uk) and GPU hardware (www.flamegpu.com) and uses a formal specification technique that acts as a universal modelling format. This not only creates an abstraction from the underlying hardware architectures, but avoids the steep learning curve associated with programming them. In benchmarking tests and simulations of advanced cellular systems, FLAME GPU has reported massive improvement in performance over more traditional ABM frameworks. This allows the time spent in the development and testing stages of modelling to be drastically reduced and creates the possibility of real-time visualisation for simple visual face-validation.

A declarative extensible markup language (SpineML) for describing the dynamics, network and experiments of large-scale spiking neural network simulations is described which builds upon the NineML standard. It utilises a level of abstraction which targets point neuron representation but addresses the limitations of existing tools by allowing arbitrary dynamics to be expressed. The use of XML promotes model sharing, is human readable and allows collaborative working. The syntax uses a high-level self explanatory format which allows straight forward code generation or translation of a model description to a native simulator format. This paper demonstrates the use of code generation in order to translate, simulate and reproduce the results of a benchmark model across a range of simulators. The flexibility of the SpineML syntax is highlighted by reproducing a pre-existing, biologically constrained model of a neural microcircuit (the striatum). The SpineML code is open source and is available at http://bimpa.group.shef.ac.uk/SpineML .

Agent based modelling (ABM) offers a powerful abstraction for scientific study in a broad range of domains. The use of agent based simulators encourages good software engineering design such as separation of concerns, that is, the uncoupling of the model description from its implementation detail. A major limitation in current approaches to ABM simulation is that of the trade off between simulator flexibility and performance. It is common that highly optimised simulations, such as those which target graphics processing units (GPU) hardware, are implemented as standalone software. This work presents a software framework (FLAME GPU 2) which balances flexibility with performance for general purpose ABM. Methods for ensuring high computational efficacy are demonstrated by, minimising data movement, and ensuring high device utilisation by exploiting opportunities for concurrent code execution within a model and through the use of ensembles of simulations. A novel hierarchical sub‐modelling approach is also presented which can be used to model certain types of recursive behaviours. This feature is shown to be essential in providing a mechanism to resolve competition for resources between agents within a parallel environment which would otherwise introduce race conditions. To understand the performance characteristics of the software, a benchmark model with millions of agents is used to explore the use of simulation ensembles and to parametrically investigate concurrent code execution within a model. Performance speedups are demonstrated of 3.5 and 10 respectively over a baseline GPU implementation. Our hierarchical sub‐modelling approach is used to demonstrate the implementation of a recursive algorithm to resolve competition of agent movement which occurs as a result of agent desire to simultaneously occupy discrete areas high in a ‘resource’. The algorithm is used to implement a classical socio‐economics model, Sugarscape, with populations of up to 16M agents.

Background: In recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts. The ABM approach is a very common technique in the biological domain due to high demand for a large scale analysis tools for the collection and interpretation of information to solve biological problems. Simulating massive multi-agent systems (i.e. simulations containing a large number of agents/entities) requires major computational effort which is only achievable through the use of parallel computing approaches. Results: This paper explores different approaches to parallelising the key component of biological and immune system models within an ABM model: pairwise interactions. The focus of this paper is on the performance and algorithmic design choices of cell interactions in continuous and discrete space where agents/entities are competing to interact with one another within a parallel environment. Conclusions: Our performance results demonstrate the applicability of these methods to a broader class of biological systems exhibiting typical cell to cell interactions. The advantage and disadvantage of each implementation is discussed showing each can be used as the basis for developing complete immune system models on parallel hardware.