Towards NeuroML: Model description methods for collaborative modelling in neuroscience

Biological nervous systems and the mechanisms underlying their operation ex hibit astonishing complexity. Computational models of these systems have be en correspondingly complex. As these models become ever more sophisticated, they become increasingly difficult to define, comprehend, manage and commu nicate. Consequently, for scientific understanding of biological nervous sy stems to progress, it is crucial for modellers to have software tools that support discussion, development and exchange of computational models. We de scribe methodologies that focus on these tasks, improving the ability of ne uroscientists to engage in the modelling process. We report our findings on the requirements for these tools and discuss the use of declarative forms of model description-equivalent to object-oriented classes and database sch ema-which we call templates. We introduce NeuroML, a mark-up language for t he neurosciences which is defined syntactically using templates, and its sp ecific component intended as a common format for communication between mode lling-related tools. Finally, we propose a template hierarchy for this mode lling component of NeuroML, sufficient for describing models ranging in str uctural levels from neuron cell membranes to neural networks. These templat es support both a framework for user-level interaction with models, and a h igh-performance framework for efficient simulation of the models.