Computational neuroscience has produced a diversity of software for simulations of networks of spiking neurons, with both negative and positive consequences. On the one hand, each simulator uses its own programming or configuration language, leading to considerable difficulty in porting models from one simulator to another. This impedes communication between investigators and makes it harder to reproduce and build on the work of others. On the other hand, simulation results can be cross-checked between different simulators, giving greater confidence in their correctness, and each simulator has different optimizations, so the most appropriate simulator can be chosen for a given modelling task. A common programming interface to multiple simulators would reduce or eliminate the problems of simulator diversity while retaining the benefits. PyNN is such an interface, making it possible to write a simulation script once, using the Python programming language, and run it without modification on any supported simulator (currently NEURON, NEST, PCSIM, Brian and the Heidelberg VLSI neuromorphic hardware). PyNN increases the productivity of neuronal network modelling by providing high-level abstraction, by promoting code sharing and reuse, and by providing a foundation for simulator-agnostic analysis, visualization and data-management tools. PyNN increases the reliability of modelling studies by making it much easier to check results on multiple simulators. PyNN is open-source software and is available from http://neuralensemble.org/PyNN .

If perception corresponds to hypothesis testing (Gregory, 1980); then visual searches might be construed as experiments that generate sensory data. In this work, we explore the idea that saccadic eye movements are optimal experiments, in which data are gathered to test hypotheses or beliefs about how those data are caused. This provides a plausible model of visual search that can be motivated from the basic principles of self-organized behavior: namely, the imperative to minimize the entropy of hidden states of the world and their sensory consequences. This imperative is met if agents sample hidden states of the world efficiently. This efficient sampling of salient information can be derived in a fairly straightforward way, using approximate Bayesian inference and variational free-energy minimization. Simulations of the resulting active inference scheme reproduce sequential eye movements that are reminiscent of empirically observed saccades and provide some counterintuitive insights into the way that sensory evidence is accumulated or assimilated into beliefs about the world.

This paper introduces a model of oculomotor control during the smooth pursuit of occluded visual targets. This model is based upon active inference, in which subjects try to minimise their (proprioceptive) prediction error based upon posterior beliefs about the hidden causes of their (exteroceptive) sensory input. Our model appeals to a single principle – the minimisation of variational free energy – to provide Bayes optimal solutions to the smooth pursuit problem. However, it tries to accommodate the cardinal features of smooth pursuit of partially occluded targets that have been observed empirically in normal subjects and schizophrenia. Specifically, we account for the ability of normal subjects to anticipate periodic target trajectories and emit pre-emptive smooth pursuit eye movements – prior to the emergence of a target from behind an occluder. Furthermore, we show that a single deficit in the postsynaptic gain of prediction error units (encoding the precision of posterior beliefs) can account for several features of smooth pursuit in schizophrenia: namely, a reduction in motor gain and anticipatory eye movements during visual occlusion, a paradoxical improvement in tracking unpredicted deviations from target trajectories and a failure to recognise and exploit regularities in the periodic motion of visual targets. This model will form the basis of subsequent (dynamic causal) models of empirical eye tracking measurements, which we hope to validate, using psychopharmacology and studies of schizophrenia.