1st INCF Workshop on Needs for Training in Neuroinformatics

The INCF workshop on Needs for Training in Neuroinformatics was organized by the INCF National Node of the UK. The scope of the workshop was to provide as overview of the current state of neuroinformatics training and recommendations for future provision of training. The report presents a summary of the workshop discussions and recommendations to the INCF

INCF Workshops on Needs for Training in Neuroinformatics: Extended and Short Course Provision

The second and third _INCF Workshops on Training in Neuroinformatics_ were organized by the INCF National Node of the UK. In these workshops, the issues arising in providing extended courses, such as a full time Masters, or short courses, of a few days or a few weeks, were discussed. There was a focus on how the INCF could facilitate training in these types of courses. In this report, the recommendations from all three Training workshops are brought together

Quantitative assessment of computational models for retinotopic map formation.

Molecular and activity-based cues acting together are thought to guide retinal axons to their terminal sites in vertebrate optic tectum or superior colliculus (SC) to form an ordered map of connections. The details of mechanisms involved, and the degree to which they might interact, are still not well understood. We have developed a framework within which existing computational models can be assessed in an unbiased and quantitative manner against a set of experimental data curated from the mouse retinocollicular system. Our framework facilitates comparison between models, testing new models against known phenotypes and simulating new phenotypes in existing models. We have used this framework to assess four representative models that combine Eph/ephrin gradients and/or activity-based mechanisms and competition. Two of the models were updated from their original form to fit into our framework. The models were tested against five different phenotypes: wild type, Isl2-EphA3(ki/ki), Isl2-EphA3(ki/+), ephrin-A2,A3,A5 triple knock-out (TKO), and Math5(-/-) (Atoh7). Two models successfully reproduced the extent of the Math5(-/-) anteromedial projection, but only one of those could account for the collapse point in Isl2-EphA3(ki/+). The models needed a weak anteroposterior gradient in the SC to reproduce the residual order in the ephrin-A2,A3,A5 TKO phenotype, suggesting either an incomplete knock-out or the presence of another guidance molecule. Our article demonstrates the importance of testing retinotopic models against as full a range of phenotypes as possible, and we have made available MATLAB software, we wrote to facilitate this process.Contract grant sponsors: Wellcome Trust; contract grant numbers: 083205, Engineering and Physical Sciences Research Council (EPSRC) (CSC).This is the published version. It's also available from Wiley at http://onlinelibrary.wiley.com/doi/10.1002/dneu.22241/abstract

Elastic net model of ocular dominance - overall stripe pattern and monocular deprivation

The elastic net (Durbin and Willshaw 1987) can account for the development of both topography and ocular dominance in the mapping from the lateral geniculate nucleus to primary visual cortex (Goodhill and Willshaw 1990). Here it is further shown for this model that (1) the overall pattern of stripes produced is strongly influenced by the shape of the cortex: in particular, stripes with a global order similar to that seen biologically can be produced under appropriate conditions, and (2) the observed changes in stripe width associated with monocular deprivation are reproduced in the model

On the Importance of Countergradients for the Development of Retinotopy: Insights from a Generalised Gierer Model

During the development of the topographic map from vertebrate retina to superior colliculus (SC), EphA receptors are expressed in a gradient along the nasotemporal retinal axis. Their ligands, ephrin-As, are expressed in a gradient along the rostrocaudal axis of the SC. Countergradients of ephrin-As in the retina and EphAs in the SC are also expressed. Disruption of any of these gradients leads to mapping errors. Gierer's (1981) model, which uses well-matched pairs of gradients and countergradients to establish the mapping, can account for the formation of wild type maps, but not the double maps found in EphA knock-in experiments. I show that these maps can be explained by models, such as Gierer's (1983), which have gradients and no countergradients, together with a powerful compensatory mechanism that helps to distribute connections evenly over the target region. However, this type of model cannot explain mapping errors found when the countergradients are knocked out partially. I examine the relative importance of countergradients as against compensatory mechanisms by generalising Gierer's (1983) model so that the strength of compensation is adjustable. Either matching gradients and countergradients alone or poorly matching gradients and countergradients together with a strong compensatory mechanism are sufficient to establish an ordered mapping. With a weaker compensatory mechanism, gradients without countergradients lead to a poorer map, but the addition of countergradients improves the mapping. This model produces the double maps in simulated EphA knock-in experiments and a map consistent with the Math5 knock-out phenotype. Simulations of a set of phenotypes from the literature substantiate the finding that countergradients and compensation can be traded off against each other to give similar maps. I conclude that a successful model of retinotopy should contain countergradients and some form of compensation mechanism, but not in the strong form put forward by Gierer

Inhomogeneities in Heteroassociative Memories with Linear Learning Rules

We investigate how various inhomogeneities present in synapses and neurons affect the performance of feedforward associative memories with linear learning, a high-level network model of hippocampal circuitry and plasticity. The inhomogeneities incorporated into the model are differential input attenuation, stochastic synaptic transmission, and memories learned with varying intensity. For a class of local learning rules, we determine the memory capacity of the model by extending previous analysis. We find that the signal-to-noise ratio (SNR), a measure of fidelity of recall, depends on the coefficients of variation (CVs) of the attenuation factors, the transmission variables, and the intensity of the memories, as well as the parameters of the learning rule, pattern sparsity and the number of memories stored. To predict the effects of attenuation due to extended dendritic trees, we use distributions of attenuations appropriate to unbranched and branched dendritic trees. Biological parameters for stochastic transmission are used to determine the CV of the transmission factors. The reduction in SNR due to differential attenuation is surprisingly low compared to the reduction due to stochastic transmission. Training a network by storing memories at different intensities is equivalent to using a learning rule incorporating weight decay. In this type of network, new memories can be stored continuously at the expense of older ones being forgotten (a palimpsest). We show that there is an optimal rate of weight decay that maximizes the capacity of the network, which is a factor of e lower than its nonpalimpsest equivalent

The Importance of Combinatorial Gene Expression in Early Mammalian Thalamic Patterning and Thalamocortical Axonal Guidance

The thalamus is essential for sensory perception. In mammals, work on the mouse has taught us most of what we know about how it develops and connects to the cortex. The mature thalamus of all mammalian species comprises numerous anatomically distinct collections of neurons called nuclei that differ in function, connectivity, and molecular constitution. At the time of its initial appearance as a distinct structure following neural tube closure, the thalamus is already patterned by the regional expression of numerous regulatory genes. This patterning, which lays down the blueprint for later development of thalamic nuclei, predates the development of thalamocortical projections. In this review we apply novel analytical methods to gene expression data available in the Allen Developing Mouse Brain Atlas to highlight the complex organized molecular heterogeneity already present among cells in the thalamus from the earliest stages at which it contains differentiating neurons. This early patterning is likely to invest in axons growing from different parts of the thalamus the ability to navigate in an ordered way to their appropriate area in the cerebral cortex. We review the mechanisms and cues that thalamic axons use, encounter, and interpret to attain the cortex. Mechanisms include guidance by previously generated guidepost cells, such as those in the subpallium that maintain thalamic axonal order and direction, and axons such as those of reciprocal projections from intermediate structures or from the cortex itself back toward the thalamus. We show how thalamocortical pathfinding involves numerous guidance cues operating at a series of steps along their route. We stress the importance of the combinatorial actions of multiple genes for the development of the numerous specific identities and functions of cells in this exquisitely complex system and their orderly innervation of the cortex

Analysis of local and global topographic order in mouse retinocollicular maps

We introduce the Lattice Method for the quantitative assessment of the topographic order within the pattern of connections between two structures. We apply this method to published visuocollicular mapping data obtained by Fourier-based intrinsic imaging of mouse colliculus. We find that, in maps from wild types and β2 knock-outs, at least 150 points on the colliculus are represented in the visual field in the correct relative order. In maps from animals with knock-out of the three ephrinA ligands (TKO), thought to specify the rostrocaudal axis of the map, the projection on the colliculus of each small circular area of visual field is elongated approximately rostrocaudally. Of these projections, 9% are made up of two distinct regions lying along the direction of ingrowth of retinal fibers. These are similar to the ectopic projections found in other ephrinA knock-out data. Coexisting with the ectopic projections, each TKO map contains a submap where neighbor–neighbor relations are preserved, which is ordered along both rostrocaudal and mediolateral axes, in the orientation found in wild-type maps. The submaps vary in size with order well above chance level, which can approach the order in wild-type maps. Knock-out of both β2 and two of the three ephrinAs yields maps with some order. The ordered TKO maps cannot be produced by correlated neural activity acting alone, as this mechanism is unable to specify map orientation. These results invite reassessment of the role of molecular signaling, particularly that of ephrinAs, in the formation of ordered nerve connections