PathwayAssist is available for commercial licensing from Ariadne Genomics, Inc. The light version with limited functionality will be available for free for academic users at www.ariadnegenomics.com/downloads/.

MedScan is available for commercial licensing from Ariadne Genomics, Inc.

The sigmoidal tuning curve that maximizes the mutual information for a Poisson neuron, or population of Poisson neurons, is obtained. The optimal tuning curve is found to have a discrete structure that results in a quantization of the input signal. The number of quantization levels undergoes a hierarchy of phase transitions as the length of the coding window is varied. We postulate, using the mammalian auditory system as an example, that the presence of a subpopulation structure within a neural population is consistent with an optimal neural code.

We study a system of two-mode stochastic oscillators coupled through their collective output. As a function of a relevant parameter four qualitatively distinct regimes of collective behavior are observed. In an extended region of the parameter space the periodicity of the collective output is enhanced by the considered coupling. This system can be used as a new model to describe synchronization-like phenomena in systems of units with two or more oscillation modes. The model can also explain how periodic dynamics can be generated by coupling largely stochastic units. Similar systems could be responsible for the emergence of rhythmic behavior in complex biological or sociological systems.

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Background: Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks. Formalization of this knowledge is necessary for computational analysis and is achieved by automatic fact extraction using various text-mining algorithms. Most of these techniques suffer from high false positive rates and redundancy of the extracted information. The extracted facts form a large network with no pathways defined.

We study the problem of detecting a small dc signal by quantifying its effect on the mean difference DeltaT in residence times in the stable steady states of a bistable dynamical measurement device, in the presence of a noise floor and a known time-sinusoidal bias signal. Errors in the measurement process occur due to a finite observation time that is present in most practical scenarios. The error is found to have a nonmonotonic dependence on the noise intensity; at a critical noise intensity, the error is minimized. This phenomenon, reminiscent of the well-known stochastic resonance effect, can also be obtained by adjusting the device tuning parameters for a given noise floor. The effect appears to be most pronounced for subthreshold bias signals in the strongly nonlinear response regime.