SUMMARY: We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. AVAILABILITY AND IMPLEMENTATION: CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. CONTACT: [email protected].

MOTIVATION: Genetic regulatory networks are often affected by stochastic noise, due to the low number of molecules taking part in certain reactions. The networks can be simulated using stochastic techniques that model each reaction as a stochastic event. As models become increasingly large and sophisticated, however, the solution time can become excessive; particularly if one wishes to determine the effect on noise of changes to a series of parameters, or the model structure. Methods are therefore required to rapidly estimate stochastic noise. RESULTS: This paper presents an algorithm, based on error growth techniques from non-linear dynamics, to rapidly estimate the noise characteristics of genetic networks of arbitrary size. The method can also be used to determine analytical solutions for simple sub-systems. It is demonstrated on a number of cases, including a prototype model of the galactose regulatory pathway in yeast. AVAILABILITY: A software tool which incorporates the algorithm is available for use as part of the stochastic simulation package Dizzy. It is available for download at http://labs.systemsbiology.net/bolouri/software/Dizzy/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: A conceptual model of the regulatory part of the galactose utilization pathway in yeast, used as an example in the paper, is available at http://labs.systemsbiology.net/bolouri/models/galconcept.dizzy

High information redundancy and strong correlations in face images result in inefficiencies when such images are used directly in recognition tasks. In this paper, discrete cosine transforms (DCT) are used to reduce image information redundancy because only a subset of the transform coefficients are necessary to preserve the most important facial features, such as hair outline, eyes and mouth. We demonstrate experimentally that when DCT coefficients are fed into a backpropagation neural network for classification, high recognition rates can be achieved using only a small proportion (0.19%) of available transform components. This makes DCT-based face recognition more than two orders of magnitude faster than other approaches.

We present a multilayer hierarchical neural system for automatic classification of complex contour patterns. The system consists of a neocognitron-like network structure combined with self-organizing maps to automatically determine feature classes. We present results showing that multilayer hierarchical networks are able to tolerate pattern distortion considerably better than standard neural network implementations.

The Neocognitron, inspired by the mammalian visual system, is a complex neural network with numerous parameters and weights which should be trained in order to utilise it for pattern recognition. However, it is not easy to optimise these parameters and weights by gradient decent algorithms. We present a staged training approach using evolutionary algorithms. The experiments demonstrate that evolutionary algorithms can successfully train the Neocognitron to perform image recognition on real world problems.