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Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and… (More)
SUMMARY The SBW-MATLAB Interface allows MATLAB users to take advantage of the wide variety of tools available through SBW, the Systems Biology Workbench (Sauro et al. (2003) OMICS, 7, 355-372). It also enables MATLAB users to themselves create SBW-enabled tools which can be freely distributed.
The singing of juvenile songbirds is highly variable and not well stereotyped, a feature that makes it difficult to analyze with existing computational techniques. We present here a method suitable for analyzing such vocalizations, windowed spectral pattern recognition (WSPR). Rather than performing pairwise sample comparisons, WSPR measures the typicality… (More)
The usual form of the Problem-Oriented Medical Record is primarily focused on the individual, and thus has serious deficiencies for the family-oriented physician. This paper presents a practical, office-tested medical charting system that incorporates features of the Problem-Oriented Medical Record and allows the recording of aspects of the family situation… (More)
In keeping with the spirit of Lamarckian evolution, variations on a simple genetic algorithm are compared, in which each individual is optimized prior to evaluation. Four different optimization techniques in all are tested: random hillclimbing, social (memetic) exchange, and two techniques using artificial neural nets (ANNs). These techniques are tested on… (More)
As a contribution to the BioSPICE project, we have developed an optimization module , for the task of fitting kinetic rate constants to time series concentration data. The algorithms use, both local searches, such as the Levenberg-Marquardt, and simplex, as well as global search methods such as simulated annealing and real coded genetic algorithms. We… (More)