Statistical analysis of the features of diatonic music with jMusic

Much has been written about the rules of melody writing and this paper reports research that uses computer-based statistical analysis to test the efficacy of these rules. As a method to assist in the computer generation of melodies, we have devised computer software that analyses melodic features. This paper will outline the melodic features identified in melody-writing literature and the results of their fit with our statistical analysis of melodies from the western music repertoire. We will also present details of the computer-based analysis software and the jMusic software environment in which it was built. The software and jMusic environment are open source software projects that are freely available, and so opportunities to develop these tools to suit other music analysis tasks will be discussed.Hosted by the Scholarly Text and Imaging Service (SETIS), the University of Sydney Library, and the Research Institute for Humanities and Social Sciences (RIHSS), the University of Sydney

Composing first species counterpoint with a variable neighbourhood search algorithm

In this article, a variable neighbourhood search (VNS) algorithm is developed that can generate musical fragments consisting of a melody for the cantus firmus and the first species counterpoint. The objective function of the algorithm is based on a quantification of existing rules for counterpoint. The VNS algorithm developed in this article is a local search algorithm that starts from a randomly generated melody and improves it by changing one or two notes at a time. A thorough parametric analysis of the VNS reveals the significance of the algorithm's parameters on the quality of the composed fragment, as well as their optimal settings. A comparison of the VNS algorithm with a developed genetic algorithm shows that the VNS is more efficient. The VNS algorithm has been implemented in a user-friendly software environment for composition, called Optimuse. Optimuse allows a user to specify a number of characteristics such as length, key and mode. Based on this information, Optimuse 'composes' both cantus firmus and first species counterpoint. Alternatively, the user may specify a cantus firmus, and let Optimuse compose the accompanying first species counterpoint. © 2012 Taylor & Francis

An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis σ66 promoters

<p>Abstract</p> <p>Background</p> <p>Promoter identification is a first step in the quest to explain gene regulation in bacteria. It has been demonstrated that the initiation of bacterial transcription depends upon the stability and topology of DNA in the promoter region as well as the binding affinity between the RNA polymerase σ-factor and promoter. However, promoter prediction algorithms to date have not explicitly used an ensemble of these factors as predictors. In addition, most promoter models have been trained on data from <it>Escherichia coli</it>. Although it has been shown that transcriptional mechanisms are similar among various bacteria, it is quite possible that the differences between <it>Escherichia coli </it>and <it>Chlamydia trachomatis </it>are large enough to recommend an organism-specific modeling effort.</p> <p>Results</p> <p>Here we present an iterative stochastic model building procedure that combines such biophysical metrics as DNA stability, curvature, twist and stress-induced DNA duplex destabilization along with duration hidden Markov model parameters to model <it>Chlamydia trachomatis </it>σ⁶⁶promoters from 29 experimentally verified sequences. Initially, iterative duration hidden Markov modeling of the training set sequences provides a scoring algorithm for <it>Chlamydia trachomatis </it>RNA polymerase σ⁶⁶/DNA binding. Subsequently, an iterative application of Stepwise Binary Logistic Regression selects multiple promoter predictors and deletes/replaces training set sequences to determine an optimal training set. The resulting model predicts the final training set with a high degree of accuracy and provides insights into the structure of the promoter region. Model based genome-wide predictions are provided so that optimal promoter candidates can be experimentally evaluated, and refined models developed. Co-predictions with three other algorithms are also supplied to enhance reliability.</p> <p>Conclusion</p> <p>This strategy and resulting model support the conjecture that DNA biophysical properties, along with RNA polymerase σ-factor/DNA binding collaboratively, contribute to a sequence's ability to promote transcription. This work provides a baseline model that can evolve as new <it>Chlamydia trachomatis </it>σ⁶⁶promoters are identified with assistance from the provided genome-wide predictions. The proposed methodology is ideal for organisms with few identified promoters and relatively small genomes.</p

Listening to ecosystems: data-rich acoustic monitoring through landscape-scale sensor networks

Ecologists have many ways to measure and monitor ecosystems, each of which can reveal details about the processes unfolding therein. Acoustic recording combined with machine learning methods for species detection can provide remote, automated monitoring of species richness and relative abundance. Such recordings also open a window into how species behave and compete for niche space in the sensory environment. These opportunities are associated with new challenges: the volume and velocity of such data require new approaches to species identification and visualization. Here we introduce a newly-initiated acoustic monitoring network across the subtropical island of Okinawa, Japan, as part of the broader OKEON (Okinawa Environmental Observation Network) project. Our aim is to monitor the acoustic environment of Okinawa’s ecosystems and use these space–time data to better understand ecosystem dynamics. We present a pilot study based on recordings from five field sites conducted over a one-month period in the summer. Our results provide a proof of concept for automated species identification on Okinawa, and reveal patterns of biogenic vs. anthropogenic noise across the landscape. In particular, we found correlations between forest land cover and detection rates of two culturally important species in the island soundscape: the Okinawa Rail and Ruddy Kingfisher. Among the soundscape indices we examined, NDSI, Acoustic Diversity and the Bioacoustic Index showed both diurnal patterns and differences among sites. Our results highlight the potential utility of remote acoustic monitoring practices that, in combination with other methods can provide a holistic picture of biodiversity. We intend this project as an open resource, and wish to extend an invitation to researchers interested in scientific collaboration

Reading the Scottish Enlightenment : libraries, readers and intellectual culture in provincial Scotland c.1750-c.1820

The thesis explores the reception of the works of the Scottish Enlightenment in provincial Scotland, broadly defined, aiming to gauge their diffusion in the libraries of private book collectors and 'public' book-lending institutions, and to suggest the meanings and uses that contemporary Scottish readers assigned to major texts like Hume's History of England and Smith's Wealth of Nations. I thereby acknowledge the relevance of more traditional quantitative approaches to the history of reading (including statistical analysis of the holdings of contemporary book collections), but prioritise the study of sources that also allow us to access the 'hows' and 'whys' of individual reading practices and experiences. Indeed, the central thrust of my work has been the discovery and interrogation of large numbers of commonplace books, marginalia, diaries, correspondence and other documentary records which can be used to illuminate the reading experience itself in an explicit attempt to develop an approach to Scottish reading practices that can contribute in comparative terms to the burgeoning field of the history of reading. More particularly, such sources allow me to assess the impact that specific texts had on the lives, thought-processes and values of a wide range of contemporary readers, and to conclude that by reading these texts in their own endlessly idiosyncratic ways, consumers of literature in Scotland assimilated many of the prevalent attitudes and priorities of the literati in the major cities. Since many of the most important and pervasive manifestations of Enlightenment in Scotland were not particularly Scottish, however, I also cast doubt on the distinctive Scottishness of the prevailing 'cultural' definition of the Scottish Enlightenment, arguing that such behaviour might more appropriately be considered alongside cultural developments in Georgian England

BioPatML.NET – a bioinformatic pattern search engine

In the present paper, we introduce BioPatML.NET, an application library for the Microsoft Windows .NET framework [2] that implements the BioPatML pattern definition language and sequence search engine. BioPatML.NET is integrated with the Microsoft Biology Foundation (MBF) application library [3], unifying the parsers and annotation services supported or emerging through MBF with the language, search framework and pattern repository of BioPatML. End users who wish to exploit the BioPatML.NET engine and repository without engaging the services of a programmer may do so via the freely accessible web-based BioPatML Editor, which we describe below