Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. Results We first used simulated reads to explore the relationship between the level of compression and the error rate, the length of the reads and the level of sampling of the underlying genome and compare choices of second-stage compression algorithm. We demonstrate that compression may be greatly improved by a particular reordering of the sequences in the collection and give a novel `implicit sorting' strategy that enables these benefits to be realised without the overhead of sorting the reads. With these techniques, a 45x coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3Gbp of sequence to fit into only 8.2Gbytes of space (trimming a small proportion of low-quality bases from the reads improves the compression still further). This is more than 4 times smaller than the size achieved by a standard BWT-based compressor (bzip2) on the untrimmed reads, but an important further advantage of our approach is that it facilitates the building of compressed full text indexes such as the FM-index on large-scale DNA sequence collections.Comment: Version here is as submitted to Bioinformatics and is same as the previously archived version. This submission registers the fact that the advanced access version is now available at http://bioinformatics.oxfordjournals.org/content/early/2012/05/02/bioinformatics.bts173.abstract . Bioinformatics should be considered as the original place of publication of this article, please cite accordingl

Emotionally Charged Aesthetic Experience

Abstract In traditional aesthetics, the typical characteristic of aesthetic experience is said to be pure disinterested beauty. However, the discussion based on this notion is burdened with the philosophical background assumptions of German idealism. In his Art as Experience John Dewey challenged the classical philosophical tradition and presented the key ideas for developing a new concept of aesthetic experience. In order to understand his pragmatist notion of aesthetic experience it is necessary to discuss a number of topics concerning pragmatist the challenge to classical philosophy. The philosophical naturalism of pragmatism questions the traditional distinction between the changing empirical world and the mind-independent real world as an object of genuine knowledge. There is only one world and we are in it. Dewey’s naturalism is, however, in important respects different from the main trend in contemporary naturalism. Further, the pragmatist conception of experience must be clearly distinguished from the traditional notion of experience as sense experience. Action and practice are modes of experiencing and understanding the world. The third topic concerns the naturalistic denial of any immaterial substances. The mind is necessarily embodied, but this is not enough to remove the classical dichotomy between internal and external. A fourth questionable dichotomy in classical philosophy is related to this: the sharp distinction between reason and experience. The pragmatist notion of meaning undermines this dualism. This notion of meaning also serves as a basis for understanding Dewey’s comments on the meanings typical in art. Finally, the emotionally expressive power of art requires an explanation. A discussion of all these points helps to clarify the character of the pragmatist notion of aesthetic experience developed below.Peer reviewe

Scapegoat: John Dewey and the character education crisis

Many conservatives, including some conservative scholars, blame the ideas and influence of John Dewey for what has frequently been called a crisis of character, a catastrophic decline in moral behavior in the schools and society of North America. Dewey’s critics claim that he is responsible for the undermining of the kinds of instruction that could lead to the development of character and the strengthening of the will, and that his educational philosophy and example exert a ubiquitous and disastrous influence on students’ conceptions of moral behavior. This article sets forth the views of some of these critics and juxtaposes them with what Dewey actually believed and wrote regarding character education. The juxtaposition demonstrates that Dewey neither called for nor exemplified the kinds of character-eroding pedagogy his critics accuse him of championing; in addition, this paper highlights the ways in which Dewey argued consistently and convincingly that the pedagogical approaches advocated by his critics are the real culprits in the decline of character and moral education

From representation to emergence: complexity's challenge to the epistemology of schooling

In modern,Western societies the purpose of schooling is to ensure that school-goers acquire knowledge of pre-existing practices, events, entities and so on.The knowledge that is learned is then tested to see if the learner has acquired a correct or adequate understanding of it. For this reason, it can be argued that schooling is organised around a representational epistemology: one which holds that knowledge is an accurate representation of something that is separate from knowledge itself. Since the object of knowledge is assumed to exist separately from the knowledge itself, this epistemology can also be considered ‘spatial.’ In this paper we show how ideas from complexity have challenged the ‘spatial epistemology’ of representation and we explore possibilities for an alternative ‘temporal’ understanding of knowledge in its relationship to reality. In addition to complexity, our alternative takes its inspiration from Deweyan ‘transactional realism’ and deconstruction. We suggest that ‘knowledge’ and ‘reality’ should not be understood as separate systems which somehow have to be brought into alignment with each other, but that they are part of the same emerging complex system which is never fully ‘present’ in any (discrete) moment in time. This not only introduces the notion of time into our understanding of the relationship between knowledge and reality, but also points to the importance of acknowledging the role of the ‘unrepresentable’ or ‘incalculable’. With this understanding knowledge reaches us not as something we receive but as a response, which brings forth new worlds because it necessarily adds something (which was not present anywhere before it appeared) to what came before. This understanding of knowledge suggests that the acquisition of curricular content should not be considered an end in itself. Rather, curricular content should be used to bring forth that which is incalculable from the perspective of the present. The epistemology of emergence therefore calls for a switch in focus for curricular thinking, away from questions about presentation and representation and towards questions about engagement and response

Spectral Line Imaging Observations of 1E0102.2-7219

E0102-72 is the second brightest X-ray source in the Small Magellanic Cloud and the brightest supernova remnant in the SMC. We observed this SNR for ~140 ksec with the High Energy Transmission Gratings (HETG) aboard the Chandra X-ray Observatory. The small angular size and high surface brightness make this an excellent target for HETG and we resolve the remnant into individual lines. We observe fluxes from several lines which include O VIII Ly$\alpha$, Ly$\beta$, and O VII along with several lines from Ne X, Ne IX and Mg XII. These line ratios provide powerful constraints on the electron temperature and the ionization age of the remnant.Comment: To appear in "Young Supernova Remnants" (11th Annual Astrophysics Conference in Maryland), S. S. Holt & U. Hwang (eds), AIP, New York (2001

Deweyan tools for inquiry and the epistemological context of critical pedagogy

This article develops the notion of resistance as articulated in the literature of critical pedagogy as being both culturally sponsored and cognitively manifested. To do so, the authors draw upon John Dewey\u27s conception of tools for inquiry. Dewey provides a way to conceptualize student resistance not as a form of willful disputation, but instead as a function of socialization into cultural models of thought that actively truncate inquiry. In other words, resistance can be construed as the cognitive and emotive dimensions of the ongoing failure of institutions to provide ideas that help individuals both recognize social problems and imagine possible solutions. Focusing on Dewey\u27s epistemological framework, specifically tools for inquiry, provides a way to grasp this problem. It also affords some innovative solutions; for instance, it helps conceive of possible links between the regular curriculum and the study of specific social justice issues, a relationship that is often under-examined. The aims of critical pedagogy depend upon students developing dexterity with the conceptual tools they use to make meaning of the evidence they confront; these are background skills that the regular curriculum can be made to serve even outside social justice-focused curricula. Furthermore, the article concludes that because such inquiry involves the exploration and potential revision of students\u27 world-ordering beliefs, developing flexibility in how one thinks may be better achieved within academic subjects and topics that are not so intimately connected to students\u27 current social lives, especially where students may be directly implicated

Precision determination of absolute neutron flux

A technique for establishing the total neutron rate of a highly-collimated monochromatic cold neutron beam was demonstrated using a method of an alpha-gamma counter. The method involves only the counting of measured rates and is independent of neutron cross sections, decay chain branching ratios, and neutron beam energy. For the measurement, a target of 10B-enriched boron carbide totally absorbed the neutrons in a monochromatic beam, and the rate of absorbed neutrons was determined by counting 478keV gamma rays from neutron capture on 10B with calibrated high-purity germanium detectors. A second measurement based on Bragg diffraction from a perfect silicon crystal was performed to determine the mean de Broglie wavelength of the beam to a precision of 0.024 %. With these measurements, the detection efficiency of a neutron monitor based on neutron absorption on 6Li was determined to an overall uncertainty of 0.058 %. We discuss the principle of the alpha-gamma method and present details of how the measurement was performed including the systematic effects. We also describe how this method may be used for applications in neutron dosimetry and metrology, fundamental neutron physics, and neutron cross section measurements.Comment: 44 page

Knowledge, the curriculum, and democratic education: the curious case of school English

Debate over subject curricula is apt to descend into internecine squabbles over which (whose?) curriculum is best. Especially so with school English, because its domain(s) of knowledge have commonly been misunderstood, or, perhaps, misrepresented in the government’s programmes of study. After brief consideration of democratic education (problems of its form and meaning), I turn to issues of knowledge and disciplinarity, outlining two conceptions of knowledge – the one constitutive and phenomenological, the other stipulative and social-realist. Drawing on Michael Young and Johan Muller, I argue that, by social-realist standards of objectivity, school English in England -- as currently framed in national curriculum documents -- falls short of the standards of ‘powerful knowledge’ and of a democratic education conceived as social justice. Having considered knowledge and disciplinarity in broad terms, I consider the curricular case of school English, for it seems to me that the curious position of English in our national curriculum has resulted in a model that is either weakly, perhaps even un-, rooted in the network of academic disciplines that make up English studies