PiGx: reproducible genomics analysis pipelines with GNU Guix

In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations or for the wider dissemination of workflows. Providing this type of reproducibility and traceability, however, is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally come in various versions. Moreover, in many fields (bioinformatics being a prime example), these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. Here, we propose a principled approach for building analysis pipelines and managing their dependencies with GNU Guix. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines called PiGx for the analysis of RNA-seq, ChIP-seq, Bisulfite-seq, and single-cell RNA-seq. All pipelines process raw experimental data, and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise beyond the use of the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own data sets or bioinformaticians seeking to automate all, or parts of, their analyses. In the long term, we hope our approach to reproducibility will serve as a blueprint for reproducible workflows in other areas. Our pipelines, along with their corresponding documentation and sample reports, are available at http://bioinformatics.mdc-berlin.de/pigx

The emergent curriculum: navigating a complex course between unguided learning and planned enculturation

This study uses the ‘logic’ of emergence to rethink the practice and purposes of modern Western schooling which, conventionally, is organized around a representational epistemology and aims to enculture the student into a particular way of being. The idea of ‘planned enculturation’ is, however, problematic for contemporary multicultural societies for it raises the question of which or whose culture should be promoted through schooling. The authors argue that emergentist challenges to representational epistemology have not released schooling from its problematic function of planned enculturation. However, if the logic of emergence is applied not only to knowledge but also to human subjectivity then the educational problem of planned enculturation disappears. When emergentist logic is applied in this double sense, it becomes possible to understand the primary responsibility of the educator not as a responsibility to promote a particular way of being, but as a responsibility to the singularity and uniqueness of each individual student. If this is what counts as ‘educational responsibility’ then this would distinguish ‘responsible’ educational practices from unguided learning on the one hand and practices of planned enculturation/socialization (training) on the other

Religious faith and psychosocial adaptation among stroke patients in Kuwait: A mixed method study

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2012 Springer Science+Business Media.Religious faith is central to life for Muslim patients in Kuwait, so it may influence adaptation and rehabilitation. This study explored quantitative associations among religious faith, self-efficacy, and life satisfaction in 40 female stroke patients and explored the influence of religion within stroke rehabilitation through qualitative interviews with 12 health professionals. The quantitative measure of religious faith did not relate to life satisfaction or self-efficacy in stroke patients. However, the health professionals described religious coping as influencing adaptation post-stroke. Fatalistic beliefs were thought to have mixed influences on rehabilitation. Measuring religious faith among Muslims through a standardized scale is debated. The qualitative accounts suggest that religious beliefs need to be acknowledged in stroke rehabilitation in Kuwait

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

Responsibility, complexity science and education: Dilemmas and uncertain responses

While complexity science is gaining interest among educational theorists, its constructs do not speak to educational responsibility or related core issues in education of power and ethics. Yet certain themes of complexity, as taken up in educational theory, can help unsettle the more controlling and problematic discourses of educational responsibility such as the potential to limit learning and subjectivity or to prescribe social justice. The purpose of this article is to critically examine complexity science against notions of responsibility in terms of implications for education. First, themes of complexity science prominent in contemporary educational writing are explained. Then dilemmas of responsibility in complexity are explored, such as what forms and meanings responsibility can have in a ‘complexified’ perspective of education, how care for others is mobilised, and how desire can be understood. Analyses of ethical action grounded in complexity science are then examined, as well as theories of the ethical subject and participatory responsibility that are congruent with certain tenets of a complexity ontology. Finally, the possibility of an educational vision of responsibility animated by complexity theories is considered, drawing from related writings of Bai, Biesta, Derrida, Levinas and Varela

Metacognitions about desire thinking predict the severity of binge eating in a sample of Italian women

In this study, our principal aim was to investigate whether metacognitions about desire thinking predict the severity of binge eating in women and, if so, whether this relationship is independent of age, self-reported body mass index (BMI), negative affect, irrational food beliefs and craving. One hundred and four women, consisting of 32 consecutive patients with binge eating disorder undergoing initial assessment for cognitive therapy for eating disorders, 39 moderate binge eaters, and 33 non-binge eaters (both from the general population), completed the following measures: Self-reported BMI, Hospital Anxiety and Depression Scale, Irrational Food Beliefs Scale, General Craving Scale, Metacognitions about Desire Thinking Questionnaire, and Binge Eating Scale. A series of Spearman's rho correlation analyses revealed that self-reported BMI, anxiety, depression, irrational food beliefs, craving, and all three factors of the metacognitions about desire thinking questionnaire were significantly associated with the severity of binge eating. A stepwise regression analysis identified self-reported BMI, craving, and negative metacognitions about desire thinking as significant predictors of the severity of binge eating. These results, taken together, highlight the possible role of metacognitions about desire thinking in predicting the severity of binge eating. The clinical implications of these findings are discussed

Income distribution: Second thoughts

As a follow-up of his book on income distribution the author reformulates his version on the scarcity theory of income from productive contributions. The need to introduce into an earnings theory several job characteristics, non-cognitive as well as cognitive, and the corresponding personality traits is stressed, the latter subdivided into innate and learnable capabilities. The theory is presented in two alternative mathematical versions: one where job and person characteristics are continuous and one where they have discrete values and their frequencies assume continuous values. Although, mainly in the United States, numerous empirical inquiries have been made, job characteristics and the corresponding personal characteristics have not been included in sufficient number. I want to express my profound gratitude to Professor Robert H. Haveman, who not only published a deep-delving review article on my book Income Distribution: Analysis and Policies but also commented on an earlier text of the present article. I also owe a great debt to Professor Jan Pen who in a long series of discussions challenged a number of my concepts and figures. Finally I want to thank Dr. S. K. Kuipers for helpful comments on an earlier draft