An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Multi-Instantons and Exact Results II: Specific Cases, Higher-Order Effects, and Numerical Calculations

In this second part of the treatment of instantons in quantum mechanics, the focus is on specific calculations related to a number of quantum mechanical potentials with degenerate minima. We calculate the leading multi-instanton constributions to the partition function, using the formalism introduced in the first part of the treatise [J. Zinn-Justin and U. D. Jentschura, e-print quant-ph/0501136]. The following potentials are considered: (i) asymmetric potentials with degenerate minima, (ii) the periodic cosine potential, (iii) anharmonic oscillators with radial symmetry, and (iv) a specific potential which bears an analogy with the Fokker-Planck equation. The latter potential has the peculiar property that the perturbation series for the ground-state energy vanishes to all orders and is thus formally convergent (the ground-state energy, however, is nonzero and positive). For the potentials (ii), (iii), and (iv), we calculate the perturbative B-function as well as the instanton A-function to fourth order in g. We also consider the double-well potential in detail, and present some higher-order analytic as well as numerical calculations to verify explicitly the related conjectures up to the order of three instantons. Strategies analogous to those outlined here could result in new conjectures for problems where our present understanding is more limited.Comment: 55 pages, LaTeX; refs. to part I preprint update

Typology of goat feeding systems in Benin

Feeding is one of the limiting factors of productivity in goat production in developing countries. That’s why this study was carried out to characterize the feeding systems used in goat farming in Benin. Accordingly, a semi-structured survey was conducted among 533 goat farmers in 6 agro-ecological zones in Benin. Data were collected on socio-demographic characteristics, breeding practices and feeding methods. A typology of goat feeding systems was developed using a factorial analysis of mixed data followed by an ascending hierarchical classification. The results of the study revealed three main types of feeding systems. These are feeding systems based on the use of: (i) natural pasture in a free-grazing system, (ii) natural pasture, crop residues and concentrates in a semi-controlled breeding system, and (iii) natural pasture, crop residues and concentrates in a controlled breeding system. The implementation of a programme to improve goat feeding and management systems will contribute significantly to increasing goat productivity. It will also contribute to food security in the rural community. Keywords: Benin, Capra hircus, feeding practices, management practice

Efficient Color-Dressed Calculation of Virtual Corrections

With the advent of generalized unitarity and parametric integration techniques, the construction of a generic Next-to-Leading Order Monte Carlo becomes feasible. Such a generator will entail the treatment of QCD color in the amplitudes. We extend the concept of color dressing to one-loop amplitudes, resulting in the formulation of an explicit algorithmic solution for the calculation of arbitrary scattering processes at Next-to-Leading order. The resulting algorithm is of exponential complexity, that is the numerical evaluation time of the virtual corrections grows by a constant multiplicative factor as the number of external partons is increased. To study the properties of the method, we calculate the virtual corrections to $n$-gluon scattering.Comment: 48 pages, 23 figure

Bell numbers and Kurepa’s conjecture

We prove under a mild condition that Kurepa's conjecture holds for the set of prime numbers $p$ such that (\frac{p-1}{2})! = {2 \overwithdelims () p\;} in $\mathbb{F}_p$

Visible and near infrared spectroscopy in soil science

This chapter provides a review on the state of soil visible–near infrared (vis–NIR) spectroscopy. Our intention is for the review to serve as a source of up-to date information on the past and current role of vis–NIR spectroscopy in soil science. It should also provide critical discussion on issues surrounding the use of vis–NIR for soil analysis and on future directions. To this end, we describe the fundamentals of visible and infrared diffuse reflectance spectroscopy and spectroscopic multivariate calibrations. A review of the past and current role of vis–NIR spectroscopy in soil analysis is provided, focusing on important soil attributes such as soil organic matter (SOM), minerals, texture, nutrients, water, pH, and heavy metals. We then discuss the performance and generalization capacity of vis–NIR calibrations, with particular attention on sample pre-tratments, co-variations in data sets, and mathematical data preprocessing. Field analyses and strategies for the practical use of vis–NIR are considered. We conclude that the technique is useful to measure soil water and mineral composition and to derive robust calibrations for SOM and clay content. Many studies show that we also can predict properties such as pH and nutrients, although their robustness may be questioned. For future work we recommend that research should focus on: (i) moving forward with more theoretical calibrations, (ii) better understanding of the complexity of soil and the physical basis for soil reflection, and (iii) applications and the use of spectra for soil mapping and monitoring, and for making inferences about soils quality, fertility and function. To do this, research in soil spectroscopy needs to be more collaborative and strategic. The development of the Global Soil Spectral Library might be a step in the right direction