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User-friendly Software (user-friendly + software)
Selected AbstractsEASY AND FLEXIBLE BAYESIAN INFERENCE OF QUANTITATIVE GENETIC PARAMETERSEVOLUTION, Issue 6 2009Patrik Waldmann There has been a tremendous advancement of Bayesian methodology in quantitative genetics and evolutionary biology. Still, there are relatively few publications that apply this methodology, probably because the availability of multipurpose and user-friendly software is somewhat limited. It is here described how only a few rows of code of the well-developed and very flexible Bayesian software WinBUGS (Lunn et al. 2000) can be used for inference of the additive polygenic variance and heritabilty in pedigrees of general design. The presented code is illustrated by application to an earlier published dataset of Scots pine. [source] Rapid and accurate quantitative phase analysis using a fast detectorJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2004A. F. Gualtieri The accuracy of the weight fractions calculated with the Rietveld method for various polycrystalline systems using data collected for very short times (5,45,min) with an RTMS (real-time multiple strip) detector was verified. The weight estimates were compared with those obtained using the same conventional Bragg,Brentano geometry, a gas proportional detector and a 13,h data acquisition. The analysed samples were monophasic and polyphasic mixtures with different degrees of complexity: the standard corundum NIST 676; a sample (labelled 1g) provided as a standard sample for the IUCr CPD Quantitative Phase Analysis Round Robin; a natural pyroclastic rock from Riano (Rome, Italy) containing zeolitic minerals and a glass phase; and a hydraulic lime. The results of the refinements show estimated weights consistent with both those obtained with a gas proportional detector and with the nominal values, indicating a very good accuracy. Only when variable slits are used, the accuracy of the estimated weights slightly decreases. The outcome of this work is a very important step forward towards fast and accurate QPA for production control and quality management, obtained by combining the use of a rapid detector and existing user-friendly software. [source] Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modellingJOURNAL OF BIOGEOGRAPHY, Issue 9 2009J. D. Lozier Abstract The availability of user-friendly software and publicly available biodiversity databases has led to a rapid increase in the use of ecological niche modelling to predict species distributions. A potential source of error in publicly available data that may affect the accuracy of ecological niche models (ENMs), and one that is difficult to correct for, is incorrect (or incomplete) taxonomy. Here we remind researchers of the need for careful evaluation of database records prior to use in modelling, especially when the presence of cryptic species is suspected or many records are based on indirect evidence. To draw attention to this potential problem, we construct ENMs for the North American Sasquatch (i.e. Bigfoot). Specifically, we use a large database of georeferenced putative sightings and footprints for Sasquatch in western North America, demonstrating how convincing environmentally predicted distributions of a taxon's potential range can be generated from questionable site-occurrence data. We compare the distribution of Bigfoot with an ENM for the black bear, Ursus americanus, and suggest that many sightings of this cryptozoid may be cases of mistaken identity. [source] Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resourcesANIMAL GENETICS, Issue 2010P. J. Boettcher Summary The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization. [source] Combining experimental data for structure determination of flexible multimeric macromolecules by molecular replacementACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2006Stefano Trapani A major effort has been made by the structural biology community to develop user-friendly software for the use of biologists. However, structural projects become more and more challenging and their solution often relies on a combination of information from various sources. Here, it is described how X-ray data, normal-mode analysis (NMA) and electron-microscopy (EM) data can be successfully combined in order to obtain a molecular-replacement (MR) solution for crystal structures containing multimeric molecules. NMA is used to simulate computationally the inherent internal flexibility of the monomer and thus enhance, together with the crystal noncrystallographic symmetry (NCS), the MR capabilities. NCS is also used to obtain a reliable EM reconstruction, which is then employed as a filter to construct oligomers starting from monomers. The feasibility of the direct use of EM reconstructions as a template for MR when the X-ray and EM data resolutions overlap is also discussed. [source] | |||||||||||||