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Selected AbstractsBulk-solvent correction for fast translation search in molecular replacement: service programs for AMoRe and CNSJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003Andrei Fokine A new software package, BULK, was developed to allow fast and easy use of low-resolution data for the translation problem in molecular replacement. When the search model is relatively complete but not precise, or when its orientation is imprecisely determined, low-resolution data contribute very favourably to the solution of the translation-search problem. BULK comprises a specially developed program and a set of procedures complementary to the program AMoRe, as well as an input file for the CNS suite. [source] seqphase: a web tool for interconverting phase input/output files and fasta sequence alignmentsMOLECULAR ECOLOGY RESOURCES, Issue 1 2010J-F. FLOT Abstract The program phase is widely used for Bayesian inference of haplotypes from diploid genotypes; however, manually creating phase input files from sequence alignments is an error-prone and time-consuming process, especially when dealing with numerous variable sites and/or individuals. Here, a web tool called seqphase is presented that generates phase input files from fasta sequence alignments and converts phase output files back into fasta. During the production of the phase input file, several consistency checks are performed on the dataset and suitable command line options to be used for the actual phase data analysis are suggested. seqphase was written in perl and is freely accessible over the Internet at the address http://www.mnhn.fr/jfflot/seqphase. [source] Validation of a vegetated filter strip model (VFSMOD)HYDROLOGICAL PROCESSES, Issue 5 2001Dr Majed Abu-Zreig Abstract Vegetated filter strips (VFS) are designed to reduce sediment load and other pollutants into water bodies. However, adaptation of VFS in the field has been limited owing to lack of data about their efficiency and performance under natural field conditions. A number of models are available that simulate sediment transport and trapping in VFS, but there is a general lack of confidence in VFS models owing to limited validation studies and model limitations that prevent correct application of these models under field conditions. The objective of this study is to test and validate a process-based model (VFSMOD) that simulates sediment trapping in VFS. This model links three submodels: modified Green,Ampt's infiltration, Quadratic overland flow submodel based on kinematic wave approximation and University of Kentucky sediment filtration model. A total of 20 VFS, 2, 5, 10 and 15 m long and with various vegetation covers, were tested under simulated sediment and runoff conditions. The results of these field experiments were used to validate the VFS model. The model requires 25 input parameters distributed over five input files. All input parameters were either measured or calculated using experimental data. The observed sediment trapping efficiencies varied from 65% in the 2-m long VFS to 92% in the 10-m long filters. No increase in sediment removal efficiency was observed at higher VFS length. Application of the VFS model to experimental data was satisfactory under the condition that actual flow widths are used in the model instead of the total filter width. Predicted and observed sediment trapping efficiencies and infiltration volume fitted very well, with a coefficient of determination (R2) of 0·9 and 0·95, respectively. Regression analyses revealed that the slope and intercept of the regression lines between predicted versus observed infiltration volume and trapping efficiency were not significantly different than the line of perfect agreement with a slope of 1·0 and intercept of 0·0. Copyright © 2001 John Wiley & Sons, Ltd. [source] MaSK: A visualization tool for teaching and research in computational chemistryINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2009Yevgeniy Podolyan Abstract The number of researchers using computational chemistry tools is growing every year. There are multiple programs used for calculation of various molecular and electronic properties such as optimized geometry, energy, vibrational spectra, and so forth. Another set of programs is used for the visualization of these properties. However, such programs are either too complex for a beginner or too simple for an intermediate user for everyday use. Molecular Modeling and Simulation Kit (MaSK) is designed to fill this gap by presenting an easy-to-use intuitive interface to quantum chemical programs such as GAMESS and Gaussian with an array of advanced tools. The program can be used as a postprocessor to visualize calculated properties or as a preprocessor to prepare the input files for quantum chemical programs. In addition, some properties such as the surfaces of molecular orbitals, electron and spin densities, and molecular electrostatic potentials are actually calculated by MaSK. If MaSK is combined with PC GAMESS, the preparation of the input, running of the calculations, and the display of the results can all be done without leaving the program's interface. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] INTEGRATING LANDSCAPE ASSESSMENT AND HYDROLOGIC MODELING FOR LAND COVER CHANGE ANALYSIS,JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 4 2002Scott N. Miller ABSTRACT: Significant land cover changes have occurred in the watersheds that contribute runoff to the upper San Pedro River in Sonora, Mexico, and southeast Arizona. These changes, observed using a series of remotely sensed images taken in the 1970s, 1980s, and 1990s, have been implicated in the alteration of the basin hydrologic response. The Cannonsville subwatershed, located in the Catskill/Delaware watershed complex that delivers water to New York City, provides a contrast in land cover change. In this region, the Cannonsville watershed condition has improved over a comparable time period. A landscape assessment tool using a geographic information system (GIS) has been developed that automates the parameterization of the Soil and Water Assessment Tool (SWAT) and KINEmatic Runoff and EROSion (KINEROS) hydrologic models. The Automated Geospatial Watershed Assessment (AGWA) tool was used to prepare parameter input files for the Upper San Pedro Basin, a subwatershed within the San Pedro undergoing significant changes, and the Cannonsville watershed using historical land cover data. Runoff and sediment yield were simulated using these models. In the Cannonsville watershed, land cover change had a beneficial impact on modeled watershed response due to the transition from agriculture to forest land cover. Simulation results for the San Pedro indicate that increasing urban and agricultural areas and the simultaneous invasion of woody plants and decline of grasslands resulted in increased annual and event runoff volumes, flashier flood response, and decreased water quality due to sediment loading. These results demonstrate the usefulness of integrating remote sensing and distributed hydrologic models through the use of GIS for assessing watershed condition and the relative impacts of land cover transitions on hydrologic response. [source] EPA'S BASINS MODEL: GOOD SCIENCE OR SERENDIPITOUS MODELING?,JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 3 2000Ray C. Whittemore ABSTRACT: Better Assessment Science Integrating Point and Non-point Sources (BASINS) is a geographic-based watershed assessment tool developed by EPA's Office of Water to help states more efficiently target and evaluate water-bodies that are not meeting water quality standards. BASINS (EPA, 1996a, 1998) brings together data on water quality and quantity, land uses, point source loadings, and other related spatial data with supporting nonpoint and water quality models at a quicker and more effective pace. EPA developed BASINS, to better integrate point and nonpoint source water quality assessments for the Nation's 2100+ watersheds. In its zeal to achieve this endpoint, EPA has initiated a simplistic approach that was expected to grow through scientific enhancements as TMDL developers become more familiar with modeling requirements. BASINS builds upon federal databases of water quality conditions and point source loadings for numerous parameters where quality assurance is suspect in some cases. Its design allows comprehensive assessments and modeling in typical Total Maximum Daily Load (TMDL) computations. While the TMDL utility is the primary reason BASINS was developed, other longer-range water quality assessments will become possible as the Agency expands the suite of assessment models and databases in future releases. The simplistic approach to modeling and user-friendly tools gives rise, however, to technical and philosophical concerns related to default data usage. Seamless generation of model input files and the failure of some utilities to work properly suggest to NCASI that serious problems may still exist and prompts the need for a more rigorous peer-review. Furthermore, sustainable training becomes paramount, as some older modelers will be unfamiliar with Geographic Information System (GIS) technology and associated computer skills. Overall, however, BASINS was judged to be an excellent beginning tool to meet the complex environmental modeling needs in the 21st Century. [source] seqphase: a web tool for interconverting phase input/output files and fasta sequence alignmentsMOLECULAR ECOLOGY RESOURCES, Issue 1 2010J-F. FLOT Abstract The program phase is widely used for Bayesian inference of haplotypes from diploid genotypes; however, manually creating phase input files from sequence alignments is an error-prone and time-consuming process, especially when dealing with numerous variable sites and/or individuals. Here, a web tool called seqphase is presented that generates phase input files from fasta sequence alignments and converts phase output files back into fasta. During the production of the phase input file, several consistency checks are performed on the dataset and suitable command line options to be used for the actual phase data analysis are suggested. seqphase was written in perl and is freely accessible over the Internet at the address http://www.mnhn.fr/jfflot/seqphase. [source] convert: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packagesMOLECULAR ECOLOGY RESOURCES, Issue 2 2004Jeffrey C. Glaubitz Abstract convert is a user-friendly, 32-bit Windows program that facilitates ready transfer of codominant, diploid genotypic data amongst commonly used population genetic software packages. convert reads input files in its own ,standard' data format, easily produced from an excel file of diploid, codominant marker data, and can convert these to the input formats of the following programs: gda, genepop, arlequin, popgene, microsat, phylip, and structure. convert can also read input files in genepop format. In addition, convert can produce a summary table of allele frequencies in which private alleles and the sample sizes at each locus are indicated. [source] | |||||||||||||