Benchmarking GNU Radio Kernels and Multi-Processor Scheduling

DTIC Science & Technology

2013-01-14

AMD E350 APU , comparable to Atom • ARM Cortex A8 running on a Gumstix Overo on an Ettus USRP E110 The general testing procedure consists of • Build...Intel Atom, and the AMD E350 APU . 3.2 Multi-Processor Scheduling Figure 1: GFLOPs per second through an FFT array on an Intel i7. Example output from

Automatic Astrometric and Photometric Calibration with SCAMP

NASA Astrophysics Data System (ADS)

Bertin, E.

2006-07-01

Astrometric and photometric calibrations have remained the most tiresome step in the reduction of large imaging surveys. I present a new software package, SCAMP which has been written to address this problem. SCAMP efficiently computes accurate astrometric and photometric solutions for any arbitrary sequence of FITS images in a completely automatic way. SCAMP is released under the GNU General Public Licence.

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

PubMed

Xu, Ying; Li, Yi-xue; Kong, Xiang-yin

2005-06-01

To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. Gpat, which is based on SPLASH algorithm, was developed by using open source software. GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

Gravitationally neutral dark matter-dark antimatter universe crystal with epochs of decelerated and accelerated expansion

NASA Astrophysics Data System (ADS)

Gribov, I. A.; Trigger, S. A.

2016-11-01

A large-scale self-similar crystallized phase of finite gravitationally neutral universe (GNU)—huge GNU-ball—with spherical 2D-boundary immersed into an endless empty 3D- space is considered. The main principal assumptions of this universe model are: (1) existence of stable elementary particles-antiparticles with the opposite gravitational “charges” (M+gr and M -gr), which have the same positive inertial mass M in = |M ±gr | ≥ 0 and are equally presented in the universe during all universe evolution epochs; (2) the gravitational interaction between the masses of the opposite charges” is repulsive; (3) the unbroken baryon-antibaryon symmetry; (4) M+gr-M-gr “charges” symmetry, valid for two equally presented matter-antimatter GNU-components: (a) ordinary matter (OM)-ordinary antimatter (OAM), (b) dark matter (DM)-dark antimatter (DAM). The GNU-ball is weightless crystallized dust of equally presented, mutually repulsive (OM+DM) clusters and (OAM+DAM) anticlusters. Newtonian GNU-hydrodynamics gives the observable spatial flatness and ideal Hubble flow. The GNU in the obtained large-scale self-similar crystallized phase preserves absence of the cluster-anticluster collisions and simultaneously explains the observable large-scale universe phenomena: (1) the absence of the matter-antimatter clusters annihilation, (2) the self-similar Hubble flow stability and homogeneity, (3) flatness, (4) bubble and cosmic-net structures as 3D-2D-1D decrystallization phases with decelerative (a ≤ 0) and accelerative (a ≥ 0) expansion epochs, (5) the dark energy (DE) phenomena with Λ VACUUM = 0, (6) the DE and DM fine-tuning nature and predicts (7) evaporation into isolated huge M±gr superclusters without Big Rip.

Phyx: phylogenetic tools for unix.

PubMed

Brown, Joseph W; Walker, Joseph F; Smith, Stephen A

2017-06-15

The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx : a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets. phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx. eebsmith@umich.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Phyx: phylogenetic tools for unix

PubMed Central

Brown, Joseph W.; Walker, Joseph F.; Smith, Stephen A.

2017-01-01

Abstract Summary: The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx: a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets. Availability and Implementation: phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx Contact: eebsmith@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28174903

Frame Decoder for Consultative Committee for Space Data Systems (CCSDS)

NASA Technical Reports Server (NTRS)

Reyes, Miguel A. De Jesus

2014-01-01

GNU Radio is a free and open source development toolkit that provides signal processing to implement software radios. It can be used with low-cost external RF hardware to create software defined radios, or without hardware in a simulation-like environment. GNU Radio applications are primarily written in Python and C++. The Universal Software Radio Peripheral (USRP) is a computer-hosted software radio designed by Ettus Research. The USRP connects to a host computer via high-speed Gigabit Ethernet. Using the open source Universal Hardware Driver (UHD), we can run GNU Radio applications using the USRP. An SDR is a "radio in which some or all physical layer functions are software defined"(IEEE Definition). A radio is any kind of device that wirelessly transmits or receives radio frequency (RF) signals in the radio frequency. An SDR is a radio communication system where components that have been typically implemented in hardware are implemented in software. GNU Radio has a generic packet decoder block that is not optimized for CCSDS frames. Using this generic packet decoder will add bytes to the CCSDS frames and will not permit for bit error correction using Reed-Solomon. The CCSDS frames consist of 256 bytes, including a 32-bit sync marker (0x1ACFFC1D). This frames are generated by the Space Data Processor and GNU Radio will perform the modulation and framing operations, including frame synchronization.

High precision series solutions of differential equations: Ordinary and regular singular points of second order ODEs

NASA Astrophysics Data System (ADS)

Noreen, Amna; Olaussen, Kåre

2012-10-01

A subroutine for a very-high-precision numerical solution of a class of ordinary differential equations is provided. For a given evaluation point and equation parameters the memory requirement scales linearly with precision P, and the number of algebraic operations scales roughly linearly with P when P becomes sufficiently large. We discuss results from extensive tests of the code, and how one, for a given evaluation point and equation parameters, may estimate precision loss and computing time in advance. Program summary Program title: seriesSolveOde1 Catalogue identifier: AEMW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 991 No. of bytes in distributed program, including test data, etc.: 488116 Distribution format: tar.gz Programming language: C++ Computer: PC's or higher performance computers. Operating system: Linux and MacOS RAM: Few to many megabytes (problem dependent). Classification: 2.7, 4.3 External routines: CLN — Class Library for Numbers [1] built with the GNU MP library [2], and GSL — GNU Scientific Library [3] (only for time measurements). Nature of problem: The differential equation -s2({d2}/{dz2}+{1-ν+-ν-}/{z}{d}/{dz}+{ν+ν-}/{z2})ψ(z)+{1}/{z} ∑n=0N vnznψ(z)=0, is solved numerically to very high precision. The evaluation point z and some or all of the equation parameters may be complex numbers; some or all of them may be represented exactly in terms of rational numbers. Solution method: The solution ψ(z), and optionally ψ'(z), is evaluated at the point z by executing the recursion A(z)={s-2}/{(m+1+ν-ν+)(m+1+ν-ν-)} ∑n=0N Vn(z)A(z), ψ(z)=ψ(z)+A(z), to sufficiently large m. Here ν is either ν+ or ν-, and Vn(z)=vnz. The recursion is initialized by A(z)=δzν,for n=0,1,…,N ψ(z)=A0(z). Restrictions: No solution is computed if z=0, or s=0, or if ν=ν- (assuming Reν+≥Reν-) with ν+-ν- an integer, except when ν+-ν-=1 and v =0 (i.e. when z is an ordinary point for zψ(z)). Additional comments: The code of the main algorithm is in the file seriesSolveOde1.cc, which "#include" the file checkForBreakOde1.cc. These routines, and the programs using them, must "#include" the file seriesSolveOde1.cc. Running time: On a Linux PC that is a few years old, at y=√{10} to an accuracy of P=200 decimal digits, evaluating the ground state wavefunction of the anharmonic oscillator (with the eigenvalue known in advance); (cf. Eq. (6)) takes about 2 ms, and about 40 min at an accuracy of P=100000 decimal digits. References: [1] B. Haible and R.B. Kreckel, CLN — Class Library for Numbers, http://www.ginac.de/CLN/ [2] T. Granlund and collaborators, GMP — The GNU Multiple Precision Arithmetic Library, http://gmplib.org/ [3] M. Galassi et al., GNU Scientific Library Reference Manual (3rd Ed.), ISBN 0954612078., http://www.gnu.org/software/gsl/

CRITIC2: A program for real-space analysis of quantum chemical interactions in solids

NASA Astrophysics Data System (ADS)

Otero-de-la-Roza, A.; Johnson, Erin R.; Luaña, Víctor

2014-03-01

We present CRITIC2, a program for the analysis of quantum-mechanical atomic and molecular interactions in periodic solids. This code, a greatly improved version of the previous CRITIC program (Otero-de-la Roza et al., 2009), can: (i) find critical points of the electron density and related scalar fields such as the electron localization function (ELF), Laplacian, … (ii) integrate atomic properties in the framework of Bader’s Atoms-in-Molecules theory (QTAIM), (iii) visualize non-covalent interactions in crystals using the non-covalent interactions (NCI) index, (iv) generate relevant graphical representations including lines, planes, gradient paths, contour plots, atomic basins, … and (v) perform transformations between file formats describing scalar fields and crystal structures. CRITIC2 can interface with the output produced by a variety of electronic structure programs including WIEN2k, elk, PI, abinit, Quantum ESPRESSO, VASP, Gaussian, and, in general, any other code capable of writing the scalar field under study to a three-dimensional grid. CRITIC2 is parallelized, completely documented (including illustrative test cases) and publicly available under the GNU General Public License. Catalogue identifier: AECB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 11686949 No. of bytes in distributed program, including test data, etc.: 337020731 Distribution format: tar.gz Programming language: Fortran 77 and 90. Computer: Workstations. Operating system: Unix, GNU/Linux. Has the code been vectorized or parallelized?: Shared-memory parallelization can be used for most tasks. Classification: 7.3. Catalogue identifier of previous version: AECB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 157 Nature of problem: Analysis of quantum-chemical interactions in periodic solids by means of atoms-in-molecules and related formalisms. Solution method: Critical point search using Newton’s algorithm, atomic basin integration using bisection, qtree and grid-based algorithms, diverse graphical representations and computation of the non-covalent interactions index on a three-dimensional grid. Additional comments: !!!!! The distribution file for this program is over 330 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!! Running time: Variable, depending on the crystal and the source of the underlying scalar field.

GetData: A filesystem-based, column-oriented database format for time-ordered binary data

NASA Astrophysics Data System (ADS)

Wiebe, Donald V.; Netterfield, Calvin B.; Kisner, Theodore S.

2015-12-01

The GetData Project is the reference implementation of the Dirfile Standards, a filesystem-based, column-oriented database format for time-ordered binary data. Dirfiles provide a fast, simple format for storing and reading data, suitable for both quicklook and analysis pipelines. GetData provides a C API and bindings exist for various other languages. GetData is distributed under the terms of the GNU Lesser General Public License.

MCPB.py: A Python Based Metal Center Parameter Builder.

PubMed

Li, Pengfei; Merz, Kenneth M

2016-04-25

MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

PubMed

Marchetti, Luca; Manca, Vincenzo

2015-04-15

MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A New Effort for Atmospherical Forecast: Meteorological Image Processing Software (MIPS) for Astronomical Observations

NASA Astrophysics Data System (ADS)

Shameoni Niaei, M.; Kilic, Y.; Yildiran, B. E.; Yüzlükoglu, F.; Yesilyaprak, C.

2016-12-01

We have described a new software (MIPS) about the analysis and image processing of the meteorological satellite (Meteosat) data for an astronomical observatory. This software will be able to help to make some atmospherical forecast (cloud, humidity, rain) using meteosat data for robotic telescopes. MIPS uses a python library for Eumetsat data that aims to be completely open-source and licenced under GNU/General Public Licence (GPL). MIPS is a platform independent and uses h5py, numpy, and PIL with the general-purpose and high-level programming language Python and the QT framework.

RNAbrowse: RNA-Seq de novo assembly results browser.

PubMed

Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse.

A Constant Envelope OFDM Implementation on GNU Radio

DTIC Science & Technology

2015-02-02

more advanced schemes like Decision Feedback Equalization or Turbo Equalization must be implemented to avoid the noise enhancement that all linear...block is coded in C++, and uses the phase unwrapping algorithm similar to MATLABs unwrap() function. To avoid false wraps propagating throughout the...outperform the real-time GNU radio implementation at higher SNR’s. While the unequalized experiment with the Matlab processor usually stayed within 5

Lambda: A Mathematica package for operator product expansions in vertex algebras

NASA Astrophysics Data System (ADS)

Ekstrand, Joel

2011-02-01

We give an introduction to the Mathematica package Lambda, designed for calculating λ-brackets in both vertex algebras, and in SUSY vertex algebras. This is equivalent to calculating operator product expansions in two-dimensional conformal field theory. The syntax of λ-brackets is reviewed, and some simple examples are shown, both in component notation, and in N=1 superfield notation. Program summaryProgram title: Lambda Catalogue identifier: AEHF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 18 087 No. of bytes in distributed program, including test data, etc.: 131 812 Distribution format: tar.gz Programming language: Mathematica Computer: See specifications for running Mathematica V7 or above. Operating system: See specifications for running Mathematica V7 or above. RAM: Varies greatly depending on calculation to be performed. Classification: 4.2, 5, 11.1. Nature of problem: Calculate operator product expansions (OPEs) of composite fields in 2d conformal field theory. Solution method: Implementation of the algebraic formulation of OPEs given by vertex algebras, and especially by λ-brackets. Running time: Varies greatly depending on calculation requested. The example notebook provided takes about 3 s to run.

CASS—CFEL-ASG software suite

NASA Astrophysics Data System (ADS)

Foucar, Lutz; Barty, Anton; Coppola, Nicola; Hartmann, Robert; Holl, Peter; Hoppe, Uwe; Kassemeyer, Stephan; Kimmel, Nils; Küpper, Jochen; Scholz, Mirko; Techert, Simone; White, Thomas A.; Strüder, Lothar; Ullrich, Joachim

2012-10-01

The Max Planck Advanced Study Group (ASG) at the Center for Free Electron Laser Science (CFEL) has created the CFEL-ASG Software Suite CASS to view, process and analyse multi-parameter experimental data acquired at Free Electron Lasers (FELs) using the CFEL-ASG Multi Purpose (CAMP) instrument Strüder et al. (2010) [6]. The software is based on a modular design so that it can be adjusted to accommodate the needs of all the various experiments that are conducted with the CAMP instrument. In fact, this allows the use of the software in all experiments where multiple detectors are involved. One of the key aspects of CASS is that it can be used either 'on-line', using a live data stream from the free-electron laser facility's data acquisition system to guide the experiment, and 'off-line', on data acquired from a previous experiment which has been saved to file. Program summary Program title: CASS Catalogue identifier: AEMP_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence, version 3 No. of lines in distributed program, including test data, etc.: 167073 No. of bytes in distributed program, including test data, etc.: 1065056 Distribution format: tar.gz Programming language: C++. Computer: Intel x86-64. Operating system: GNU/Linux (for information about restrictions see outlook). RAM: >8 GB Classification: 2.3, 3, 15, 16.4. External routines: Qt-Framework[1], SOAP[2], (optional HDF5[3], VIGRA[4], ROOT[5], QWT[6]) Nature of problem: Analysis and visualisation of scientific data acquired at Free-Electron-Lasers Solution method: Generalise data access and storage so that a variety of small programming pieces can be linked to form a complex analysis chain. Unusual features: Complex analysis chains can be built without recompiling the program Additional comments: An updated extensive documentation of CASS is available at [7]. Running time: Depending on the data size and complexity of analysis algorithms. References: [1] http://qt.nokia.com [2] http://www.cs.fsu.edu/~engelen/soap.html [3] http://www.hdfgroup.org/HDF5/ [4] http://hci.iwr.uni-heidelberg.de/vigra/ [5] http://root.cern.ch [6] http://qwt.sourceforge.net/ [7] http://www.mpi-hd.mpg.de/personalhomes/gitasg/cass

Accelerating numerical solution of stochastic differential equations with CUDA

NASA Astrophysics Data System (ADS)

Januszewski, M.; Kostur, M.

2010-01-01

Numerical integration of stochastic differential equations is commonly used in many branches of science. In this paper we present how to accelerate this kind of numerical calculations with popular NVIDIA Graphics Processing Units using the CUDA programming environment. We address general aspects of numerical programming on stream processors and illustrate them by two examples: the noisy phase dynamics in a Josephson junction and the noisy Kuramoto model. In presented cases the measured speedup can be as high as 675× compared to a typical CPU, which corresponds to several billion integration steps per second. This means that calculations which took weeks can now be completed in less than one hour. This brings stochastic simulation to a completely new level, opening for research a whole new range of problems which can now be solved interactively. Program summaryProgram title: SDE Catalogue identifier: AEFG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu GPL v3 No. of lines in distributed program, including test data, etc.: 978 No. of bytes in distributed program, including test data, etc.: 5905 Distribution format: tar.gz Programming language: CUDA C Computer: any system with a CUDA-compatible GPU Operating system: Linux RAM: 64 MB of GPU memory Classification: 4.3 External routines: The program requires the NVIDIA CUDA Toolkit Version 2.0 or newer and the GNU Scientific Library v1.0 or newer. Optionally gnuplot is recommended for quick visualization of the results. Nature of problem: Direct numerical integration of stochastic differential equations is a computationally intensive problem, due to the necessity of calculating multiple independent realizations of the system. We exploit the inherent parallelism of this problem and perform the calculations on GPUs using the CUDA programming environment. The GPU's ability to execute hundreds of threads simultaneously makes it possible to speed up the computation by over two orders of magnitude, compared to a typical modern CPU. Solution method: The stochastic Runge-Kutta method of the second order is applied to integrate the equation of motion. Ensemble-averaged quantities of interest are obtained through averaging over multiple independent realizations of the system. Unusual features: The numerical solution of the stochastic differential equations in question is performed on a GPU using the CUDA environment. Running time: < 1 minute

Mushu, a free- and open source BCI signal acquisition, written in Python.

PubMed

Venthur, Bastian; Blankertz, Benjamin

2012-01-01

The following paper describes Mushu, a signal acquisition software for retrieval and online streaming of Electroencephalography (EEG) data. It is written, but not limited, to the needs of Brain Computer Interfacing (BCI). It's main goal is to provide a unified interface to EEG data regardless of the amplifiers used. It runs under all major operating systems, like Windows, Mac OS and Linux, is written in Python and is free- and open source software licensed under the terms of the GNU General Public License.

UTM: Universal Transit Modeller

NASA Astrophysics Data System (ADS)

Deeg, Hans J.

2014-12-01

The Universal Transit Modeller (UTM) is a light-curve simulator for all kinds of transiting or eclipsing configurations between arbitrary numbers of several types of objects, which may be stars, planets, planetary moons, and planetary rings. A separate fitting program, UFIT (Universal Fitter) is part of the UTM distribution and may be used to derive best fits to light-curves for any set of continuously variable parameters. UTM/UFIT is written in IDL code and its source is released in the public domain under the GNU General Public License.

A Model for Atomic and Molecular Interstellar Gas: The Meudon PDR Code

NASA Astrophysics Data System (ADS)

Le Petit, Franck; Nehmé, Cyrine; Le Bourlot, Jacques; Roueff, Evelyne

2006-06-01

We present the revised ``Meudon'' model of photon-dominated region (PDR) code, available on the Web under the GNU Public License. General organization of the code is described down to a level that should allow most observers to use it as an interpretation tool with minimal help from our part. Two grids of models, one for low-excitation diffuse clouds and one for dense highly illuminated clouds, are discussed, and some new results on PDR modelization highlighted.

Taverna: a tool for building and running workflows of services

PubMed Central

Hull, Duncan; Wolstencroft, Katy; Stevens, Robert; Goble, Carole; Pocock, Mathew R.; Li, Peter; Oinn, Tom

2006-01-01

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from . PMID:16845108

DOVIS 2.0: An Efficient and Easy to Use Parallel Virtual Screening Tool Based on AutoDock 4.0

DTIC Science & Technology

2008-09-08

under the GNU General Public License. Background Molecular docking is a computational method that pre- dicts how a ligand interacts with a receptor...Hence, it is an important tool in studying receptor-ligand interactions and plays an essential role in drug design. Particularly, molecular docking has...libraries from OpenBabel and setup a molecular data structure as a C++ object in our program. This makes handling of molecular structures (e.g., atoms

RNAbrowse: RNA-Seq De Novo Assembly Results Browser

PubMed Central

Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

SiGN-SSM: open source parallel software for estimating gene networks with state space models.

PubMed

Tamada, Yoshinori; Yamaguchi, Rui; Imoto, Seiya; Hirose, Osamu; Yoshida, Ryo; Nagasaki, Masao; Miyano, Satoru

2011-04-15

SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles. SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http://sign.hgc.jp/signssm/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site. tamada@ims.u-tokyo.ac.jp.

Evaluation of HITRAN 2012 H2O linelist

NASA Astrophysics Data System (ADS)

Toon, Geoffrey C.

2014-06-01

The HITRAN 2012 H2O linelist has been evaluated in spectral regions used for ground-based remote sensing, such as the NDACC and TCCON networks. Both atmospheric and laboratory spectra have been used in the evaluation, which covers selected regions in the mid-IR and Near-IR. Results are compared with some other linelists. as part of the GNU EPrints system , and is freely redistributable under the GPL .

Rapid Prototyping of Application Specific Signal Processors (RASSP)

DTIC Science & Technology

1993-12-23

Compilers 2-9 - Cadre Teamwork 2-13 - CodeCenter (Centerline) 2-15 - dbx/dbxtool (UNIXm) 2-17 - Falcon (Mentor) 2-19 - FrameMaker (Frame Tech) 2-21 - gprof...UNIXm C debuggers Falcon Mentor ECAD Framework FrameMaker Frame Tech Word Processing gcc GNU CIC++ compiler gprof GNU Software profiling tool...organization can put their own documentation on-line using the BOLD Com- poser for Framemaker . " The AMPLE programming language is a C like language used for

SCTE: An open-source Perl framework for testing equipment control and data acquisition

NASA Astrophysics Data System (ADS)

Mostaço-Guidolin, Luiz C.; Frigori, Rafael B.; Ruchko, Leonid; Galvão, Ricardo M. O.

2012-07-01

SCTE intends to provide a simple, yet powerful, framework for building data acquisition and equipment control systems for experimental Physics, and correlated areas. Via its SCTE::Instrument module, RS-232, USB, and LAN buses are supported, and the intricacies of hardware communication are encapsulated underneath an object oriented abstraction layer. Written in Perl, and using the SCPI protocol, enabled instruments can be easily programmed to perform a wide variety of tasks. While this work presents general aspects of the development of data acquisition systems using the SCTE framework, it is illustrated by particular applications designed for the calibration of several in-house developed devices for power measurement in the tokamak TCABR Alfvén Waves Excitement System. Catalogue identifier: AELZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License Version 3 No. of lines in distributed program, including test data, etc.: 13 811 No. of bytes in distributed program, including test data, etc.: 743 709 Distribution format: tar.gz Programming language: Perl version 5.10.0 or higher. Computer: PC. SCPI capable digital oscilloscope, with RS-232, USB, or LAN communication ports, null modem, USB, or Ethernet cables Operating system: GNU/Linux (2.6.28-11), should also work on any Unix-based operational system Classification: 4.14 External routines: Perl modules: Device::SerialPort, Term::ANSIColor, Math::GSL, Net::HTTP. Gnuplot 4.0 or higher Nature of problem: Automation of experiments and data acquisition often requires expensive equipment and in-house development of software applications. Nowadays personal computers and test equipment come with fast and easy-to-use communication ports. Instrument vendors often supply application programs capable of controlling such devices, but are very restricted in terms of functionalities. For instance, they are not capable of controlling more than one test equipment at a same time or to automate repetitive tasks. SCTE provides a way of using auxiliary equipment in order to automate experiment procedures at low cost using only free, and open-source operational system and libraries. Solution method: SCTE provides a Perl module that implements RS-232, USB, and LAN communication allowing the use of SCPI capable instruments [1]. Therefore providing a straightforward way of creating automation and data acquisition applications using personal computers and testing instruments [2]. SCPI Consortium, Standard Commands for Programmable Instruments, 1999, http://www.scpiconsortium.org. L.C.B. Mostaço-Guidolin, Determinação da configuração de ondas de Alfvén excitadas no tokamak TCABR, Master's thesis, Universidade de São Paulo (2007), http://www.teses.usp.br/teses/disponiveis/43/43134/tde-23042009-230419/.

Continuous-time quantum Monte Carlo impurity solvers

NASA Astrophysics Data System (ADS)

Gull, Emanuel; Werner, Philipp; Fuchs, Sebastian; Surer, Brigitte; Pruschke, Thomas; Troyer, Matthias

2011-04-01

Continuous-time quantum Monte Carlo impurity solvers are algorithms that sample the partition function of an impurity model using diagrammatic Monte Carlo techniques. The present paper describes codes that implement the interaction expansion algorithm originally developed by Rubtsov, Savkin, and Lichtenstein, as well as the hybridization expansion method developed by Werner, Millis, Troyer, et al. These impurity solvers are part of the ALPS-DMFT application package and are accompanied by an implementation of dynamical mean-field self-consistency equations for (single orbital single site) dynamical mean-field problems with arbitrary densities of states. Program summaryProgram title: dmft Catalogue identifier: AEIL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: ALPS LIBRARY LICENSE version 1.1 No. of lines in distributed program, including test data, etc.: 899 806 No. of bytes in distributed program, including test data, etc.: 32 153 916 Distribution format: tar.gz Programming language: C++ Operating system: The ALPS libraries have been tested on the following platforms and compilers: Linux with GNU Compiler Collection (g++ version 3.1 and higher), and Intel C++ Compiler (icc version 7.0 and higher) MacOS X with GNU Compiler (g++ Apple-version 3.1, 3.3 and 4.0) IBM AIX with Visual Age C++ (xlC version 6.0) and GNU (g++ version 3.1 and higher) compilers Compaq Tru64 UNIX with Compq C++ Compiler (cxx) SGI IRIX with MIPSpro C++ Compiler (CC) HP-UX with HP C++ Compiler (aCC) Windows with Cygwin or coLinux platforms and GNU Compiler Collection (g++ version 3.1 and higher) RAM: 10 MB-1 GB Classification: 7.3 External routines: ALPS [1], BLAS/LAPACK, HDF5 Nature of problem: (See [2].) Quantum impurity models describe an atom or molecule embedded in a host material with which it can exchange electrons. They are basic to nanoscience as representations of quantum dots and molecular conductors and play an increasingly important role in the theory of "correlated electron" materials as auxiliary problems whose solution gives the "dynamical mean field" approximation to the self-energy and local correlation functions. Solution method: Quantum impurity models require a method of solution which provides access to both high and low energy scales and is effective for wide classes of physically realistic models. The continuous-time quantum Monte Carlo algorithms for which we present implementations here meet this challenge. Continuous-time quantum impurity methods are based on partition function expansions of quantum impurity models that are stochastically sampled to all orders using diagrammatic quantum Monte Carlo techniques. For a review of quantum impurity models and their applications and of continuous-time quantum Monte Carlo methods for impurity models we refer the reader to [2]. Additional comments: Use of dmft requires citation of this paper. Use of any ALPS program requires citation of the ALPS [1] paper. Running time: 60 s-8 h per iteration.

MinFinder v2.0: An improved version of MinFinder

NASA Astrophysics Data System (ADS)

Tsoulos, Ioannis G.; Lagaris, Isaac E.

2008-10-01

A new version of the "MinFinder" program is presented that offers an augmented linking procedure for Fortran-77 subprograms, two additional stopping rules and a new start-point rejection mechanism that saves a significant portion of gradient and function evaluations. The method is applied on a set of standard test functions and the results are reported. New version program summaryProgram title: MinFinder v2.0 Catalogue identifier: ADWU_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWU_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC Licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 14 150 No. of bytes in distributed program, including test data, etc.: 218 144 Distribution format: tar.gz Programming language used: GNU C++, GNU FORTRAN, GNU C Computer: The program is designed to be portable in all systems running the GNU C++ compiler Operating system: Linux, Solaris, FreeBSD RAM: 200 000 bytes Classification: 4.9 Catalogue identifier of previous version: ADWU_v1_0 Journal reference of previous version: Computer Physics Communications 174 (2006) 166-179 Does the new version supersede the previous version?: Yes Nature of problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques can be trapped in any local minimum. Global optimization is then the appropriate tool. For example, solving a non-linear system of equations via optimization, one may encounter many local minima that do not correspond to solutions, i.e. they are far from zero. Solution method: Using a uniform pdf, points are sampled from a rectangular domain. A clustering technique, based on a typical distance and a gradient criterion, is used to decide from which points a local search should be started. Further searching is terminated when all the local minima inside the search domain are thought to be found. This is accomplished via three stopping rules: the "double-box" stopping rule, the "observables" stopping rule and the "expected minimizers" stopping rule. Reasons for the new version: The link procedure for source code in Fortran 77 is enhanced, two additional stopping rules are implemented and a new criterion for accepting-start points, that economizes on function and gradient calls, is introduced. Summary of revisions:Addition of command line parameters to the utility program make_program. Augmentation of the link process for Fortran 77 subprograms, by linking the final executable with the g2c library. Addition of two probabilistic stopping rules. Introduction of a rejection mechanism to the Checking step of the original method, that reduces the number of gradient evaluations. Additional comments: A technical report describing the revisions, experiments and test runs is packaged with the source code. Running time: Depending on the objective function.

Status of GDL - GNU Data Language

NASA Astrophysics Data System (ADS)

Coulais, A.; Schellens, M.; Gales, J.; Arabas, S.; Boquien, M.; Chanial, P.; Messmer, P.; Fillmore, D.; Poplawski, O.; Maret, S.; Marchal, G.; Galmiche, N.; Mermet, T.

2010-12-01

Gnu Data Language (GDL) is an open-source interpreted language aimed at numerical data analysis and visualisation. It is a free implementation of the Interactive Data Language (IDL) widely used in Astronomy. GDL has a full syntax compatibility with IDL, and includes a large set of library routines targeting advanced matrix manipulation, plotting, time-series and image analysis, mapping, and data input/output including numerous scientific data formats. We will present the current status of the project, the key accomplishments, and the weaknesses - areas where contributions are welcome!

Porting the Starlink Software Collection to GNU Autotools

NASA Astrophysics Data System (ADS)

Gray, N.; Jenness, T.; Allan, A.; Berry, D. S.; Currie, M. J.; Draper, P. W.; Taylor, M. B.; Cavanagh, B.

2005-12-01

The Starlink software collection currently runs on three different Unix platforms and contains around 100 separate software items, totaling 2.5 million lines of code, in a mixture of languages. We have changed the build system from a hand-maintained collection of makefiles with hard-wired OS variants to a scheme involving feature-discovery via GNU Autoconf. As a result of this work, we have already ported the collection to Mac OS X and Cygwin. This had some unexpected benefits and costs, and valuable lessons.

Application of the GNU Radio platform in the multistatic radar

NASA Astrophysics Data System (ADS)

Szlachetko, Boguslaw; Lewandowski, Andrzej

2009-06-01

This document presents the application of the Software Defined Radio-based platform in the multistatic radar. This platform consists of four-sensor linear antenna, Universal Software Radio Peripheral (USRP) hardware (radio frequency frontend) and GNU-Radio PC software. The paper provides information about architecture of digital signal processing performed by USRP's FPGA (digital down converting blocks) and PC host (implementation of the multichannel digital beamforming). The preliminary results of the signal recording performed by our experimental platform are presented.

FindGDPs: fast identification of primers for labeling microbial transcriptomes for DNA microarray analysis

PubMed Central

Blick, Robert J.; Revel, Andrew T.; Hansen, Eric J.

2008-01-01

Summary FindGDPs is a program that uses a greedy algorithm to quickly identify a set of genome-directed primers that specifically anneal to all of the open reading frames in a genome and that do not exhibit full-length complementarity to the members of another user-supplied set of nucleotide sequences. Availability The program code is distributed under the GNU General Public License at http://www8.utsouthwestern.edu/utsw/cda/dept131456/files/159331.html Contact eric.hansen@utsouthwestern.edu PMID:15593406

Lambert W function for applications in physics

NASA Astrophysics Data System (ADS)

Veberič, Darko

2012-12-01

The Lambert W(x) function and its possible applications in physics are presented. The actual numerical implementation in C++ consists of Halley's and Fritsch's iterations with initial approximations based on branch-point expansion, asymptotic series, rational fits, and continued-logarithm recursion. Program summaryProgram title: LambertW Catalogue identifier: AENC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 1335 No. of bytes in distributed program, including test data, etc.: 25 283 Distribution format: tar.gz Programming language: C++ (with suitable wrappers it can be called from C, Fortran etc.), the supplied command-line utility is suitable for other scripting languages like sh, csh, awk, perl etc. Computer: All systems with a C++ compiler. Operating system: All Unix flavors, Windows. It might work with others. RAM: Small memory footprint, less than 1 MB Classification: 1.1, 4.7, 11.3, 11.9. Nature of problem: Find fast and accurate numerical implementation for the Lambert W function. Solution method: Halley's and Fritsch's iterations with initial approximations based on branch-point expansion, asymptotic series, rational fits, and continued logarithm recursion. Additional comments: Distribution file contains the command-line utility lambert-w. Doxygen comments, included in the source files. Makefile. Running time: The tests provided take only a few seconds to run.

The GMOD Drupal bioinformatic server framework.

PubMed

Papanicolaou, Alexie; Heckel, David G

2010-12-15

Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.

Optimized multiple quantum MAS lineshape simulations in solid state NMR

NASA Astrophysics Data System (ADS)

Brouwer, William J.; Davis, Michael C.; Mueller, Karl T.

2009-10-01

The majority of nuclei available for study in solid state Nuclear Magnetic Resonance have half-integer spin I>1/2, with corresponding electric quadrupole moment. As such, they may couple with a surrounding electric field gradient. This effect introduces anisotropic line broadening to spectra, arising from distinct chemical species within polycrystalline solids. In Multiple Quantum Magic Angle Spinning (MQMAS) experiments, a second frequency dimension is created, devoid of quadrupolar anisotropy. As a result, the center of gravity of peaks in the high resolution dimension is a function of isotropic second order quadrupole and chemical shift alone. However, for complex materials, these parameters take on a stochastic nature due in turn to structural and chemical disorder. Lineshapes may still overlap in the isotropic dimension, complicating the task of assignment and interpretation. A distributed computational approach is presented here which permits simulation of the two-dimensional MQMAS spectrum, generated by random variates from model distributions of isotropic chemical and quadrupole shifts. Owing to the non-convex nature of the residual sum of squares (RSS) function between experimental and simulated spectra, simulated annealing is used to optimize the simulation parameters. In this manner, local chemical environments for disordered materials may be characterized, and via a re-sampling approach, error estimates for parameters produced. Program summaryProgram title: mqmasOPT Catalogue identifier: AEEC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3650 No. of bytes in distributed program, including test data, etc.: 73 853 Distribution format: tar.gz Programming language: C, OCTAVE Computer: UNIX/Linux Operating system: UNIX/Linux Has the code been vectorised or parallelized?: Yes RAM: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 3.5M, SMP AMD opteron Classification: 2.3 External routines: OCTAVE ( http://www.gnu.org/software/octave/), GNU Scientific Library ( http://www.gnu.org/software/gsl/), OPENMP ( http://openmp.org/wp/) Nature of problem: The optimal simulation and modeling of multiple quantum magic angle spinning NMR spectra, for general systems, especially those with mild to significant disorder. The approach outlined and implemented in C and OCTAVE also produces model parameter error estimates. Solution method: A model for each distinct chemical site is first proposed, for the individual contribution of crystallite orientations to the spectrum. This model is averaged over all powder angles [1], as well as the (stochastic) parameters; isotropic chemical shift and quadrupole coupling constant. The latter is accomplished via sampling from a bi-variate Gaussian distribution, using the Box-Muller algorithm to transform Sobol (quasi) random numbers [2]. A simulated annealing optimization is performed, and finally the non-linear jackknife [3] is applied in developing model parameter error estimates. Additional comments: The distribution contains a script, mqmasOpt.m, which runs in the OCTAVE language workspace. Running time: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 58.35 seconds, SMP AMD opteron. References:S.K. Zaremba, Annali di Matematica Pura ed Applicata 73 (1966) 293. H. Niederreiter, Random Number Generation and Quasi-Monte Carlo Methods, SIAM, 1992. T. Fox, D. Hinkley, K. Larntz, Technometrics 22 (1980) 29.

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

PubMed

Drummond, A; Strimmer, K

2001-07-01

Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.

InDEx: Open Source iOS and Android Software for Self-Reporting and Monitoring of Alcohol Consumption.

PubMed

Leightley, Daniel; Puddephatt, Jo-Anne; Goodwin, Laura; Rona, Roberto; Fear, Nicola T

2018-03-23

InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub (https://github.com/DrDanL/index-app-public).

InDEx: Open Source iOS and Android Software for Self-Reporting and Monitoring of Alcohol Consumption

PubMed Central

Leightley, Daniel; Puddephatt, Jo-Anne; Goodwin, Laura; Rona, Roberto; Fear, Nicola T.

2018-01-01

InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub (https://github.com/DrDanL/index-app-public). PMID:29795769

PhyLIS: a simple GNU/Linux distribution for phylogenetics and phyloinformatics.

PubMed

Thomson, Robert C

2009-07-30

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/.

PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics

PubMed Central

Thomson, Robert C.

2009-01-01

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/. PMID:19812729

FROG: Time Series Analysis for the Web Service Era

NASA Astrophysics Data System (ADS)

Allan, A.

2005-12-01

The FROG application is part of the next generation Starlink{http://www.starlink.ac.uk} software work (Draper et al. 2005) and released under the GNU Public License{http://www.gnu.org/copyleft/gpl.html} (GPL). Written in Java, it has been designed for the Web and Grid Service era as an extensible, pluggable, tool for time series analysis and display. With an integrated SOAP server the packages functionality is exposed to the user for use in their own code, and to be used remotely over the Grid, as part of the Virtual Observatory (VO).

Comparative Analysis of Active and Passive Mapping Techniques in an Internet-Based Local Area Network

DTIC Science & Technology

2004-03-01

PIII/500 (K) 512 A11 3C905 Honeynet PIII/1000 (C) 512 A11 3C905 Generator PIII/800 (C) 256 A11 3C905 Each system is running Debian GNU / Linux “unstable...Network,” September 2000. http://www.issues.af.mil/notams/notam00-5.html; accessed January 16, 2004. 5. “Debian GNU / Linux 3.0 Released,” Debian News...interact with those servers. 1.5 Summary The remainder of this document is organized into four chapters. Chapter 2 con - tains the literature review where

1 CFR 304.1 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 1 General Provisions 1 2013-01-01 2012-01-01 true General provisions. 304.1 Section 304.1 General Provisions ADMINISTRATIVE CONFERENCE OF THE UNITED STATES DISCLOSURE OF RECORDS OR INFORMATION Procedures for Disclosure of Records Under the Freedom of Information Act § 304.1 General provisions. (a) This subpart...

1 CFR 304.1 - General provisions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 1 General Provisions 1 2012-01-01 2012-01-01 false General provisions. 304.1 Section 304.1 General Provisions ADMINISTRATIVE CONFERENCE OF THE UNITED STATES DISCLOSURE OF RECORDS OR INFORMATION Procedures for Disclosure of Records Under the Freedom of Information Act § 304.1 General provisions. (a) This subpart...

1 CFR 304.1 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 1 General Provisions 1 2014-01-01 2012-01-01 true General provisions. 304.1 Section 304.1 General Provisions ADMINISTRATIVE CONFERENCE OF THE UNITED STATES DISCLOSURE OF RECORDS OR INFORMATION Procedures for Disclosure of Records Under the Freedom of Information Act § 304.1 General provisions. (a) This subpart...

XTALOPT: An open-source evolutionary algorithm for crystal structure prediction

NASA Astrophysics Data System (ADS)

Lonie, David C.; Zurek, Eva

2011-02-01

The implementation and testing of XTALOPT, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XTALOPT are optimized using a novel benchmarking scheme. XTALOPT is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface. Program summaryProgram title:XTALOPT Catalogue identifier: AEGX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.1 or later [1] No. of lines in distributed program, including test data, etc.: 36 849 No. of bytes in distributed program, including test data, etc.: 1 149 399 Distribution format: tar.gz Programming language: C++ Computer: PCs, workstations, or clusters Operating system: Linux Classification: 7.7 External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7]. Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics. Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XTALOPT, is freely available to the scientific community for use and collaboration under the GNU Public License. Running time: User dependent. The program runs until stopped by the user.

CoSMoMVPA: Multi-Modal Multivariate Pattern Analysis of Neuroimaging Data in Matlab/GNU Octave.

PubMed

Oosterhof, Nikolaas N; Connolly, Andrew C; Haxby, James V

2016-01-01

Recent years have seen an increase in the popularity of multivariate pattern (MVP) analysis of functional magnetic resonance (fMRI) data, and, to a much lesser extent, magneto- and electro-encephalography (M/EEG) data. We present CoSMoMVPA, a lightweight MVPA (MVP analysis) toolbox implemented in the intersection of the Matlab and GNU Octave languages, that treats both fMRI and M/EEG data as first-class citizens. CoSMoMVPA supports all state-of-the-art MVP analysis techniques, including searchlight analyses, classification, correlations, representational similarity analysis, and the time generalization method. These can be used to address both data-driven and hypothesis-driven questions about neural organization and representations, both within and across: space, time, frequency bands, neuroimaging modalities, individuals, and species. It uses a uniform data representation of fMRI data in the volume or on the surface, and of M/EEG data at the sensor and source level. Through various external toolboxes, it directly supports reading and writing a variety of fMRI and M/EEG neuroimaging formats, and, where applicable, can convert between them. As a result, it can be integrated readily in existing pipelines and used with existing preprocessed datasets. CoSMoMVPA overloads the traditional volumetric searchlight concept to support neighborhoods for M/EEG and surface-based fMRI data, which supports localization of multivariate effects of interest across space, time, and frequency dimensions. CoSMoMVPA also provides a generalized approach to multiple comparison correction across these dimensions using Threshold-Free Cluster Enhancement with state-of-the-art clustering and permutation techniques. CoSMoMVPA is highly modular and uses abstractions to provide a uniform interface for a variety of MVP measures. Typical analyses require a few lines of code, making it accessible to beginner users. At the same time, expert programmers can easily extend its functionality. CoSMoMVPA comes with extensive documentation, including a variety of runnable demonstration scripts and analysis exercises (with example data and solutions). It uses best software engineering practices including version control, distributed development, an automated test suite, and continuous integration testing. It can be used with the proprietary Matlab and the free GNU Octave software, and it complies with open source distribution platforms such as NeuroDebian. CoSMoMVPA is Free/Open Source Software under the permissive MIT license. Website: http://cosmomvpa.org Source code: https://github.com/CoSMoMVPA/CoSMoMVPA.

CoSMoMVPA: Multi-Modal Multivariate Pattern Analysis of Neuroimaging Data in Matlab/GNU Octave

PubMed Central

Oosterhof, Nikolaas N.; Connolly, Andrew C.; Haxby, James V.

2016-01-01

Recent years have seen an increase in the popularity of multivariate pattern (MVP) analysis of functional magnetic resonance (fMRI) data, and, to a much lesser extent, magneto- and electro-encephalography (M/EEG) data. We present CoSMoMVPA, a lightweight MVPA (MVP analysis) toolbox implemented in the intersection of the Matlab and GNU Octave languages, that treats both fMRI and M/EEG data as first-class citizens. CoSMoMVPA supports all state-of-the-art MVP analysis techniques, including searchlight analyses, classification, correlations, representational similarity analysis, and the time generalization method. These can be used to address both data-driven and hypothesis-driven questions about neural organization and representations, both within and across: space, time, frequency bands, neuroimaging modalities, individuals, and species. It uses a uniform data representation of fMRI data in the volume or on the surface, and of M/EEG data at the sensor and source level. Through various external toolboxes, it directly supports reading and writing a variety of fMRI and M/EEG neuroimaging formats, and, where applicable, can convert between them. As a result, it can be integrated readily in existing pipelines and used with existing preprocessed datasets. CoSMoMVPA overloads the traditional volumetric searchlight concept to support neighborhoods for M/EEG and surface-based fMRI data, which supports localization of multivariate effects of interest across space, time, and frequency dimensions. CoSMoMVPA also provides a generalized approach to multiple comparison correction across these dimensions using Threshold-Free Cluster Enhancement with state-of-the-art clustering and permutation techniques. CoSMoMVPA is highly modular and uses abstractions to provide a uniform interface for a variety of MVP measures. Typical analyses require a few lines of code, making it accessible to beginner users. At the same time, expert programmers can easily extend its functionality. CoSMoMVPA comes with extensive documentation, including a variety of runnable demonstration scripts and analysis exercises (with example data and solutions). It uses best software engineering practices including version control, distributed development, an automated test suite, and continuous integration testing. It can be used with the proprietary Matlab and the free GNU Octave software, and it complies with open source distribution platforms such as NeuroDebian. CoSMoMVPA is Free/Open Source Software under the permissive MIT license. Website: http://cosmomvpa.org Source code: https://github.com/CoSMoMVPA/CoSMoMVPA PMID:27499741

The GMOD Drupal Bioinformatic Server Framework

PubMed Central

Papanicolaou, Alexie; Heckel, David G.

2010-01-01

Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com Contact: alexie@butterflybase.org PMID:20971988

MNPBEM - A Matlab toolbox for the simulation of plasmonic nanoparticles

NASA Astrophysics Data System (ADS)

Hohenester, Ulrich; Trügler, Andreas

2012-02-01

MNPBEM is a Matlab toolbox for the simulation of metallic nanoparticles (MNP), using a boundary element method (BEM) approach. The main purpose of the toolbox is to solve Maxwell's equations for a dielectric environment where bodies with homogeneous and isotropic dielectric functions are separated by abrupt interfaces. Although the approach is in principle suited for arbitrary body sizes and photon energies, it is tested (and probably works best) for metallic nanoparticles with sizes ranging from a few to a few hundreds of nanometers, and for frequencies in the optical and near-infrared regime. The toolbox has been implemented with Matlab classes. These classes can be easily combined, which has the advantage that one can adapt the simulation programs flexibly for various applications. Program summaryProgram title: MNPBEM Catalogue identifier: AEKJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v2 No. of lines in distributed program, including test data, etc.: 15 700 No. of bytes in distributed program, including test data, etc.: 891 417 Distribution format: tar.gz Programming language: Matlab 7.11.0 (R2010b) Computer: Any which supports Matlab 7.11.0 (R2010b) Operating system: Any which supports Matlab 7.11.0 (R2010b) RAM: ⩾1 GByte Classification: 18 Nature of problem: Solve Maxwell's equations for dielectric particles with homogeneous dielectric functions separated by abrupt interfaces. Solution method: Boundary element method using electromagnetic potentials. Running time: Depending on surface discretization between seconds and hours.

WebGLORE: a web service for Grid LOgistic REgression.

PubMed

Jiang, Wenchao; Li, Pinghao; Wang, Shuang; Wu, Yuan; Xue, Meng; Ohno-Machado, Lucila; Jiang, Xiaoqian

2013-12-15

WebGLORE is a free web service that enables privacy-preserving construction of a global logistic regression model from distributed datasets that are sensitive. It only transfers aggregated local statistics (from participants) through Hypertext Transfer Protocol Secure to a trusted server, where the global model is synthesized. WebGLORE seamlessly integrates AJAX, JAVA Applet/Servlet and PHP technologies to provide an easy-to-use web service for biomedical researchers to break down policy barriers during information exchange. http://dbmi-engine.ucsd.edu/webglore3/. WebGLORE can be used under the terms of GNU general public license as published by the Free Software Foundation.

PFMCal : Photonic force microscopy calibration extended for its application in high-frequency microrheology

NASA Astrophysics Data System (ADS)

Butykai, A.; Domínguez-García, P.; Mor, F. M.; Gaál, R.; Forró, L.; Jeney, S.

2017-11-01

The present document is an update of the previously published MatLab code for the calibration of optical tweezers in the high-resolution detection of the Brownian motion of non-spherical probes [1]. In this instance, an alternative version of the original code, based on the same physical theory [2], but focused on the automation of the calibration of measurements using spherical probes, is outlined. The new added code is useful for high-frequency microrheology studies, where the probe radius is known but the viscosity of the surrounding fluid maybe not. This extended calibration methodology is automatic, without the need of a user's interface. A code for calibration by means of thermal noise analysis [3] is also included; this is a method that can be applied when using viscoelastic fluids if the trap stiffness is previously estimated [4]. The new code can be executed in MatLab and using GNU Octave. Program Files doi:http://dx.doi.org/10.17632/s59f3gz729.1 Licensing provisions: GPLv3 Programming language: MatLab 2016a (MathWorks Inc.) and GNU Octave 4.0 Operating system: Linux and Windows. Supplementary material: A new document README.pdf includes basic running instructions for the new code. Journal reference of previous version: Computer Physics Communications, 196 (2015) 599 Does the new version supersede the previous version?: No. It adds alternative but compatible code while providing similar calibration factors. Nature of problem (approx. 50-250 words): The original code uses a MatLab-provided user's interface, which is not available in GNU Octave, and cannot be used outside of a proprietary software as MatLab. Besides, the process of calibration when using spherical probes needs an automatic method when calibrating big amounts of different data focused to microrheology. Solution method (approx. 50-250 words): The new code can be executed in the latest version of MatLab and using GNU Octave, a free and open-source alternative to MatLab. This code generates an automatic calibration process which requires only to write the input data in the main script. Additionally, we include a calibration method based on thermal noise statistics, which can be used with viscoelastic fluids if the trap stiffness is previously estimated. Reasons for the new version: This version extends the functionality of PFMCal for the particular case of spherical probes and unknown fluid viscosities. The extended code is automatic, works in different operating systems and it is compatible with GNU Octave. Summary of revisions: The original MatLab program in the previous version, which is executed by PFMCal.m, is not changed. Here, we have added two additional main archives named PFMCal_auto.m and PFMCal_histo.m, which implement automatic calculations of the calibration process and calibration through Boltzmann statistics, respectively. The process of calibration using this code for spherical beads is described in the README.pdf file provided in the new code submission. Here, we obtain different calibration factors, β (given in μm/V), according to [2], related to two statistical quantities: the mean-squared displacement (MSD), βMSD, and the velocity autocorrelation function (VAF), βVAF. Using that methodology, the trap stiffness, k, and the zero-shear viscosity of the fluid, η, can be calculated if the value of the particle's radius, a, is previously known. For comparison, we include in the extended code the method of calibration using the corner frequency of the power-spectral density (PSD) [5], providing a calibration factor βPSD. Besides, with the prior estimation of the trap stiffness, along with the known value of the particle's radius, we can use thermal noise statistics to obtain calibration factors, β, according to the quadratic form of the optical potential, βE, and related to the Gaussian distribution of the bead's positions, βσ2. This method has been demonstrated to be applicable to the calibration of optical tweezers when using non-Newtonian viscoelastic polymeric liquids [4]. An example of the results using this calibration process is summarized in Table 1. Using the data provided in the new code submission, for water and acetone fluids, we calculate all the calibration factors by using the original PFMCal.m and by the new non-GUI code PFMCal_auto.m and PFMCal_histo.m. Regarding the new code, PFMCal_auto.m returns η, k, βMSD, βVAF and βPSD, while PFMCal_histo.m provides βσ2 and βE. Table 1 shows how we obtain the expected viscosity of the two fluids at this temperature and how the different methods provide good agreement between trap stiffnesses and calibration factors. Additional comments including Restrictions and Unusual features (approx. 50-250 words): The original code, PFMCal.m, runs under MatLab using the Statistics Toolbox. The extended code, PFMCal_auto.m and PFMCal_histo.m, can be executed without modification using MatLab or GNU Octave. The code has been tested in Linux and Windows operating systems.

78 FR 48660 - Agency Information Collection Activities; Comment Request; Student Assistance General Provisions...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-09

...; Comment Request; Student Assistance General Provisions--Subpart K--Cash Management AGENCY: Federal Student... of Collection: Student Assistance General Provisions--Subpart K--Cash Management OMB Control Number... administration of 34 CFR 668 Subpart K Cash Management of the Student Assistance General Provisions. The...

1993 Wholesale Power and Transmission Rate Schedules.

DOE Office of Scientific and Technical Information (OSTI.GOV)

US Bonneville Power Administration

1993-10-01

Bonneville Power Administration 1993 Wholesale Power Rate Schedules and General Rate Schedule Provisions and 1993 Transmission Rate Schedules and General Transmission Rate Schedule Provisions, contained herein, were approved on an interim basis effective October 1, 1993. These rate schedules and provisions were approved by the Federal Energy Commission, United States Department of Energy, in September, 1993. These rate schedules and provisions supersede the Administration`s Wholesale Power Rate Schedules and General Rate Schedule Provisions and Transmission Rate Schedules and General Transmission Rate Schedule Provisions effective October 1, 1991.

21 CFR 172.5 - General provisions for direct food additives.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true General provisions for direct food additives. 172.5... (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) FOOD ADDITIVES PERMITTED FOR DIRECT ADDITION TO FOOD FOR HUMAN CONSUMPTION General Provisions § 172.5 General provisions for direct food additives. (a...

21 CFR 172.5 - General provisions for direct food additives.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 3 2013-04-01 2013-04-01 false General provisions for direct food additives. 172... (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) FOOD ADDITIVES PERMITTED FOR DIRECT ADDITION TO FOOD FOR HUMAN CONSUMPTION General Provisions § 172.5 General provisions for direct food additives. (a...

21 CFR 172.5 - General provisions for direct food additives.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 3 2011-04-01 2011-04-01 false General provisions for direct food additives. 172... (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) FOOD ADDITIVES PERMITTED FOR DIRECT ADDITION TO FOOD FOR HUMAN CONSUMPTION General Provisions § 172.5 General provisions for direct food additives. (a...

21 CFR 172.5 - General provisions for direct food additives.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 3 2014-04-01 2014-04-01 false General provisions for direct food additives. 172... (CONTINUED) FOOD ADDITIVES PERMITTED FOR DIRECT ADDITION TO FOOD FOR HUMAN CONSUMPTION General Provisions § 172.5 General provisions for direct food additives. (a) Regulations prescribing conditions under which...

21 CFR 172.5 - General provisions for direct food additives.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 3 2012-04-01 2012-04-01 false General provisions for direct food additives. 172... (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) FOOD ADDITIVES PERMITTED FOR DIRECT ADDITION TO FOOD FOR HUMAN CONSUMPTION General Provisions § 172.5 General provisions for direct food additives. (a...

SOCIB Glider toolbox: from sensor to data repository

NASA Astrophysics Data System (ADS)

Pau Beltran, Joan; Heslop, Emma; Ruiz, Simón; Troupin, Charles; Tintoré, Joaquín

2015-04-01

Nowadays in oceanography, gliders constitutes a mature, cost-effective technology for the acquisition of measurements independently of the sea state (unlike ships), providing subsurface data during sustained periods, including extreme weather events. The SOCIB glider toolbox is a set of MATLAB/Octave scripts and functions developed in order to manage the data collected by a glider fleet. They cover the main stages of the data management process, both in real-time and delayed-time modes: metadata aggregation, downloading, processing, and automatic generation of data products and figures. The toolbox is distributed under the GNU licence (http://www.gnu.org/copyleft/gpl.html) and is available at http://www.socib.es/users/glider/glider_toolbox.

WeBIAS: a web server for publishing bioinformatics applications.

PubMed

Daniluk, Paweł; Wilczyński, Bartek; Lesyng, Bogdan

2015-11-02

One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well as impairs actual usefulness to the scientific community at large. In this note we present WeBIAS-a simple, self-contained solution to make command-line programs accessible through web forms. It comprises a web portal capable of serving several applications and backend schedulers which carry out computations. The server handles user registration and authentication, stores queries and results, and provides a convenient administrator interface. WeBIAS is implemented in Python and available under GNU Affero General Public License. It has been developed and tested on GNU/Linux compatible platforms covering a vast majority of operational WWW servers. Since it is written in pure Python, it should be easy to deploy also on all other platforms supporting Python (e.g. Windows, Mac OS X). Documentation and source code, as well as a demonstration site are available at http://bioinfo.imdik.pan.pl/webias . WeBIAS has been designed specifically with ease of installation and deployment of services in mind. Setting up a simple application requires minimal effort, yet it is possible to create visually appealing, feature-rich interfaces for query submission and presentation of results.

WebGLORE: a Web service for Grid LOgistic REgression

PubMed Central

Jiang, Wenchao; Li, Pinghao; Wang, Shuang; Wu, Yuan; Xue, Meng; Ohno-Machado, Lucila; Jiang, Xiaoqian

2013-01-01

WebGLORE is a free web service that enables privacy-preserving construction of a global logistic regression model from distributed datasets that are sensitive. It only transfers aggregated local statistics (from participants) through Hypertext Transfer Protocol Secure to a trusted server, where the global model is synthesized. WebGLORE seamlessly integrates AJAX, JAVA Applet/Servlet and PHP technologies to provide an easy-to-use web service for biomedical researchers to break down policy barriers during information exchange. Availability and implementation: http://dbmi-engine.ucsd.edu/webglore3/. WebGLORE can be used under the terms of GNU general public license as published by the Free Software Foundation. Contact: x1jiang@ucsd.edu PMID:24072732

The PLUTO code for astrophysical gasdynamics .

NASA Astrophysics Data System (ADS)

Mignone, A.

Present numerical codes appeal to a consolidated theory based on finite difference and Godunov-type schemes. In this context we have developed a versatile numerical code, PLUTO, suitable for the solution of high-mach number flow in 1, 2 and 3 spatial dimensions and different systems of coordinates. Different hydrodynamic modules and algorithms may be independently selected to properly describe Newtonian, relativistic, MHD, or relativistic MHD fluids. The modular structure exploits a general framework for integrating a system of conservation laws, built on modern Godunov-type shock-capturing schemes. The code is freely distributed under the GNU public license and it is available for download to the astrophysical community at the URL http://plutocode.to.astro.it.

Automatic generation of randomized trial sequences for priming experiments.

PubMed

Ihrke, Matthias; Behrendt, Jörg

2011-01-01

In most psychological experiments, a randomized presentation of successive displays is crucial for the validity of the results. For some paradigms, this is not a trivial issue because trials are interdependent, e.g., priming paradigms. We present a software that automatically generates optimized trial sequences for (negative-) priming experiments. Our implementation is based on an optimization heuristic known as genetic algorithms that allows for an intuitive interpretation due to its similarity to natural evolution. The program features a graphical user interface that allows the user to generate trial sequences and to interactively improve them. The software is based on freely available software and is released under the GNU General Public License.

The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology.

PubMed

Blakes, Jonathan; Twycross, Jamie; Romero-Campero, Francisco Jose; Krasnogor, Natalio

2011-12-01

The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking. Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3. Natalio.Krasnogor@nottingham.ac.uk.

40 CFR 63.215 - What General Provisions apply to me?

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 10 2013-07-01 2013-07-01 false What General Provisions apply to me? 63.215 Section 63.215 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Other Requirements and Information § 63.215 What General Provisions apply to me? (a) All the provisions...

40 CFR 63.215 - What General Provisions apply to me?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 10 2012-07-01 2012-07-01 false What General Provisions apply to me? 63.215 Section 63.215 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Other Requirements and Information § 63.215 What General Provisions apply to me? (a) All the provisions...

40 CFR 1068.15 - What general provisions apply for EPA decision-making?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false What general provisions apply for EPA decision-making? 1068.15 Section 1068.15 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Miscellaneous Provisions § 1068.15 What general provisions apply for EPA decision-making? (a) The Administrator...

QuTiP: An open-source Python framework for the dynamics of open quantum systems

NASA Astrophysics Data System (ADS)

Johansson, J. R.; Nation, P. D.; Nori, Franco

2012-08-01

We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum object class, and then passed on to a choice of master equation or Monte Carlo solvers. We give an overview of the basic structure for the framework before detailing the numerical simulation of open system dynamics. Several examples are given to illustrate the build up to a complete calculation. Finally, we measure the performance of our library against that of current implementations. The framework described here is particularly well suited to the fields of quantum optics, superconducting circuit devices, nanomechanics, and trapped ions, while also being ideal for use in classroom instruction. Catalogue identifier: AEMB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 16 482 No. of bytes in distributed program, including test data, etc.: 213 438 Distribution format: tar.gz Programming language: Python Computer: i386, x86-64 Operating system: Linux, Mac OSX, Windows RAM: 2+ Gigabytes Classification: 7 External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.org/), Matplotlib (http://matplotlib.sourceforge.net/) Nature of problem: Dynamics of open quantum systems. Solution method: Numerical solutions to Lindblad master equation or Monte Carlo wave function method. Restrictions: Problems must meet the criteria for using the master equation in Lindblad form. Running time: A few seconds up to several tens of minutes, depending on size of underlying Hilbert space.

Sharing electronic structure and crystallographic data with ETSF_IO

NASA Astrophysics Data System (ADS)

Caliste, D.; Pouillon, Y.; Verstraete, M. J.; Olevano, V.; Gonze, X.

2008-11-01

We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines. Catalogue identifier: AEBG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu Lesser General Public License No. of lines in distributed program, including test data, etc.: 63 156 No. of bytes in distributed program, including test data, etc.: 363 390 Distribution format: tar.gz Programming language: Fortran 95 Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Classification: 7.3, 8 External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdf Nature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating software Solution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)

A Matlab-based finite-difference solver for the Poisson problem with mixed Dirichlet-Neumann boundary conditions

NASA Astrophysics Data System (ADS)

Reimer, Ashton S.; Cheviakov, Alexei F.

2013-03-01

A Matlab-based finite-difference numerical solver for the Poisson equation for a rectangle and a disk in two dimensions, and a spherical domain in three dimensions, is presented. The solver is optimized for handling an arbitrary combination of Dirichlet and Neumann boundary conditions, and allows for full user control of mesh refinement. The solver routines utilize effective and parallelized sparse vector and matrix operations. Computations exhibit high speeds, numerical stability with respect to mesh size and mesh refinement, and acceptable error values even on desktop computers. Catalogue identifier: AENQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3.0 No. of lines in distributed program, including test data, etc.: 102793 No. of bytes in distributed program, including test data, etc.: 369378 Distribution format: tar.gz Programming language: Matlab 2010a. Computer: PC, Macintosh. Operating system: Windows, OSX, Linux. RAM: 8 GB (8, 589, 934, 592 bytes) Classification: 4.3. Nature of problem: To solve the Poisson problem in a standard domain with “patchy surface”-type (strongly heterogeneous) Neumann/Dirichlet boundary conditions. Solution method: Finite difference with mesh refinement. Restrictions: Spherical domain in 3D; rectangular domain or a disk in 2D. Unusual features: Choice between mldivide/iterative solver for the solution of large system of linear algebraic equations that arise. Full user control of Neumann/Dirichlet boundary conditions and mesh refinement. Running time: Depending on the number of points taken and the geometry of the domain, the routine may take from less than a second to several hours to execute.

40 CFR 1068.301 - What general provisions apply?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false What general provisions apply? 1068.301 Section 1068.301 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS GENERAL COMPLIANCE PROVISIONS FOR ENGINE PROGRAMS Imports § 1068.301 What general...

40 CFR 1068.301 - What general provisions apply?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false What general provisions apply? 1068.301 Section 1068.301 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS GENERAL COMPLIANCE PROVISIONS FOR ENGINE PROGRAMS Imports § 1068.301 What general...

40 CFR 63.215 - What General Provisions apply to me?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 9 2011-07-01 2011-07-01 false What General Provisions apply to me? 63.215 Section 63.215 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... and Information § 63.215 What General Provisions apply to me? (a) All the provisions in 40 CFR part 61...

40 CFR 63.215 - What General Provisions apply to me?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 9 2010-07-01 2010-07-01 false What General Provisions apply to me? 63.215 Section 63.215 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... and Information § 63.215 What General Provisions apply to me? (a) All the provisions in 40 CFR part 61...

Libsharp - spherical harmonic transforms revisited

NASA Astrophysics Data System (ADS)

Reinecke, M.; Seljebotn, D. S.

2013-06-01

We present libsharp, a code library for spherical harmonic transforms (SHTs), which evolved from the libpsht library and addresses several of its shortcomings, such as adding MPI support for distributed memory systems and SHTs of fields with arbitrary spin, but also supporting new developments in CPU instruction sets like the Advanced Vector Extensions (AVX) or fused multiply-accumulate (FMA) instructions. The library is implemented in portable C99 and provides an interface that can be easily accessed from other programming languages such as C++, Fortran, Python, etc. Generally, libsharp's performance is at least on par with that of its predecessor; however, significant improvements were made to the algorithms for scalar SHTs, which are roughly twice as fast when using the same CPU capabilities. The library is available at http://sourceforge.net/projects/libsharp/ under the terms of the GNU General Public License.

CRPropa 2.0 - A public framework for propagating high energy nuclei, secondary gamma rays and neutrinos

NASA Astrophysics Data System (ADS)

Kampert, Karl-Heinz; Kulbartz, Jörg; Maccione, Luca; Nierstenhoefer, Nils; Schiffer, Peter; Sigl, Günter; van Vliet, Arjen René

2013-02-01

Version 2.0 of CRPropa [CRPropa is published under the 3rd version of the GNU General Public License (GPLv3). It is available, together with a detailed documentation of the code, at https://crpropa.desy.de.] is public software to model the extra-galactic propagation of ultra-high energy nuclei of atomic number Z⩽26 through structured magnetic fields and ambient photon backgrounds taking into account all relevant particle interactions. CRPropa covers the energy range 7×1016

SEGY to ASCII: Conversion and Plotting Program

USGS Publications Warehouse

Goldman, Mark R.

1999-01-01

This report documents a computer program to convert standard 4 byte, IBM floating point SEGY files to ASCII xyz format. The program then optionally plots the seismic data using the GMT plotting package. The material for this publication is contained in a standard tar file (of99-126.tar) that is uncompressed and 726 K in size. It can be downloaded by any Unix machine. Move the tar file to the directory you wish to use it in, then type 'tar xvf of99-126.tar' The archive files (and diskette) contain a NOTE file, a README file, a version-history file, source code, a makefile for easy compilation, and an ASCII version of the documentation. The archive files (and diskette) also contain example test files, including a typical SEGY file along with the resulting ASCII xyz and postscript files. Requirements for compiling the source code into an executable are a C++ compiler. The program has been successfully compiled using Gnu's g++ version 2.8.1, and use of other compilers may require modifications to the existing source code. The g++ compiler is a free, high quality C++ compiler and may be downloaded from the ftp site: ftp://ftp.gnu.org/gnu Requirements for plotting the seismic data is the existence of the GMT plotting package. The GMT plotting package may be downloaded from the web site: http://www.soest.hawaii.edu/gmt/

78 FR 45517 - Agency Information Collection Activities; Comment Request; Student Assistance General Provisions...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-29

...; Comment Request; Student Assistance General Provisions--Subpart K--Cash Management AGENCY: Federal Student...)(A)), provides the general public and Federal agencies with an opportunity to comment on proposed... notice will be considered public records. Title of Collection: Student Assistance General Provisions...

40 CFR 75.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 17 2012-07-01 2012-07-01 false General Acid Rain Program provisions. 75.3 Section 75.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING General § 75.3 General Acid Rain Program provisions. The...

40 CFR 75.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 16 2011-07-01 2011-07-01 false General Acid Rain Program provisions. 75.3 Section 75.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING General § 75.3 General Acid Rain Program provisions. The...

40 CFR 75.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 17 2014-07-01 2014-07-01 false General Acid Rain Program provisions. 75.3 Section 75.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING General § 75.3 General Acid Rain Program provisions. The...

40 CFR 75.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 16 2010-07-01 2010-07-01 false General Acid Rain Program provisions. 75.3 Section 75.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING General § 75.3 General Acid Rain Program provisions. The...

40 CFR 75.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 17 2013-07-01 2013-07-01 false General Acid Rain Program provisions. 75.3 Section 75.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) CONTINUOUS EMISSION MONITORING General § 75.3 General Acid Rain Program provisions. The...

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission.

PubMed

Hankeln, Wolfgang; Buttigieg, Pier Luigi; Fink, Dennis; Kottmann, Renzo; Yilmaz, Pelin; Glöckner, Frank Oliver

2010-06-30

Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

PubMed Central

2010-01-01

Background Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft® Excel® spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data. PMID:20591175

24 CFR 5.506 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false General provisions. 5.506 Section 5.506 Housing and Urban Development Office of the Secretary, Department of Housing and Urban Development GENERAL HUD PROGRAM REQUIREMENTS; WAIVERS Restrictions on Assistance to Noncitizens § 5.506 General provisions. (a) Restrictions on assistance....

19 CFR 10.114 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... ARTICLES CONDITIONALLY FREE, SUBJECT TO A REDUCED RATE, ETC. General Provisions Instruments and Apparatus for Educational and Scientific Institutions § 10.114 General provisions. The consolidated regulations of the Commerce and Treasury Departments relating to the entry of instruments and apparatus for...

19 CFR 10.114 - General provisions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... ARTICLES CONDITIONALLY FREE, SUBJECT TO A REDUCED RATE, ETC. General Provisions Instruments and Apparatus for Educational and Scientific Institutions § 10.114 General provisions. The consolidated regulations of the Commerce and Treasury Departments relating to the entry of instruments and apparatus for...

19 CFR 10.114 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... ARTICLES CONDITIONALLY FREE, SUBJECT TO A REDUCED RATE, ETC. General Provisions Instruments and Apparatus for Educational and Scientific Institutions § 10.114 General provisions. The consolidated regulations of the Commerce and Treasury Departments relating to the entry of instruments and apparatus for...

19 CFR 10.114 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... ARTICLES CONDITIONALLY FREE, SUBJECT TO A REDUCED RATE, ETC. General Provisions Instruments and Apparatus for Educational and Scientific Institutions § 10.114 General provisions. The consolidated regulations of the Commerce and Treasury Departments relating to the entry of instruments and apparatus for...

Achieving Lower Nitrogen Balance and Higher Nitrogen Recovery Efficiency Reduces Nitrous Oxide Emissions in North America's Maize Cropping Systems

PubMed Central

Omonode, Rex A.; Halvorson, Ardell D.; Gagnon, Bernard; Vyn, Tony J.

2017-01-01

Few studies have assessed the common, yet unproven, hypothesis that an increase of plant nitrogen (N) uptake and/or recovery efficiency (NRE) will reduce nitrous oxide (N2O) emission during crop production. Understanding the relationships between N2O emissions and crop N uptake and use efficiency parameters can help inform crop N management recommendations for both efficiency and environmental goals. Analyses were conducted to determine which of several commonly used crop N uptake-derived parameters related most strongly to growing season N2O emissions under varying N management practices in North American maize systems. Nitrogen uptake-derived variables included total aboveground N uptake (TNU), grain N uptake (GNU), N recovery efficiency (NRE), net N balance (NNB) in relation to GNU [NNB(GNU)] and TNU [NNB(TNU)], and surplus N (SN). The relationship between N2O and N application rate was sigmoidal with relatively small emissions for N rates <130 kg ha−1, and a sharp increase for N rates from 130 to 220 kg ha−1; on average, N2O increased linearly by about 5 g N per kg of N applied for rates up to 220 kg ha−1. Fairly strong and significant negative relationships existed between N2O and NRE when management focused on N application rate (r2 = 0.52) or rate and timing combinations (r2 = 0.65). For every percentage point increase, N2O decreased by 13 g N ha−1 in response to N rates, and by 20 g N ha−1 for NRE changes in response to rate-by-timing treatments. However, more consistent positive relationships (R2 = 0.73–0.77) existed between N2O and NNB(TNU), NNB(GNU), and SN, regardless of rate and timing of N application; on average N2O emission increased by about 5, 7, and 8 g N, respectively, per kg increase of NNB(GNU), NNB(TNU), and SN. Neither N source nor placement influenced the relationship between N2O and NRE. Overall, our analysis indicated that a careful selection of appropriate N rate applied at the right time can both increase NRE and reduce N2O. However, N2O reduction benefits of optimum N rate-by-timing practices were achieved most consistently with management systems that reduced NNB through an increase of grain N removal or total plant N uptake relative to the total fertilizer N applied to maize. Future research assessing crop or N management effects on N2O should include N uptake parameter measurements to better understand N2O emission relationships to plant NRE and N uptake. PMID:28690623

46 CFR 502.201 - General provisions governing discovery.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 9 2010-10-01 2010-10-01 false General provisions governing discovery. 502.201 Section... AND PROCEDURE Depositions, Written Interrogatories, and Discovery § 502.201 General provisions governing discovery. (a) Applicability. The procedures described in this subpart are available in all...

78 FR 63974 - Student Assistance General Provisions-Subpart K-Cash Management; Extension of Public Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-25

... DEPARTMENT OF EDUCATION Student Assistance General Provisions--Subpart K--Cash Management; Extension of Public Comment Period; Correction AGENCY: Department of Education. ACTION: Correction notice... an information collection entitled, ``Student Assistance General Provisions--Subpart K--Cash...

40 CFR 94.1107 - Warranty provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... were in general use with engines prior to 1999. For diesel engines, this would generally include...) CONTROL OF EMISSIONS FROM MARINE COMPRESSION-IGNITION ENGINES General Enforcement Provisions and Prohibited Acts § 94.1107 Warranty provisions. (a) The manufacturer of each engine must warrant to the...

40 CFR 94.1107 - Warranty provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... were in general use with engines prior to 1999. For diesel engines, this would generally include...) CONTROL OF EMISSIONS FROM MARINE COMPRESSION-IGNITION ENGINES General Enforcement Provisions and Prohibited Acts § 94.1107 Warranty provisions. (a) The manufacturer of each engine must warrant to the...

40 CFR 94.1107 - Warranty provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... were in general use with engines prior to 1999. For diesel engines, this would generally include...) CONTROL OF EMISSIONS FROM MARINE COMPRESSION-IGNITION ENGINES General Enforcement Provisions and Prohibited Acts § 94.1107 Warranty provisions. (a) The manufacturer of each engine must warrant to the...

40 CFR 94.1107 - Warranty provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... were in general use with engines prior to 1999. For diesel engines, this would generally include...) CONTROL OF EMISSIONS FROM MARINE COMPRESSION-IGNITION ENGINES General Enforcement Provisions and Prohibited Acts § 94.1107 Warranty provisions. (a) The manufacturer of each engine must warrant to the...

40 CFR 94.1107 - Warranty provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... were in general use with engines prior to 1999. For diesel engines, this would generally include...) CONTROL OF EMISSIONS FROM MARINE COMPRESSION-IGNITION ENGINES General Enforcement Provisions and Prohibited Acts § 94.1107 Warranty provisions. (a) The manufacturer of each engine must warrant to the...

Low-cost approach for a software-defined radio based ground station receiver for CCSDS standard compliant S-band satellite communications

NASA Astrophysics Data System (ADS)

Boettcher, M. A.; Butt, B. M.; Klinkner, S.

2016-10-01

A major concern of a university satellite mission is to download the payload and the telemetry data from a satellite. While the ground station antennas are in general easy and with limited afford to procure, the receiving unit is most certainly not. The flexible and low-cost software-defined radio (SDR) transceiver "BladeRF" is used to receive the QPSK modulated and CCSDS compliant coded data of a satellite in the HAM radio S-band. The control software is based on the Open Source program GNU Radio, which also is used to perform CCSDS post processing of the binary bit stream. The test results show a good performance of the receiving system.

The moving mesh code SHADOWFAX

NASA Astrophysics Data System (ADS)

Vandenbroucke, B.; De Rijcke, S.

2016-07-01

We introduce the moving mesh code SHADOWFAX, which can be used to evolve a mixture of gas, subject to the laws of hydrodynamics and gravity, and any collisionless fluid only subject to gravity, such as cold dark matter or stars. The code is written in C++ and its source code is made available to the scientific community under the GNU Affero General Public Licence. We outline the algorithm and the design of our implementation, and demonstrate its validity through the results of a set of basic test problems, which are also part of the public version. We also compare SHADOWFAX with a number of other publicly available codes using different hydrodynamical integration schemes, illustrating the advantages and disadvantages of the moving mesh technique.

Tatool: a Java-based open-source programming framework for psychological studies.

PubMed

von Bastian, Claudia C; Locher, André; Ruflin, Michael

2013-03-01

Tatool (Training and Testing Tool) was developed to assist researchers with programming training software, experiments, and questionnaires. Tatool is Java-based, and thus is a platform-independent and object-oriented framework. The architecture was designed to meet the requirements of experimental designs and provides a large number of predefined functions that are useful in psychological studies. Tatool comprises features crucial for training studies (e.g., configurable training schedules, adaptive training algorithms, and individual training statistics) and allows for running studies online via Java Web Start. The accompanying "Tatool Online" platform provides the possibility to manage studies and participants' data easily with a Web-based interface. Tatool is published open source under the GNU Lesser General Public License, and is available at www.tatool.ch.

AMIDE: a free software tool for multimodality medical image analysis.

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves.

PubMed

Sprouffske, Kathleen; Wagner, Andreas

2016-04-19

Plate readers can measure the growth curves of many microbial strains in a high-throughput fashion. The hundreds of absorbance readings collected simultaneously for hundreds of samples create technical hurdles for data analysis. Growthcurver summarizes the growth characteristics of microbial growth curve experiments conducted in a plate reader. The data are fitted to a standard form of the logistic equation, and the parameters have clear interpretations on population-level characteristics, like doubling time, carrying capacity, and growth rate. Growthcurver is an easy-to-use R package available for installation from the Comprehensive R Archive Network (CRAN). The source code is available under the GNU General Public License and can be obtained from Github (Sprouffske K, Growthcurver sourcecode, 2016).

78 FR 21114 - Magnuson-Stevens Act Provisions; General Provisions for Domestic Fisheries; Application for...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-09

...-Stevens Act Provisions; General Provisions for Domestic Fisheries; Application for Exempted Fishing... preliminary determination that an Exempted Fishing Permit (EFP) application contains all of the required information and warrants further consideration. This Exempted Fishing Permit would exempt commercial fishing...

14 CFR 201.4 - General provisions concerning contents.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false General provisions concerning contents. 201.4 Section 201.4 Aeronautics and Space OFFICE OF THE SECRETARY, DEPARTMENT OF TRANSPORTATION... UNITED STATES CODE-[AMENDED] Application Procedures § 201.4 General provisions concerning contents. (a...

19 CFR 10.114 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... ARTICLES CONDITIONALLY FREE, SUBJECT TO A REDUCED RATE, ETC. General Provisions Instruments and Apparatus for Educational and Scientific Institutions § 10.114 General provisions. The consolidated regulations... educational and scientific institutions are contained in 15 CFR part 301. [T.D. 82-224, 47 FR 53727, Nov. 29...

10 CFR 835.701 - General provisions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false General provisions. 835.701 Section 835.701 Energy DEPARTMENT OF ENERGY OCCUPATIONAL RADIATION PROTECTION Records § 835.701 General provisions. (a) Records shall be maintained to document compliance with this part and with radiation protection programs...

10 CFR 835.701 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false General provisions. 835.701 Section 835.701 Energy DEPARTMENT OF ENERGY OCCUPATIONAL RADIATION PROTECTION Records § 835.701 General provisions. (a) Records shall be maintained to document compliance with this part and with radiation protection programs...

10 CFR 835.701 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false General provisions. 835.701 Section 835.701 Energy DEPARTMENT OF ENERGY OCCUPATIONAL RADIATION PROTECTION Records § 835.701 General provisions. (a) Records shall be maintained to document compliance with this part and with radiation protection programs...

10 CFR 835.701 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false General provisions. 835.701 Section 835.701 Energy DEPARTMENT OF ENERGY OCCUPATIONAL RADIATION PROTECTION Records § 835.701 General provisions. (a) Records shall be maintained to document compliance with this part and with radiation protection programs...

10 CFR 835.701 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false General provisions. 835.701 Section 835.701 Energy DEPARTMENT OF ENERGY OCCUPATIONAL RADIATION PROTECTION Records § 835.701 General provisions. (a) Records shall be maintained to document compliance with this part and with radiation protection programs...

32 CFR 728.51 - General provisions-the “Economy Act.”

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 5 2011-07-01 2011-07-01 false General provisions-the âEconomy Act.â 728.51... Federal Agencies § 728.51 General provisions—the “Economy Act.” The Economy Act, 31 U.S.C. 1535, generally... convenient, or less expensive, than commercial procurement. Provisions of the Economy Act apply to requests...

32 CFR 728.51 - General provisions-the “Economy Act.”

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 5 2012-07-01 2012-07-01 false General provisions-the âEconomy Act.â 728.51... Federal Agencies § 728.51 General provisions—the “Economy Act.” The Economy Act, 31 U.S.C. 1535, generally... convenient, or less expensive, than commercial procurement. Provisions of the Economy Act apply to requests...

32 CFR 728.51 - General provisions-the “Economy Act.”

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 5 2013-07-01 2013-07-01 false General provisions-the âEconomy Act.â 728.51... Federal Agencies § 728.51 General provisions—the “Economy Act.” The Economy Act, 31 U.S.C. 1535, generally... convenient, or less expensive, than commercial procurement. Provisions of the Economy Act apply to requests...

32 CFR 728.51 - General provisions-the “Economy Act.”

Code of Federal Regulations, 2014 CFR

2014-07-01

... 32 National Defense 5 2014-07-01 2014-07-01 false General provisions-the âEconomy Act.â 728.51... Federal Agencies § 728.51 General provisions—the “Economy Act.” The Economy Act, 31 U.S.C. 1535, generally... convenient, or less expensive, than commercial procurement. Provisions of the Economy Act apply to requests...

28 CFR 30.13 - May the Attorney General waive any provision of these regulations?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 1 2010-07-01 2010-07-01 false May the Attorney General waive any... INTERGOVERNMENTAL REVIEW OF DEPARTMENT OF JUSTICE PROGRAMS AND ACTIVITIES § 30.13 May the Attorney General waive any provision of these regulations? In an emergency, the Attorney General may waive any provision of these...

42 CFR 71.31 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 1 2014-10-01 2014-10-01 false General provisions. 71.31 Section 71.31 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES QUARANTINE, INSPECTION, LICENSING FOREIGN QUARANTINE Health Measures at U.S. Ports: Communicable Diseases § 71.31 General provisions. (a...

42 CFR 71.41 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 1 2013-10-01 2013-10-01 false General provisions. 71.41 Section 71.41 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES QUARANTINE, INSPECTION, LICENSING FOREIGN QUARANTINE Requirements Upon Arrival at U.S. Ports: Sanitary Inspection § 71.41 General provisions...

42 CFR 71.31 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 1 2013-10-01 2013-10-01 false General provisions. 71.31 Section 71.31 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES QUARANTINE, INSPECTION, LICENSING FOREIGN QUARANTINE Health Measures at U.S. Ports: Communicable Diseases § 71.31 General provisions. (a...

42 CFR 71.31 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 1 2011-10-01 2011-10-01 false General provisions. 71.31 Section 71.31 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES QUARANTINE, INSPECTION, LICENSING FOREIGN QUARANTINE Health Measures at U.S. Ports: Communicable Diseases § 71.31 General provisions. (a...

42 CFR 71.41 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 1 2014-10-01 2014-10-01 false General provisions. 71.41 Section 71.41 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES QUARANTINE, INSPECTION, LICENSING FOREIGN QUARANTINE Requirements Upon Arrival at U.S. Ports: Sanitary Inspection § 71.41 General provisions...

42 CFR 71.41 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 1 2011-10-01 2011-10-01 false General provisions. 71.41 Section 71.41 Public Health PUBLIC HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES QUARANTINE, INSPECTION, LICENSING FOREIGN QUARANTINE Requirements Upon Arrival at U.S. Ports: Sanitary Inspection § 71.41 General provisions...

10 CFR 20.2101 - General provisions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false General provisions. 20.2101 Section 20.2101 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Records § 20.2101 General provisions. (a) Each licensee shall use the units: curie, rad, rem, including multiples and subdivisions, and shall...

10 CFR 20.2101 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General provisions. 20.2101 Section 20.2101 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Records § 20.2101 General provisions. (a) Each licensee shall use the units: curie, rad, rem, including multiples and subdivisions, and shall...

10 CFR 20.2101 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false General provisions. 20.2101 Section 20.2101 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Records § 20.2101 General provisions. (a) Each licensee shall use the units: curie, rad, rem, including multiples and subdivisions, and shall...

10 CFR 20.2101 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false General provisions. 20.2101 Section 20.2101 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Records § 20.2101 General provisions. (a) Each licensee shall use the units: curie, rad, rem, including multiples and subdivisions, and shall...

10 CFR 20.2101 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false General provisions. 20.2101 Section 20.2101 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Records § 20.2101 General provisions. (a) Each licensee shall use the units: curie, rad, rem, including multiples and subdivisions, and shall...

20 CFR 71.1 - General administrative provisions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... HIDING FROM THE IMPERIAL JAPANESE GOVERNMENT GENERAL PROVISIONS § 71.1 General administrative provisions... Imperial Japanese Government to the same extent as if such civilian American citizen were an employee... Japanese Government on or after December 7, 1941, at Midway, Guam, Wake Island, the Philippine Islands, or...

Provision of medical student teaching in UK general practices: a cross-sectional questionnaire study

PubMed Central

Harding, Alex; Rosenthal, Joe; Al-Seaidy, Marwa; Gray, Denis Pereira; McKinley, Robert K

2015-01-01

Background Health care is increasingly provided in general practice. To meet this demand, the English Department of Health recommends that 50% of all medical students should train for general practice after qualification. Currently 19% of medical students express general practice as their first career choice. Undergraduate exposure to general practice positively influences future career choice. Appropriate undergraduate exposure to general practice is therefore highly relevant to workforce planning Aim This study seeks to quantify current exposure of medical students to general practice and compare it with past provision and also with postgraduate provision. Design and setting A cross-sectional questionnaire in the UK. Method A questionnaire regarding provision of undergraduate teaching was sent to the general practice teaching leads in all UK medical schools. Information was gathered on the amount of undergraduate teaching, how this was supported financially, and whether there was an integrated department of general practice. The data were then compared with results from previous studies of teaching provision. The provision of postgraduate teaching in general practice was also examined. Results General practice teaching for medical students increased from <1.0% of clinical teaching in 1968 to 13.0% by 2008; since then, the percentage has plateaued. The total amount of general practice teaching per student has fallen by 2 weeks since 2002. Medical schools providing financial data delivered 14.6% of the clinical curriculum and received 7.1% of clinical teaching funding. The number of departments of general practice has halved since 2002. Provision of postgraduate teaching has tripled since 2000. Conclusion Current levels of undergraduate teaching in general practice are too low to fulfil future workforce requirements and may be falling. Financial support for current teaching is disproportionately low and the mechanism counterproductive. Central intervention may be required to solve this. PMID:26009536

BOINC: compute for science

Science.gov Websites

. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation.

29 CFR 570.103 - Comparison with wage and hour provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... REGULATIONS CHILD LABOR REGULATIONS, ORDERS AND STATEMENTS OF INTERPRETATION General Statements of Interpretation of the Child Labor Provisions of the Fair Labor Standards Act of 1938, as Amended General § 570.103 Comparison with wage and hour provisions. A comparison of the child labor provisions with the so...

29 CFR 570.103 - Comparison with wage and hour provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... REGULATIONS CHILD LABOR REGULATIONS, ORDERS AND STATEMENTS OF INTERPRETATION General Statements of Interpretation of the Child Labor Provisions of the Fair Labor Standards Act of 1938, as Amended General § 570.103 Comparison with wage and hour provisions. A comparison of the child labor provisions with the so...

29 CFR 570.103 - Comparison with wage and hour provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... REGULATIONS CHILD LABOR REGULATIONS, ORDERS AND STATEMENTS OF INTERPRETATION General Statements of Interpretation of the Child Labor Provisions of the Fair Labor Standards Act of 1938, as Amended General § 570.103 Comparison with wage and hour provisions. A comparison of the child labor provisions with the so...

29 CFR 570.103 - Comparison with wage and hour provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... REGULATIONS CHILD LABOR REGULATIONS, ORDERS AND STATEMENTS OF INTERPRETATION General Statements of Interpretation of the Child Labor Provisions of the Fair Labor Standards Act of 1938, as Amended General § 570.103 Comparison with wage and hour provisions. A comparison of the child labor provisions with the so...

30 CFR 1206.452 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Coal subject to royalties-general provisions... INTERIOR NATURAL RESOURCES REVENUE PRODUCT VALUATION Indian Coal § 1206.452 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM pursuant to 43 CFR...

30 CFR 1206.253 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Coal subject to royalties-general provisions..., DEPARTMENT OF THE INTERIOR Natural Resources Revenue PRODUCT VALUATION Federal Coal § 1206.253 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM...

30 CFR 1206.452 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Coal subject to royalties-general provisions... INTERIOR NATURAL RESOURCES REVENUE PRODUCT VALUATION Indian Coal § 1206.452 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM pursuant to 43 CFR...

30 CFR 1206.452 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Coal subject to royalties-general provisions... INTERIOR NATURAL RESOURCES REVENUE PRODUCT VALUATION Indian Coal § 1206.452 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM pursuant to 43 CFR...

6 CFR 5.1 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 6 Domestic Security 1 2010-01-01 2010-01-01 false General provisions. 5.1 Section 5.1 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY DISCLOSURE OF RECORDS AND INFORMATION Freedom of Information Act § 5.1 General provisions. (a)(1) This subpart A contains the rules that the...

7 CFR 1.15 - General provisions respecting release of records.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 1 2013-01-01 2013-01-01 false General provisions respecting release of records. 1.15 Section 1.15 Agriculture Office of the Secretary of Agriculture ADMINISTRATIVE REGULATIONS Official Records § 1.15 General provisions respecting release of records. (a) When releasing documents, agencies...

50 CFR 26.21 - General trespass provision.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 9 2013-10-01 2013-10-01 false General trespass provision. 26.21 Section... (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM PUBLIC ENTRY AND USE Public Entry § 26.21 General trespass provision. (a) No person shall trespass, including but not limited to entering, occupying, using, or being...

50 CFR 26.21 - General trespass provision.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false General trespass provision. 26.21 Section... (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM PUBLIC ENTRY AND USE Public Entry § 26.21 General trespass provision. (a) No person shall trespass, including but not limited to entering, occupying, using, or being...

50 CFR 26.21 - General trespass provision.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 9 2012-10-01 2012-10-01 false General trespass provision. 26.21 Section... (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM PUBLIC ENTRY AND USE Public Entry § 26.21 General trespass provision. (a) No person shall trespass, including but not limited to entering, occupying, using, or being...

50 CFR 26.21 - General trespass provision.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 8 2011-10-01 2011-10-01 false General trespass provision. 26.21 Section... (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM PUBLIC ENTRY AND USE Public Entry § 26.21 General trespass provision. (a) No person shall trespass, including but not limited to entering, occupying, using, or being...

50 CFR 26.21 - General trespass provision.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 9 2014-10-01 2014-10-01 false General trespass provision. 26.21 Section... (CONTINUED) THE NATIONAL WILDLIFE REFUGE SYSTEM PUBLIC ENTRY AND USE Public Entry § 26.21 General trespass provision. (a) No person shall trespass, including but not limited to entering, occupying, using, or being...

28 CFR 700.10 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 2 2010-07-01 2010-07-01 false General provisions. 700.10 Section 700.10... Privacy Act of 1974 § 700.10 General provisions. (a) Purpose and scope. The subpart contains the... pertaining to him, may request correction of such records, or may seek an accounting of disclosures of such...

10 CFR 20.1401 - General provisions and scope.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General provisions and scope. 20.1401 Section 20.1401 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Radiological Criteria for License Termination § 20.1401 General provisions and scope. (a) The criteria in this subpart apply to the...

10 CFR 20.1401 - General provisions and scope.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false General provisions and scope. 20.1401 Section 20.1401 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Radiological Criteria for License Termination § 20.1401 General provisions and scope. (a) The criteria in this subpart apply to the...

10 CFR 20.1401 - General provisions and scope.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false General provisions and scope. 20.1401 Section 20.1401 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Radiological Criteria for License Termination § 20.1401 General provisions and scope. (a) The criteria in this subpart apply to the...

10 CFR 20.1401 - General provisions and scope.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false General provisions and scope. 20.1401 Section 20.1401 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Radiological Criteria for License Termination § 20.1401 General provisions and scope. (a) The criteria in this subpart apply to the...

10 CFR 20.1401 - General provisions and scope.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false General provisions and scope. 20.1401 Section 20.1401 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Radiological Criteria for License Termination § 20.1401 General provisions and scope. (a) The criteria in this subpart apply to the...

40 CFR 60.4218 - What parts of the General Provisions apply to me?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What parts of the General Provisions apply to me? 60.4218 Section 60.4218 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Performance for Stationary Compression Ignition Internal Combustion Engines General Provisions § 60.4218 What...

10 CFR 26.53 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false General provisions. 26.53 Section 26.53 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Granting and Maintaining Authorization § 26.53 General provisions. (a) In order to grant authorization to an individual, a licensee or other entity shall ensure...

10 CFR 26.53 - General provisions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false General provisions. 26.53 Section 26.53 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Granting and Maintaining Authorization § 26.53 General provisions. (a) In order to grant authorization to an individual, a licensee or other entity shall ensure...

10 CFR 26.53 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false General provisions. 26.53 Section 26.53 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Granting and Maintaining Authorization § 26.53 General provisions. (a) In order to grant authorization to an individual, a licensee or other entity shall ensure...

10 CFR 26.203 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General provisions. 26.203 Section 26.203 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Managing Fatigue § 26.203 General provisions. (a) Policy. Licensees shall establish a policy for the management of fatigue for all individuals who are subject to the...

10 CFR 26.53 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false General provisions. 26.53 Section 26.53 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Granting and Maintaining Authorization § 26.53 General provisions. (a) In order to grant authorization to an individual, a licensee or other entity shall ensure...

10 CFR 26.203 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false General provisions. 26.203 Section 26.203 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Managing Fatigue § 26.203 General provisions. (a) Policy. Licensees shall establish a policy for the management of fatigue for all individuals who are subject to the...

10 CFR 26.53 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General provisions. 26.53 Section 26.53 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Granting and Maintaining Authorization § 26.53 General provisions. (a) In order to grant authorization to an individual, a licensee or other entity shall ensure...

40 CFR 76.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 17 2013-07-01 2013-07-01 false General Acid Rain Program provisions. 76.3 Section 76.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.3 General Acid Rain Program provisions...

40 CFR 76.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 16 2010-07-01 2010-07-01 false General Acid Rain Program provisions. 76.3 Section 76.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.3 General Acid Rain Program provisions...

40 CFR 76.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 17 2014-07-01 2014-07-01 false General Acid Rain Program provisions. 76.3 Section 76.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.3 General Acid Rain Program provisions...

40 CFR 76.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 17 2012-07-01 2012-07-01 false General Acid Rain Program provisions. 76.3 Section 76.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.3 General Acid Rain Program provisions...

40 CFR 76.3 - General Acid Rain Program provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 16 2011-07-01 2011-07-01 false General Acid Rain Program provisions. 76.3 Section 76.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.3 General Acid Rain Program provisions...

21 CFR 179.25 - General provisions for food irradiation.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 3 2011-04-01 2011-04-01 false General provisions for food irradiation. 179.25... (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) IRRADIATION IN THE PRODUCTION, PROCESSING AND HANDLING OF FOOD Radiation and Radiation Sources § 179.25 General provisions for food irradiation. For the purposes...

21 CFR 179.25 - General provisions for food irradiation.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 3 2012-04-01 2012-04-01 false General provisions for food irradiation. 179.25... (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) IRRADIATION IN THE PRODUCTION, PROCESSING AND HANDLING OF FOOD Radiation and Radiation Sources § 179.25 General provisions for food irradiation. For the purposes...

21 CFR 179.25 - General provisions for food irradiation.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 3 2014-04-01 2014-04-01 false General provisions for food irradiation. 179.25... (CONTINUED) IRRADIATION IN THE PRODUCTION, PROCESSING AND HANDLING OF FOOD Radiation and Radiation Sources § 179.25 General provisions for food irradiation. For the purposes of § 179.26, current good...

21 CFR 179.25 - General provisions for food irradiation.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true General provisions for food irradiation. 179.25... (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) IRRADIATION IN THE PRODUCTION, PROCESSING AND HANDLING OF FOOD Radiation and Radiation Sources § 179.25 General provisions for food irradiation. For the purposes...

21 CFR 179.25 - General provisions for food irradiation.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 3 2013-04-01 2013-04-01 false General provisions for food irradiation. 179.25... (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) IRRADIATION IN THE PRODUCTION, PROCESSING AND HANDLING OF FOOD Radiation and Radiation Sources § 179.25 General provisions for food irradiation. For the purposes...

40 CFR 1068.301 - What general provisions apply?

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 33 2014-07-01 2014-07-01 false What general provisions apply? 1068.301 Section 1068.301 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... § 1068.301 What general provisions apply? (a) This subpart applies to you if you import into the United...

SAWdoubler: A program for counting self-avoiding walks

NASA Astrophysics Data System (ADS)

Schram, Raoul D.; Barkema, Gerard T.; Bisseling, Rob H.

2013-03-01

This article presents SAWdoubler, a package for counting the total number ZN of self-avoiding walks (SAWs) on a regular lattice by the length-doubling method, of which the basic concept has been published previously by us. We discuss an algorithm for the creation of all SAWs of length N, efficient storage of these SAWs in a tree data structure, and an algorithm for the computation of correction terms to the count Z2N for SAWs of double length, removing all combinations of two intersecting single-length SAWs. We present an efficient numbering of the lattice sites that enables exploitation of symmetry and leads to a smaller tree data structure; this numbering is by increasing Euclidean distance from the origin of the lattice. Furthermore, we show how the computation can be parallelised by distributing the iterations of the main loop of the algorithm over the cores of a multicore architecture. Experimental results on the 3D cubic lattice demonstrate that Z28 can be computed on a dual-core PC in only 1 h and 40 min, with a speedup of 1.56 compared to the single-core computation and with a gain by using symmetry of a factor of 26. We present results for memory use and show how the computation is made to fit in 4 GB RAM. It is easy to extend the SAWdoubler software to other lattices; it is publicly available under the GNU LGPL license. Catalogue identifier: AEOB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Lesser General Public Licence No. of lines in distributed program, including test data, etc.: 2101 No. of bytes in distributed program, including test data, etc.: 19816 Distribution format: tar.gz Programming language: C. Computer: Any computer with a UNIX-like operating system and a C compiler. For large problems, use is made of specific 128-bit integer arithmetic provided by the gcc compiler. Operating system: Any UNIX-like system; developed under Linux and Mac OS 10. Has the code been vectorised or parallelised?: Yes. A parallel version of the code is available in the “Extras” directory of the distribution file. RAM: Problem dependent (2 GB for counting SAWs of length 28 on the 3D cubic lattice) Classification: 16.11. Nature of problem: Computing the number of self-avoiding walks of a given length on a given lattice. Solution method: Length-doubling. Restrictions: The length of the walk must be even. Lattice is 3D simple cubic. Additional comments: The lattice can be replaced by other lattices, such as BCC, FCC, or a 2D square lattice. Running time: Problem dependent (2.5 h using one processor core for length 28 on the 3D cubic lattice).

30 CFR 1206.253 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Coal subject to royalties-general provisions... INTERIOR NATURAL RESOURCES REVENUE PRODUCT VALUATION Federal Coal § 1206.253 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM under 43 CFR part 3400...

30 CFR 206.452 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Coal subject to royalties-general provisions... MINERALS REVENUE MANAGEMENT PRODUCT VALUATION Indian Coal § 206.452 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM pursuant to 43 CFR group 3400...

30 CFR 206.253 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Coal subject to royalties-general provisions... MINERALS REVENUE MANAGEMENT PRODUCT VALUATION Federal Coal § 206.253 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM under 43 CFR part 3400) from a...

30 CFR 1206.253 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Coal subject to royalties-general provisions... INTERIOR NATURAL RESOURCES REVENUE PRODUCT VALUATION Federal Coal § 1206.253 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM under 43 CFR part 3400...

30 CFR 1206.452 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Coal subject to royalties-general provisions..., DEPARTMENT OF THE INTERIOR Natural Resources Revenue PRODUCT VALUATION Indian Coal § 1206.452 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM pursuant to 43...

30 CFR 1206.253 - Coal subject to royalties-general provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Coal subject to royalties-general provisions... INTERIOR NATURAL RESOURCES REVENUE PRODUCT VALUATION Federal Coal § 1206.253 Coal subject to royalties—general provisions. (a) All coal (except coal unavoidably lost as determined by BLM under 43 CFR part 3400...

40 CFR 86.1707-99 - General provisions; opt-outs.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) General Provisions for the Voluntary National Low Emission Vehicle Program for Light-Duty Vehicles and Light-Duty Trucks § 86.1707-99 General provisions; opt-outs. A covered manufacturer or covered state may... manufacturer until the opt-out has come into effect under paragraph (d)(1) of this section and EPA or a...

40 CFR 86.1707-99 - General provisions; opt-outs.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) General Provisions for the Voluntary National Low Emission Vehicle Program for Light-Duty Vehicles and Light-Duty Trucks § 86.1707-99 General provisions; opt-outs. A covered manufacturer or covered state may... manufacturer until the opt-out has come into effect under paragraph (d)(1) of this section and EPA or a...

45 CFR 613.1 - General Provisions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 3 2011-10-01 2011-10-01 false General Provisions. 613.1 Section 613.1 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION PRIVACY ACT REGULATIONS § 613.1 General Provisions. This part sets forth the National Science Foundation procedures under the Privacy Act of 1974. The rules in this...

45 CFR 613.1 - General Provisions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 3 2010-10-01 2010-10-01 false General Provisions. 613.1 Section 613.1 Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION PRIVACY ACT REGULATIONS § 613.1 General Provisions. This part sets forth the National Science Foundation procedures under the Privacy Act of 1974. The rules in this...

40 CFR 60.4246 - What parts of the General Provisions apply to me?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What parts of the General Provisions apply to me? 60.4246 Section 60.4246 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Performance for Stationary Spark Ignition Internal Combustion Engines General Provisions § 60.4246 What parts...

DynamO: a free O(N) general event-driven molecular dynamics simulator.

PubMed

Bannerman, M N; Sargant, R; Lue, L

2011-11-30

Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo. Copyright © 2011 Wiley Periodicals, Inc.

40 CFR Table 2 to Subpart Ssss of... - Applicability of General Provisions to Subpart SSSS

Code of Federal Regulations, 2010 CFR

2010-07-01

... Subpart SSSS 2 Table 2 to Subpart SSSS of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION... Pt. 63, Subpt. SSSS, Table 2 Table 2 to Subpart SSSS of Part 63—Applicability of General Provisions to Subpart SSSS You must comply with the applicable General Provisions requirements according to the...

40 CFR 63.11150 - What General Provisions apply to this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 14 2010-07-01 2010-07-01 false What General Provisions apply to this... Area Sources Other Requirements and Information § 63.11150 What General Provisions apply to this... a gas cleaning system controlling PM and to a sulfuric acid plant in accordance with § 63.11148(a)(2...

40 CFR Table 1 to Subpart Mm of... - General Provisions Applicability to Subpart MM

Code of Federal Regulations, 2014 CFR

2014-07-01

... Subpart MM 1 Table 1 to Subpart MM of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Combustion Sources at Kraft, Soda, Sulfite, and Stand-Alone Semichemical Pulp Mills Pt. 63, Subpt. MM, Table 1 Table 1 to Subpart MM of Part 63—General Provisions Applicability to Subpart MM General provisions...

40 CFR Table 1 to Subpart Mm of... - General Provisions Applicability to Subpart MM

Code of Federal Regulations, 2010 CFR

2010-07-01

... Subpart MM 1 Table 1 to Subpart MM of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Combustion Sources at Kraft, Soda, Sulfite, and Stand-Alone Semichemical Pulp Mills Pt. 63, Subpt. MM, Table 1 Table 1 to Subpart MM of Part 63—General Provisions Applicability to Subpart MM General provisions...

40 CFR Table 1 to Subpart Mm of... - General Provisions Applicability to Subpart MM

Code of Federal Regulations, 2011 CFR

2011-07-01

... Subpart MM 1 Table 1 to Subpart MM of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Combustion Sources at Kraft, Soda, Sulfite, and Stand-Alone Semichemical Pulp Mills Pt. 63, Subpt. MM, Table 1 Table 1 to Subpart MM of Part 63—General Provisions Applicability to Subpart MM General provisions...

40 CFR Table 1 to Subpart Mm of... - General Provisions Applicability to Subpart MM

Code of Federal Regulations, 2013 CFR

2013-07-01

... Subpart MM 1 Table 1 to Subpart MM of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Combustion Sources at Kraft, Soda, Sulfite, and Stand-Alone Semichemical Pulp Mills Pt. 63, Subpt. MM, Table 1 Table 1 to Subpart MM of Part 63—General Provisions Applicability to Subpart MM General provisions...

40 CFR Table 1 to Subpart Mm of... - General Provisions Applicability to Subpart MM

Code of Federal Regulations, 2012 CFR

2012-07-01

... Subpart MM 1 Table 1 to Subpart MM of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Combustion Sources at Kraft, Soda, Sulfite, and Stand-Alone Semichemical Pulp Mills Pt. 63, Subpt. MM, Table 1 Table 1 to Subpart MM of Part 63—General Provisions Applicability to Subpart MM General provisions...

1 CFR 2.4 - General authority of Director.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 1 General Provisions 1 2011-01-01 2011-01-01 false General authority of Director. 2.4 Section 2.4 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER GENERAL GENERAL INFORMATION § 2.4 General authority of Director. (a) The Director of the Federal Register is delegated authority to...

1 CFR 2.4 - General authority of Director.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 1 General Provisions 1 2010-01-01 2010-01-01 false General authority of Director. 2.4 Section 2.4 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER GENERAL GENERAL INFORMATION § 2.4 General authority of Director. (a) The Director of the Federal Register is delegated authority to...

1 CFR 2.4 - General authority of Director.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 1 General Provisions 1 2014-01-01 2012-01-01 true General authority of Director. 2.4 Section 2.4 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER GENERAL GENERAL INFORMATION § 2.4 General authority of Director. (a) The Director of the Federal Register is delegated authority to...

1 CFR 2.4 - General authority of Director.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 1 General Provisions 1 2012-01-01 2012-01-01 false General authority of Director. 2.4 Section 2.4 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER GENERAL GENERAL INFORMATION § 2.4 General authority of Director. (a) The Director of the Federal Register is delegated authority to...

1 CFR 2.4 - General authority of Director.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 1 General Provisions 1 2013-01-01 2012-01-01 true General authority of Director. 2.4 Section 2.4 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER GENERAL GENERAL INFORMATION § 2.4 General authority of Director. (a) The Director of the Federal Register is delegated authority to...

CompariMotif: quick and easy comparisons of sequence motifs.

PubMed

Edwards, Richard J; Davey, Norman E; Shields, Denis C

2008-05-15

CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples

PubMed Central

Turchin, Michael C.; Hirschhorn, Joel N.

2012-01-01

Summary: Meta-analysis across genome-wide association studies is a common approach for discovering genetic associations. However, in some meta-analysis efforts, individual-level data cannot be broadly shared by study investigators due to privacy and Institutional Review Board concerns. In such cases, researchers cannot confirm that each study represents a unique group of people, leading to potentially inflated test statistics and false positives. To resolve this problem, we created a software tool, Gencrypt, which utilizes a security protocol known as one-way cryptographic hashes to allow overlapping participants to be identified without sharing individual-level data. Availability: Gencrypt is freely available under the GNU general public license v3 at http://www.broadinstitute.org/software/gencrypt/ Contact: joelh@broadinstitute.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22302573

TRIQS: A toolbox for research on interacting quantum systems

NASA Astrophysics Data System (ADS)

Parcollet, Olivier; Ferrero, Michel; Ayral, Thomas; Hafermann, Hartmut; Krivenko, Igor; Messio, Laura; Seth, Priyanka

2015-11-01

We present the TRIQS library, a Toolbox for Research on Interacting Quantum Systems. It is an open-source, computational physics library providing a framework for the quick development of applications in the field of many-body quantum physics, and in particular, strongly-correlated electronic systems. It supplies components to develop codes in a modern, concise and efficient way: e.g. Green's function containers, a generic Monte Carlo class, and simple interfaces to HDF5. TRIQS is a C++/Python library that can be used from either language. It is distributed under the GNU General Public License (GPLv3). State-of-the-art applications based on the library, such as modern quantum many-body solvers and interfaces between density-functional-theory codes and dynamical mean-field theory (DMFT) codes are distributed along with it.

ParTIES: a toolbox for Paramecium interspersed DNA elimination studies.

PubMed

Denby Wilkes, Cyril; Arnaiz, Olivier; Sperling, Linda

2016-02-15

Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available. We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms. ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

UTM, a universal simulator for lightcurves of transiting systems

NASA Astrophysics Data System (ADS)

Deeg, Hans

2009-02-01

The Universal Transit Modeller (UTM) is a light-curve simulator for all kinds of transiting or eclipsing configurations between arbitrary numbers of several types of objects, which may be stars, planets, planetary moons, and planetary rings. Applications of UTM to date have been mainly in the generation of light-curves for the testing of detection algorithms. For the preparation of such test for the Corot Mission, a special version has been used to generate multicolour light-curves in Corot's passbands. A separate fitting program, UFIT (Universal Fitter) is part of the UTM distribution and may be used to derive best fits to light-curves for any set of continuously variable parameters. UTM/UFIT is written in IDL code and its source is released in the public domain under the GNU General Public License.

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

PubMed

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

50 CFR 71.12 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-10-01

...) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL FISH HATCHERY AREAS Fishing § 71.12 General provisions. The following provisions shall apply to public sport fishing on a national... may be amended as needed to meet management responsibilities for the area. ...

50 CFR 71.12 - General provisions.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL FISH HATCHERY AREAS Fishing § 71.12 General provisions. The following provisions shall apply to public sport fishing on a national... may be amended as needed to meet management responsibilities for the area. ...

50 CFR 71.12 - General provisions.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL FISH HATCHERY AREAS Fishing § 71.12 General provisions. The following provisions shall apply to public sport fishing on a national... may be amended as needed to meet management responsibilities for the area. ...

50 CFR 71.12 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-10-01

...) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL FISH HATCHERY AREAS Fishing § 71.12 General provisions. The following provisions shall apply to public sport fishing on a national... may be amended as needed to meet management responsibilities for the area. ...

50 CFR 71.12 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL FISH HATCHERY AREAS Fishing § 71.12 General provisions. The following provisions shall apply to public sport fishing on a national... may be amended as needed to meet management responsibilities for the area. ...

40 CFR Table 1 to Subpart Wwwwww... - Table 1 to Subpart WWWWWW of Part 63. Applicability of General Provisions to Plating and...

Code of Federal Regulations, 2010 CFR

2010-07-01

.... Applicability of General Provisions to Plating and Polishing Area Sources 1 Table 1 to Subpart WWWWWW of Part 63. Applicability of General Provisions to Plating and Polishing Area Sources Protection of Environment... Pollutants: Area Source Standards for Plating and Polishing Operations Pt. 63, Subpt. WWWWWW, Table 1 Table 1...

40 CFR Table 1 to Subpart Wwwwww... - Table 1 to Subpart WWWWWW of Part 63. Applicability of General Provisions to Plating and...

Code of Federal Regulations, 2011 CFR

2011-07-01

.... Applicability of General Provisions to Plating and Polishing Area Sources 1 Table 1 to Subpart WWWWWW of Part 63. Applicability of General Provisions to Plating and Polishing Area Sources Protection of Environment... Pollutants: Area Source Standards for Plating and Polishing Operations Pt. 63, Subpt. WWWWWW, Table 1 Table 1...

14 CFR Sec. 2-1 - Generally accepted accounting principles.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false Generally accepted accounting principles... AIR CARRIERS General Accounting Provisions Sec. 2-1 Generally accepted accounting principles. (a) The accounting provisions contained in this part are based on generally accepted accounting principles (GAAP...

OpenMP GNU and Intel Fortran programs for solving the time-dependent Gross-Pitaevskii equation

NASA Astrophysics Data System (ADS)

Young-S., Luis E.; Muruganandam, Paulsamy; Adhikari, Sadhan K.; Lončar, Vladimir; Vudragović, Dušan; Balaž, Antun

2017-11-01

We present Open Multi-Processing (OpenMP) version of Fortran 90 programs for solving the Gross-Pitaevskii (GP) equation for a Bose-Einstein condensate in one, two, and three spatial dimensions, optimized for use with GNU and Intel compilers. We use the split-step Crank-Nicolson algorithm for imaginary- and real-time propagation, which enables efficient calculation of stationary and non-stationary solutions, respectively. The present OpenMP programs are designed for computers with multi-core processors and optimized for compiling with both commercially-licensed Intel Fortran and popular free open-source GNU Fortran compiler. The programs are easy to use and are elaborated with helpful comments for the users. All input parameters are listed at the beginning of each program. Different output files provide physical quantities such as energy, chemical potential, root-mean-square sizes, densities, etc. We also present speedup test results for new versions of the programs. Program files doi:http://dx.doi.org/10.17632/y8zk3jgn84.2 Licensing provisions: Apache License 2.0 Programming language: OpenMP GNU and Intel Fortran 90. Computer: Any multi-core personal computer or workstation with the appropriate OpenMP-capable Fortran compiler installed. Number of processors used: All available CPU cores on the executing computer. Journal reference of previous version: Comput. Phys. Commun. 180 (2009) 1888; ibid.204 (2016) 209. Does the new version supersede the previous version?: Not completely. It does supersede previous Fortran programs from both references above, but not OpenMP C programs from Comput. Phys. Commun. 204 (2016) 209. Nature of problem: The present Open Multi-Processing (OpenMP) Fortran programs, optimized for use with commercially-licensed Intel Fortran and free open-source GNU Fortran compilers, solve the time-dependent nonlinear partial differential (GP) equation for a trapped Bose-Einstein condensate in one (1d), two (2d), and three (3d) spatial dimensions for six different trap symmetries: axially and radially symmetric traps in 3d, circularly symmetric traps in 2d, fully isotropic (spherically symmetric) and fully anisotropic traps in 2d and 3d, as well as 1d traps, where no spatial symmetry is considered. Solution method: We employ the split-step Crank-Nicolson algorithm to discretize the time-dependent GP equation in space and time. The discretized equation is then solved by imaginary- or real-time propagation, employing adequately small space and time steps, to yield the solution of stationary and non-stationary problems, respectively. Reasons for the new version: Previously published Fortran programs [1,2] have now become popular tools [3] for solving the GP equation. These programs have been translated to the C programming language [4] and later extended to the more complex scenario of dipolar atoms [5]. Now virtually all computers have multi-core processors and some have motherboards with more than one physical computer processing unit (CPU), which may increase the number of available CPU cores on a single computer to several tens. The C programs have been adopted to be very fast on such multi-core modern computers using general-purpose graphic processing units (GPGPU) with Nvidia CUDA and computer clusters using Message Passing Interface (MPI) [6]. Nevertheless, previously developed Fortran programs are also commonly used for scientific computation and most of them use a single CPU core at a time in modern multi-core laptops, desktops, and workstations. Unless the Fortran programs are made aware and capable of making efficient use of the available CPU cores, the solution of even a realistic dynamical 1d problem, not to mention the more complicated 2d and 3d problems, could be time consuming using the Fortran programs. Previously, we published auto-parallel Fortran programs [2] suitable for Intel (but not GNU) compiler for solving the GP equation. Hence, a need for the full OpenMP version of the Fortran programs to reduce the execution time cannot be overemphasized. To address this issue, we provide here such OpenMP Fortran programs, optimized for both Intel and GNU Fortran compilers and capable of using all available CPU cores, which can significantly reduce the execution time. Summary of revisions: Previous Fortran programs [1] for solving the time-dependent GP equation in 1d, 2d, and 3d with different trap symmetries have been parallelized using the OpenMP interface to reduce the execution time on multi-core processors. There are six different trap symmetries considered, resulting in six programs for imaginary-time propagation and six for real-time propagation, totaling to 12 programs included in BEC-GP-OMP-FOR software package. All input data (number of atoms, scattering length, harmonic oscillator trap length, trap anisotropy, etc.) are conveniently placed at the beginning of each program, as before [2]. Present programs introduce a new input parameter, which is designated by Number_of_Threads and defines the number of CPU cores of the processor to be used in the calculation. If one sets the value 0 for this parameter, all available CPU cores will be used. For the most efficient calculation it is advisable to leave one CPU core unused for the background system's jobs. For example, on a machine with 20 CPU cores such that we used for testing, it is advisable to use up to 19 CPU cores. However, the total number of used CPU cores can be divided into more than one job. For instance, one can run three simulations simultaneously using 10, 4, and 5 CPU cores, respectively, thus totaling to 19 used CPU cores on a 20-core computer. The Fortran source programs are located in the directory src, and can be compiled by the make command using the makefile in the root directory BEC-GP-OMP-FOR of the software package. The examples of produced output files can be found in the directory output, although some large density files are omitted, to save space. The programs calculate the values of actually used dimensionless nonlinearities from the physical input parameters, where the input parameters correspond to the identical nonlinearity values as in the previously published programs [1], so that the output files of the old and new programs can be directly compared. The output files are conveniently named such that their contents can be easily identified, following the naming convention introduced in Ref. [2]. For example, a file named -out.txt, where is a name of the individual program, represents the general output file containing input data, time and space steps, nonlinearity, energy and chemical potential, and was named fort.7 in the old Fortran version of programs [1]. A file named -den.txt is the output file with the condensate density, which had the names fort.3 and fort.4 in the old Fortran version [1] for imaginary- and real-time propagation programs, respectively. Other possible density outputs, such as the initial density, are commented out in the programs to have a simpler set of output files, but users can uncomment and re-enable them, if needed. In addition, there are output files for reduced (integrated) 1d and 2d densities for different programs. In the real-time programs there is also an output file reporting the dynamics of evolution of root-mean-square sizes after a perturbation is introduced. The supplied real-time programs solve the stationary GP equation, and then calculate the dynamics. As the imaginary-time programs are more accurate than the real-time programs for the solution of a stationary problem, one can first solve the stationary problem using the imaginary-time programs, adapt the real-time programs to read the pre-calculated wave function and then study the dynamics. In that case the parameter NSTP in the real-time programs should be set to zero and the space mesh and nonlinearity parameters should be identical in both programs. The reader is advised to consult our previous publication where a complete description of the output files is given [2]. A readme.txt file, included in the root directory, explains the procedure to compile and run the programs. We tested our programs on a workstation with two 10-core Intel Xeon E5-2650 v3 CPUs. The parameters used for testing are given in sample input files, provided in the corresponding directory together with the programs. In Table 1 we present wall-clock execution times for runs on 1, 6, and 19 CPU cores for programs compiled using Intel and GNU Fortran compilers. The corresponding columns "Intel speedup" and "GNU speedup" give the ratio of wall-clock execution times of runs on 1 and 19 CPU cores, and denote the actual measured speedup for 19 CPU cores. In all cases and for all numbers of CPU cores, although the GNU Fortran compiler gives excellent results, the Intel Fortran compiler turns out to be slightly faster. Note that during these tests we always ran only a single simulation on a workstation at a time, to avoid any possible interference issues. Therefore, the obtained wall-clock times are more reliable than the ones that could be measured with two or more jobs running simultaneously. We also studied the speedup of the programs as a function of the number of CPU cores used. The performance of the Intel and GNU Fortran compilers is illustrated in Fig. 1, where we plot the speedup and actual wall-clock times as functions of the number of CPU cores for 2d and 3d programs. We see that the speedup increases monotonically with the number of CPU cores in all cases and has large values (between 10 and 14 for 3d programs) for the maximal number of cores. This fully justifies the development of OpenMP programs, which enable much faster and more efficient solving of the GP equation. However, a slow saturation in the speedup with the further increase in the number of CPU cores is observed in all cases, as expected. The speedup tends to increase for programs in higher dimensions, as they become more complex and have to process more data. This is why the speedups of the supplied 2d and 3d programs are larger than those of 1d programs. Also, for a single program the speedup increases with the size of the spatial grid, i.e., with the number of spatial discretization points, since this increases the amount of calculations performed by the program. To demonstrate this, we tested the supplied real2d-th program and varied the number of spatial discretization points NX=NY from 20 to 1000. The measured speedup obtained when running this program on 19 CPU cores as a function of the number of discretization points is shown in Fig. 2. The speedup first increases rapidly with the number of discretization points and eventually saturates. Additional comments: Example inputs provided with the programs take less than 30 minutes to run on a workstation with two Intel Xeon E5-2650 v3 processors (2 QPI links, 10 CPU cores, 25 MB cache, 2.3 GHz).