It's Time to Consider Open Source Software

ERIC Educational Resources Information Center

Pfaffman, Jay

2007-01-01

In 1985 Richard Stallman, a computer programmer, released "The GNU Manifesto" in which he proclaimed a golden rule: One must share computer programs. Software vendors required him to agree to license agreements that forbade sharing programs with others, but he refused to "break solidarity" with other computer users whom he assumed also wanted to…

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.

XtalOpt  version r9: An open-source evolutionary algorithm for crystal structure prediction

DOE PAGES

Falls, Zackary; Lonie, David C.; Avery, Patrick; ...

2015-10-23

This is a new version of XtalOpt, an evolutionary algorithm for crystal structure prediction available for download from the CPC library or the XtalOpt website, http://xtalopt.github.io. XtalOpt is published under the Gnu Public License (GPL), which is an open source license that is recognized by the Open Source Initiative. We have detailed the new version incorporates many bug-fixes and new features here and predict the crystal structure of a system from its stoichiometry alone, using evolutionary algorithms.

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.

XTALOPT version r11: An open-source evolutionary algorithm for crystal structure prediction

NASA Astrophysics Data System (ADS)

Avery, Patrick; Falls, Zackary; Zurek, Eva

2018-01-01

Version 11 of XTALOPT, an evolutionary algorithm for crystal structure prediction, has now been made available for download from the CPC library or the XTALOPT website, http://xtalopt.github.io. Whereas the previous versions of XTALOPT were published under the Gnu Public License (GPL), the current version is made available under the 3-Clause BSD License, which is an open source license that is recognized by the Open Source Initiative. Importantly, the new version can be executed via a command line interface (i.e., it does not require the use of a Graphical User Interface). Moreover, the new version is written as a stand-alone program, rather than an extension to AVOGADRO.

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.

Limits, discovery and cut optimization for a Poisson process with uncertainty in background and signal efficiency: TRolke 2.0

NASA Astrophysics Data System (ADS)

Lundberg, J.; Conrad, J.; Rolke, W.; Lopez, A.

2010-03-01

A C++ class was written for the calculation of frequentist confidence intervals using the profile likelihood method. Seven combinations of Binomial, Gaussian, Poissonian and Binomial uncertainties are implemented. The package provides routines for the calculation of upper and lower limits, sensitivity and related properties. It also supports hypothesis tests which take uncertainties into account. It can be used in compiled C++ code, in Python or interactively via the ROOT analysis framework. Program summaryProgram title: TRolke version 2.0 Catalogue identifier: AEFT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 3431 No. of bytes in distributed program, including test data, etc.: 21 789 Distribution format: tar.gz Programming language: ISO C++. Computer: Unix, GNU/Linux, Mac. Operating system: Linux 2.6 (Scientific Linux 4 and 5, Ubuntu 8.10), Darwin 9.0 (Mac-OS X 10.5.8). RAM:˜20 MB Classification: 14.13. External routines: ROOT ( http://root.cern.ch/drupal/) Nature of problem: The problem is to calculate a frequentist confidence interval on the parameter of a Poisson process with statistical or systematic uncertainties in signal efficiency or background. Solution method: Profile likelihood method, Analytical Running time:<10 seconds per extracted limit.

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.

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.

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

Klise, Katherine A.; Siirola, John Daniel; Hart, David

The Water Security Toolkit (WST) is a suite of open source software tools that can be used by water utilities to create response strategies to reduce the impact of contamination in a water distribution network . WST includes hydraulic and water quality modeling software , optimizati on methodologies , and visualization tools to identify: (1) sensor locations to detect contamination, (2) locations in the network in which the contamination was introduced, (3) hydrants to remove contaminated water from the distribution system, (4) locations in the network to inject decontamination agents to inactivate, remove, or destroy contaminants, (5) locations in themore » network to take grab sample s to help identify the source of contamination and (6) valves to close in order to isolate contaminate d areas of the network. This user manual describes the different components of WST , along w ith examples and case studies. License Notice The Water Security Toolkit (WST) v.1.2 Copyright c 2012 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive license for use of this work by or on behalf of the U.S. government. This software is distributed under the Revised BSD License (see below). In addition, WST leverages a variety of third-party software packages, which have separate licensing policies: Acro Revised BSD License argparse Python Software Foundation License Boost Boost Software License Coopr Revised BSD License Coverage BSD License Distribute Python Software Foundation License / Zope Public License EPANET Public Domain EPANET-ERD Revised BSD License EPANET-MSX GNU Lesser General Public License (LGPL) v.3 gcovr Revised BSD License GRASP AT&T Commercial License for noncommercial use; includes randomsample and sideconstraints executable files LZMA SDK Public Domain nose GNU Lesser General Public License (LGPL) v.2.1 ordereddict MIT License pip MIT License PLY BSD License PyEPANET Revised BSD License Pyro MIT License PyUtilib Revised BSD License PyYAML MIT License runpy2 Python Software Foundation License setuptools Python Software Foundation License / Zope Public License six MIT License TinyXML zlib License unittest2 BSD License Utilib Revised BSD License virtualenv MIT License Vol Common Public License vpykit Revised BSD License Additionally, some precompiled WST binary distributions might bundle other third-party executables files: Coliny Revised BSD License (part of Acro project) Dakota GNU Lesser General Public License (LGPL) v.2.1 PICO Revised BSD License (part of Acro project) i Revised BSD License Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Sandia National Laboratories nor Sandia Corporation nor the names of its con- tributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IM- PLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUD- ING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ii Acknowledgements This work was supported by the U.S. Environmental Protection Agency through its Office of Research and Development (Interagency Agreement # DW8992192801). The material in this document has been subject to technical and policy review by the U.S. EPA, and approved for publication. The views expressed by individual authors, however, are their own, and do not necessarily reflect those of the U.S. Environmental Protection Agency. Mention of trade names, products, or services does not convey official U.S. EPA approval, endorsement, or recommendation. The Water Security Toolkit is an extension of the Threat Ensemble Vulnerability Assessment-Sensor Place- ment Optimization Tool (TEVA-SPOT), which was also developed with funding from the U.S. Environ- mental Protection Agency through its Office of Research and Development (Interagency Agreement # DW8992192801). The authors acknowledge the following individuals for their contributions to the devel- opment of TEVA-SPOT: Jonathan Berry (Sandia National Laboratories), Erik Boman (Sandia National Laboratories), Lee Ann Riesen (Sandia National Laboratories), James Uber (University of Cincinnati), and Jean-Paul Watson (Sandia National Laboratories). iii Acronyms ATUS American Time-Use Survey BLAS Basic linear algebra sub-routines CFU Colony-forming unit CVAR Conditional value at risk CWS Contamination warning system EA Evolutionary algorithm EDS Event detection system EPA U.S. Environmental Protection Agency EC Extent of Contamination ERD EPANET results database file GLPK GNU Linear Programming Kit GRASP Greedy randomized adaptive sampling process HEX Hexadecimal HTML HyperText markup language INP EPANET input file LP Linear program MC Mass consumed MILP Mixed integer linear program MIP Mixed integer program MSX Multi-species extension for EPANET NFD Number of failed detections NS Number of sensors NZD Non-zero demand PD Population dosed PE Population exposed PK Population killed TAI Threat assessment input file TCE Tailed-conditioned expectation TD Time to detection TEC Timed extent of contamination TEVA Threat ensemble vulnerability assessment TSB Tryptic soy broth TSG Threat scenario generation file TSI Threat simulation input file VAR Value at risk VC Volume consumed WST Water Security Toolkit YML YAML configuration file format for WST iv Symbols Notation Definition Example { , } set brackets { 1,2,3 } means a set containing the values 1,2, and 3. [?] is an element of s [?] S means that s is an element of the set S . [?] for all s = 1 [?] s [?] S means that the statement s = 1 is true for all s in set S . P summation P n i =1 s i means s 1 + s 2 + * * * + s n . \\ set minus S \\ T means the set that contains all those elements of S that are not in set T . %7C given %7C is used to define conditional probability. P ( s %7C t ) means the prob- ability of s occurring given that t occurs. %7C ... %7C cardinality Cardinality of a set is the number of elements of the set. If set S = { 2,4,6 } , then %7C S %7C = 3. v« less

47 CFR 25.135 - Licensing provisions for earth station networks in the non-voice, non-geostationary Mobile...

Code of Federal Regulations, 2014 CFR

2014-10-01

... Applications and Licenses Earth Stations § 25.135 Licensing provisions for earth station networks in the non... 47 Telecommunication 2 2014-10-01 2014-10-01 false Licensing provisions for earth station networks in the non-voice, non-geostationary Mobile-Satellite Service. 25.135 Section 25.135 Telecommunication...

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/

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.

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

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.

MYRaf: An Easy Aperture Photometry GUI for IRAF

NASA Astrophysics Data System (ADS)

Niaei, M. S.; KiliÇ, Y.; Özeren, F. F.

2015-07-01

We describe the design and development of MYRaf, a GUI (Graphical User Interface) that aims to be completely open-source under General Public License (GPL). MYRaf is an easy to use, reliable, and a fast IRAF aperture photometry GUI tool for those who are conversant with text-based software and command-line procedures in GNU/Linux OSs. MYRaf uses IRAF, PyRAF, matplotlib, ginga, alipy, and SExtractor with the general-purpose and high-level programming language Python, and uses the Qt framework.

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

Computerized Testing Software for Assessing Interference Suppression in Children and Adults: The Bivalent Shape Task (BST)

PubMed Central

Mueller, Shane T.; Esposito, Alena G.

2015-01-01

We describe the Bivalent Shape Task (BST), software using the Psychology Experiment Building Language (PEBL), for testing of cognitive interference and the ability to suppress interference. The test is available via the GNU Public License, Version 3 (GPLv3), is freely modifiable, and has been tested on both children and adults and found to provide a simple and fast non-verbal measure of cognitive interference and suppression that requires no reading. PMID:26702358

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

10 CFR 34.11 - Application for a specific license.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL RADIOGRAPHIC OPERATIONS Specific Licensing Provisions § 34.11 Application for a... industrial radiography on NRC Form 313, “Application for Material License,” in accordance with the provisions...

10 CFR 34.11 - Application for a specific license.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL RADIOGRAPHIC OPERATIONS Specific Licensing Provisions § 34.11 Application for a... industrial radiography on NRC Form 313, “Application for Material License,” in accordance with the provisions...

10 CFR 34.11 - Application for a specific license.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL RADIOGRAPHIC OPERATIONS Specific Licensing Provisions § 34.11 Application for a... industrial radiography on NRC Form 313, “Application for Material License,” in accordance with the provisions...

10 CFR 34.11 - Application for a specific license.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL RADIOGRAPHIC OPERATIONS Specific Licensing Provisions § 34.11 Application for a... industrial radiography on NRC Form 313, “Application for Material License,” in accordance with the provisions...

10 CFR 34.11 - Application for a specific license.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL RADIOGRAPHIC OPERATIONS Specific Licensing Provisions § 34.11 Application for a... industrial radiography on NRC Form 313, “Application for Material License,” in accordance with the provisions...

47 CFR 25.142 - Licensing provisions for the non-voice, non-geostationary mobile-satellite service.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 2 2011-10-01 2011-10-01 false Licensing provisions for the non-voice, non... Stations § 25.142 Licensing provisions for the non-voice, non-geostationary mobile-satellite service. (a... the non-voice, non-geostationary mobile-satellite service shall describe in detail the proposed non...

47 CFR 25.142 - Licensing provisions for the non-voice, non-geostationary Mobile-Satellite Service.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 2 2013-10-01 2013-10-01 false Licensing provisions for the non-voice, non... Stations § 25.142 Licensing provisions for the non-voice, non-geostationary Mobile-Satellite Service. (a... the non-voice, non-geostationary mobile-satellite service shall describe in detail the proposed non...

47 CFR 25.142 - Licensing provisions for the non-voice, non-geostationary mobile-satellite service.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 2 2012-10-01 2012-10-01 false Licensing provisions for the non-voice, non... Stations § 25.142 Licensing provisions for the non-voice, non-geostationary mobile-satellite service. (a... the non-voice, non-geostationary mobile-satellite service shall describe in detail the proposed non...

47 CFR 25.142 - Licensing provisions for the non-voice, non-geostationary mobile-satellite service.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Licensing provisions for the non-voice, non... Stations § 25.142 Licensing provisions for the non-voice, non-geostationary mobile-satellite service. (a... the non-voice, non-geostationary mobile-satellite service shall describe in detail the proposed non...

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.

An introduction to intellectual property licensing for technology companies

NASA Astrophysics Data System (ADS)

Meier, Lawrence H.

2001-05-01

Intellectual property licensing is an important issue facing all technology companies. Before entering into license agreements a number of issues need to be addressed, including invention ownership, obtaining and identifying licensable subject matter, and developing a licensing strategy. There are a number of important provisions that are included in most intellectual property license agreements. These provisions include definitions, the license grant, consideration, audit rights confidentiality, warranties, indemnification, and limitation of liability. Special licensing considerations exist relative to each type of intellectual property, and when the other party is a foreign company or a university.

Opendf - An Implementation of the Dual Fermion Method for Strongly Correlated Systems

NASA Astrophysics Data System (ADS)

Antipov, Andrey E.; LeBlanc, James P. F.; Gull, Emanuel

The dual fermion method is a multiscale approach for solving lattice problems of interacting strongly correlated systems. In this paper, we present the opendfcode, an open-source implementation of the dual fermion method applicable to fermionic single- orbital lattice models in dimensions D = 1, 2, 3 and 4. The method is built on a dynamical mean field starting point, which neglects all local correlations, and perturbatively adds spatial correlations. Our code is distributed as an open-source package under the GNU public license version 2.

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

BioMake: a GNU make-compatible utility for declarative workflow management.

PubMed

Holmes, Ian H; Mungall, Christopher J

2017-11-01

The Unix 'make' program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. We present BioMake, a make-like utility that is compatible with most features of GNU Make and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog. BioMake is available for MacOSX and Linux systems from https://github.com/evoldoers/biomake under the BSD3 license. The only dependency is SWI-Prolog (version 7), available from http://www.swi-prolog.org/. ihholmes + biomake@gmail.com or cmungall + biomake@gmail.com. Feature table comparing BioMake to similar tools. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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.

47 CFR 25.147 - Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz.

Code of Federal Regulations, 2014 CFR

2014-10-01

... COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25.147 Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz. If an NGSO...

47 CFR 25.147 - Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz.

Code of Federal Regulations, 2012 CFR

2012-10-01

... COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25.147 Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz. If an NGSO...

47 CFR 25.147 - Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz.

Code of Federal Regulations, 2010 CFR

2010-10-01

... COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25.147 Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz. If an NGSO...

47 CFR 25.147 - Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz.

Code of Federal Regulations, 2011 CFR

2011-10-01

... COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25.147 Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz. If an NGSO...

47 CFR 25.147 - Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz.

Code of Federal Regulations, 2013 CFR

2013-10-01

... COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses Space Stations § 25.147 Licensing provision for NGSO MSS feeder downlinks in the band 6700-6875 MHz. If an NGSO...

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.

47 CFR 25.135 - Licensing provisions for earth station networks in the non-voice, non-geostationary mobile...

Code of Federal Regulations, 2013 CFR

2013-10-01

... Applications and Licenses Earth Stations § 25.135 Licensing provisions for earth station networks in the non... systems shall not transmit communications to or from user transceivers in the United States unless such communications are authorized under a service contract with the holder of a pertinent FCC blanket license or...

47 CFR 25.135 - Licensing provisions for earth station networks in the non-voice, non-geostationary mobile...

Code of Federal Regulations, 2010 CFR

2010-10-01

... Applications and Licenses Earth Stations § 25.135 Licensing provisions for earth station networks in the non... systems shall not transmit communications to or from user transceivers in the United States unless such communications are authorized under a service contract with the holder of a pertinent FCC blanket license or...

47 CFR 25.135 - Licensing provisions for earth station networks in the non-voice, non-geostationary mobile...

Code of Federal Regulations, 2012 CFR

2012-10-01

... Applications and Licenses Earth Stations § 25.135 Licensing provisions for earth station networks in the non... systems shall not transmit communications to or from user transceivers in the United States unless such communications are authorized under a service contract with the holder of a pertinent FCC blanket license or...

47 CFR 25.135 - Licensing provisions for earth station networks in the non-voice, non-geostationary mobile...

Code of Federal Regulations, 2011 CFR

2011-10-01

... Applications and Licenses Earth Stations § 25.135 Licensing provisions for earth station networks in the non... systems shall not transmit communications to or from user transceivers in the United States unless such communications are authorized under a service contract with the holder of a pertinent FCC blanket license or...

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.

Fluorescence techniques in agricultural applications

NASA Astrophysics Data System (ADS)

McMurtrey, James E.; Corp, Lawrence A.; Kim, Moon S.; Chappelle, Emmett W.; Daughtry, Craig S. T.; DiBenedetto, J. D.

2001-03-01

Intellectual property licensing is an important issue facing all technology companies. Before entering into license agreements a number of issues need to be addressed, including invention ownership, obtaining and identifying licensable subject matter, and developing a licensing strategy. There are a number of important provisions that are included in most intellectual property license agreements. These provisions include definitions, the license grant, consideration, audit rights, confidentiality, warranties, indemnification, and limitation of liability. Special licensing considerations exist relative to each type of intellectual property, and when the other party is a foreign company or a university.

47 CFR 25.134 - Licensing provisions of Very Small Aperture Terminal (VSAT) and C-band Small Aperture Terminal...

Code of Federal Regulations, 2012 CFR

2012-10-01

... Applications and Licenses Earth Stations § 25.134 Licensing provisions of Very Small Aperture Terminal (VSAT... maximum outbound downlink EIRP density of +10.0 dBW/4 kHz per carrier and earth station antennas with... Order in the Matter of Routine Licensing of Earth Stations in the 6 GHz and 14 GHz Bands Using Antennas...

47 CFR 25.134 - Licensing provisions for Very Small Aperture Terminal (VSAT) and C-band Small Aperture Terminal...

Code of Federal Regulations, 2013 CFR

2013-10-01

... Applications and Licenses Earth Stations § 25.134 Licensing provisions for Very Small Aperture Terminal (VSAT... maximum outbound downlink EIRP density of +10.0 dBW/4 kHz per carrier and earth station antennas with... Order in the Matter of Routine Licensing of Earth Stations in the 6 GHz and 14 GHz Bands Using Antennas...

18 CFR 4.108 - Contents of application for exemption from provisions other than licensing.

Code of Federal Regulations, 2012 CFR

2012-04-01

... POWER ACT LICENSES, PERMITS, EXEMPTIONS, AND DETERMINATION OF PROJECT COSTS Exemption of Small Hydroelectric Power Projects of 5 Megawatts or Less § 4.108 Contents of application for exemption from provisions other than licensing. An application for exemption of a small hydroelectric power project from...

18 CFR 4.108 - Contents of application for exemption from provisions other than licensing.

Code of Federal Regulations, 2013 CFR

2013-04-01

... POWER ACT LICENSES, PERMITS, EXEMPTIONS, AND DETERMINATION OF PROJECT COSTS Exemption of Small Hydroelectric Power Projects of 5 Megawatts or Less § 4.108 Contents of application for exemption from provisions other than licensing. An application for exemption of a small hydroelectric power project from...

18 CFR 4.108 - Contents of application for exemption from provisions other than licensing.

Code of Federal Regulations, 2011 CFR

2011-04-01

... POWER ACT LICENSES, PERMITS, EXEMPTIONS, AND DETERMINATION OF PROJECT COSTS Exemption of Small Hydroelectric Power Projects of 5 Megawatts or Less § 4.108 Contents of application for exemption from provisions other than licensing. An application for exemption of a small hydroelectric power project from...

18 CFR 4.108 - Contents of application for exemption from provisions other than licensing.

Code of Federal Regulations, 2010 CFR

2010-04-01

... POWER ACT LICENSES, PERMITS, EXEMPTIONS, AND DETERMINATION OF PROJECT COSTS Exemption of Small Hydroelectric Power Projects of 5 Megawatts or Less § 4.108 Contents of application for exemption from provisions other than licensing. An application for exemption of a small hydroelectric power project from...

18 CFR 4.108 - Contents of application for exemption from provisions other than licensing.

Code of Federal Regulations, 2014 CFR

2014-04-01

... POWER ACT LICENSES, PERMITS, EXEMPTIONS, AND DETERMINATION OF PROJECT COSTS Exemption of Small Hydroelectric Power Projects of 5 Megawatts or Less § 4.108 Contents of application for exemption from provisions other than licensing. An application for exemption of a small hydroelectric power project from...

77 FR 31019 - Agency Information Collection Activities; Submission for Office of Management and Budget Review...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-24

... Request; General Licensing Provisions; Section 351(k) Biosimilar Applications AGENCY: Food and Drug... Provisions; Section 351(k) Biosimilar Applications''. Also include the FDA docket number found in brackets in.... General Licensing Provisions; Section 351(k) Biosimilar Applications-- (OMB Control Number 0910--New) On...

A general spectral method for the numerical simulation of one-dimensional interacting fermions

NASA Astrophysics Data System (ADS)

Clason, Christian; von Winckel, Gregory

2012-08-01

This software implements a general framework for the direct numerical simulation of systems of interacting fermions in one spatial dimension. The approach is based on a specially adapted nodal spectral Galerkin method, where the basis functions are constructed to obey the antisymmetry relations of fermionic wave functions. An efficient Matlab program for the assembly of the stiffness and potential matrices is presented, which exploits the combinatorial structure of the sparsity pattern arising from this discretization to achieve optimal run-time complexity. This program allows the accurate discretization of systems with multiple fermions subject to arbitrary potentials, e.g., for verifying the accuracy of multi-particle approximations such as Hartree-Fock in the few-particle limit. It can be used for eigenvalue computations or numerical solutions of the time-dependent Schrödinger equation. The new version includes a Python implementation of the presented approach. New version program summaryProgram title: assembleFermiMatrix Catalogue identifier: AEKO_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKO_v1_1.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.: 332 No. of bytes in distributed program, including test data, etc.: 5418 Distribution format: tar.gz Programming language: MATLAB/GNU Octave, Python Computer: Any architecture supported by MATLAB, GNU Octave or Python Operating system: Any supported by MATLAB, GNU Octave or Python RAM: Depends on the data Classification: 4.3, 2.2. External routines: Python 2.7+, NumPy 1.3+, SciPy 0.10+ Catalogue identifier of previous version: AEKO_v1_0 Journal reference of previous version: Comput. Phys. Commun. 183 (2012) 405 Does the new version supersede the previous version?: Yes Nature of problem: The direct numerical solution of the multi-particle one-dimensional Schrödinger equation in a quantum well is challenging due to the exponential growth in the number of degrees of freedom with increasing particles. Solution method: A nodal spectral Galerkin scheme is used where the basis functions are constructed to obey the antisymmetry relations of the fermionic wave function. The assembly of these matrices is performed efficiently by exploiting the combinatorial structure of the sparsity patterns. Reasons for new version: A Python implementation is now included. Summary of revisions: Added a Python implementation; small documentation fixes in Matlab implementation. No change in features of the package. Restrictions: Only one-dimensional computational domains with homogeneous Dirichlet or periodic boundary conditions are supported. Running time: Seconds to minutes.

A-Track: A new approach for detection of moving objects in FITS images

NASA Astrophysics Data System (ADS)

Atay, T.; Kaplan, M.; Kilic, Y.; Karapinar, N.

2016-10-01

We have developed a fast, open-source, cross-platform pipeline, called A-Track, for detecting the moving objects (asteroids and comets) in sequential telescope images in FITS format. The pipeline is coded in Python 3. The moving objects are detected using a modified line detection algorithm, called MILD. We tested the pipeline on astronomical data acquired by an SI-1100 CCD with a 1-meter telescope. We found that A-Track performs very well in terms of detection efficiency, stability, and processing time. The code is hosted on GitHub under the GNU GPL v3 license.

orthAgogue: an agile tool for the rapid prediction of orthology relations.

PubMed

Ekseth, Ole Kristian; Kuiper, Martin; Mironov, Vladimir

2014-03-01

The comparison of genes and gene products across species depends on high-quality tools to determine the relationships between gene or protein sequences from various species. Although some excellent applications are available and widely used, their performance leaves room for improvement. We developed orthAgogue: a multithreaded C application for high-speed estimation of homology relations in massive datasets, operated via a flexible and easy command-line interface. The orthAgogue software is distributed under the GNU license. The source code and binaries compiled for Linux are available at https://code.google.com/p/orthagogue/.

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.

MOCCASIN: converting MATLAB ODE models to SBML.

PubMed

Gómez, Harold F; Hucka, Michael; Keating, Sarah M; Nudelman, German; Iber, Dagmar; Sealfon, Stuart C

2016-06-15

MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging-especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format. MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin : mhucka@caltech.edu More information is available at https://github.com/sbmlteam/moccasin. © The Author 2016. Published by Oxford University Press.

7 CFR 226.18 - Day care home provisions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 4 2014-01-01 2014-01-01 false Day care home provisions. 226.18 Section 226.18... care home provisions. (a) Day care homes shall have current Federal, State or local licensing or approval to provide day care services to children. Day care homes which cannot obtain their license because...

7 CFR 226.18 - Day care home provisions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 4 2013-01-01 2013-01-01 false Day care home provisions. 226.18 Section 226.18... care home provisions. (a) Day care homes shall have current Federal, State or local licensing or approval to provide day care services to children. Day care homes which cannot obtain their license because...

7 CFR 226.18 - Day care home provisions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 4 2012-01-01 2012-01-01 false Day care home provisions. 226.18 Section 226.18... care home provisions. (a) Day care homes shall have current Federal, State or local licensing or approval to provide day care services to children. Day care homes which cannot obtain their license because...

10 CFR 50.43 - Additional standards and provisions affecting class 103 licenses and certifications for...

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Additional standards and provisions affecting class 103... Regulatory Approvals § 50.43 Additional standards and provisions affecting class 103 licenses and... propose nuclear reactor designs which differ significantly from light-water reactor designs that were...

10 CFR 50.43 - Additional standards and provisions affecting class 103 licenses and certifications for...

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Additional standards and provisions affecting class 103... Regulatory Approvals § 50.43 Additional standards and provisions affecting class 103 licenses and... propose nuclear reactor designs which differ significantly from light-water reactor designs that were...

10 CFR 50.43 - Additional standards and provisions affecting class 103 licenses and certifications for...

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Additional standards and provisions affecting class 103... Regulatory Approvals § 50.43 Additional standards and provisions affecting class 103 licenses and... propose nuclear reactor designs which differ significantly from light-water reactor designs that were...

10 CFR 50.43 - Additional standards and provisions affecting class 103 licenses and certifications for...

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Additional standards and provisions affecting class 103... Regulatory Approvals § 50.43 Additional standards and provisions affecting class 103 licenses and... propose nuclear reactor designs which differ significantly from light-water reactor designs that were...

Your EHR license agreement: critical issues.

PubMed

Shay, Daniel F

2014-01-01

This article discusses several key provisions and concepts in software license agreements for electronic health records. It offers insight into what physician practices can expect to find in their license agreements, as well as practical advice on beneficial provisions. The article examines contractual language relating to term and termination, technical specifications and support, and compliance with governmental programs.

47 CFR 25.143 - Licensing provisions for the 1.6/2.4 GHz Mobile-Satellite Service and 2 GHz Mobile-Satellite...

Code of Federal Regulations, 2013 CFR

2013-10-01

... authorization with no further action required on the Commission's part. (f) Safety and distress communications... 47 Telecommunication 2 2013-10-01 2013-10-01 false Licensing provisions for the 1.6/2.4 GHz Mobile... COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses...

47 CFR 25.143 - Licensing provisions for the 1.6/2.4 GHz Mobile-Satellite Service and 2 GHz Mobile-Satellite...

Code of Federal Regulations, 2014 CFR

2014-10-01

... space stations authorized by the Commission. (d)-(e) [Reserved] (f) Safety and distress communications... 47 Telecommunication 2 2014-10-01 2014-10-01 false Licensing provisions for the 1.6/2.4 GHz Mobile... COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Applications and Licenses...

47 CFR 25.145 - Licensing provisions for the Fixed-Satellite Service in the 20/30 GHz bands.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 2 2014-10-01 2014-10-01 false Licensing provisions for the Fixed-Satellite Service in the 20/30 GHz bands. 25.145 Section 25.145 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... indicating the number of earth stations actually brought into service under its blanket licensing authority...

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/.

47 CFR 25.134 - Licensing provisions for Very Small Aperture Terminal (VSAT) and C-band Small Aperture Terminal...

Code of Federal Regulations, 2014 CFR

2014-10-01

... Applications and Licenses Earth Stations § 25.134 Licensing provisions for Very Small Aperture Terminal (VSAT... affected adjacent satellite operators by the operation of the non-conforming earth station. (b) VSAT...) VSAT networks operating in the 12/14 GHz bands may use more than one hub earth station, and the hubs...

31 CFR 598.507 - Provision of certain legal services authorized.

Code of Federal Regulations, 2012 CFR

2012-07-01

... authorized. 598.507 Section 598.507 Money and Finance: Treasury Regulations Relating to Money and Finance... REGULATIONS Licenses, Authorizations, and Statements of Licensing Policy § 598.507 Provision of certain legal... accordance with § 598.205(e). ...

31 CFR 598.507 - Provision of certain legal services authorized.

Code of Federal Regulations, 2010 CFR

2010-07-01

... authorized. 598.507 Section 598.507 Money and Finance: Treasury Regulations Relating to Money and Finance... REGULATIONS Licenses, Authorizations, and Statements of Licensing Policy § 598.507 Provision of certain legal... accordance with § 598.205(e). ...

31 CFR 598.507 - Provision of certain legal services authorized.

Code of Federal Regulations, 2011 CFR

2011-07-01

... authorized. 598.507 Section 598.507 Money and Finance: Treasury Regulations Relating to Money and Finance... REGULATIONS Licenses, Authorizations, and Statements of Licensing Policy § 598.507 Provision of certain legal... accordance with § 598.205(e). ...

31 CFR 598.507 - Provision of certain legal services authorized.

Code of Federal Regulations, 2014 CFR

2014-07-01

... authorized. 598.507 Section 598.507 Money and Finance: Treasury Regulations Relating to Money and Finance... REGULATIONS Licenses, Authorizations, and Statements of Licensing Policy § 598.507 Provision of certain legal... accordance with § 598.205(e). ...

31 CFR 598.507 - Provision of certain legal services authorized.

Code of Federal Regulations, 2013 CFR

2013-07-01

... authorized. 598.507 Section 598.507 Money and Finance: Treasury Regulations Relating to Money and Finance... REGULATIONS Licenses, Authorizations, and Statements of Licensing Policy § 598.507 Provision of certain legal... accordance with § 598.205(e). ...

GNuMe: A Galerkin-based Numerical Modeliing Environment for modeling geophysical fluid dynamics applications ranging from the Atmosphere to the Ocean

NASA Astrophysics Data System (ADS)

Giraldo, Francis; Abdi, Daniel; Kopera, Michal

2017-04-01

We have built a Galerkin-based Numerical Modeling Environment (GNuMe) for non hydrostatic atmospheric and ocean processes. GNuMe uses continuous Galerkin and Discontinuous Galerkin (CG/DG) discetizations as well as non-conforming adaptive mesh refinement (AMR), along with advanced time-integration methods that exploits both CG/DG and AMR capabilities. GNuMe currently solves the compressible and incompressible Navier-Stokes equations, the shallow water equations (with wetting and drying), and work is underway for inclusion of other types of equations. Moreover, GNuMe can run in both 2D and 3D modes on any type of accelerator hardware such as Nvidia GPUs and Intel KNL, and on standard X86 cores. In this talk, we shall present representative solutions obtained with GNuMe and will discuss where we think such a modeling framework could fit within standard Earth Systems Models. For further information on GNuMe please visit: http://frankgiraldo.wixsite.com/mysite/gnume.

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.

Distributed databases for materials study of thermo-kinetic properties

NASA Astrophysics Data System (ADS)

Toher, Cormac

2015-03-01

High-throughput computational materials science provides researchers with the opportunity to rapidly generate large databases of materials properties. To rapidly add thermal properties to the AFLOWLIB consortium and Materials Project repositories, we have implemented an automated quasi-harmonic Debye model, the Automatic GIBBS Library (AGL). This enables us to screen thousands of materials for thermal conductivity, bulk modulus, thermal expansion and related properties. The search and sort functions of the online database can then be used to identify suitable materials for more in-depth study using more precise computational or experimental techniques. AFLOW-AGL source code is public domain and will soon be released within the GNU-GPL license.

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

49 CFR 383.23 - Commercial driver's license.

Code of Federal Regulations, 2010 CFR

2010-10-01

... STANDARDS; REQUIREMENTS AND PENALTIES Single License Requirement § 383.23 Commercial driver's license. (a... the single license provision of § 383.21, a driver holding a commercial driver's license issued under... be considered valid commercial drivers' licenses for purposes of behind-the-wheel training on public...

Licensing Process | NREL

Science.gov Websites

Agreement After the company and NREL agree on license financial terms, NREL will draft a license agreement Group Licensing Guide and Sample License. 4. Negotiate License Language After a draft agreement has been created, NREL can tailor many of the license provisions to ensure an agreement that works for all parties

31 CFR 515.542 - Mail and telecommunications-related transactions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Mail and telecommunications-related... Licenses, Authorizations, and Statements of Licensing Policy § 515.542 Mail and telecommunications-related..., incident to the provision of telecommunications services between the United States and Cuba, the provision...

31 CFR 515.542 - Mail and telecommunications-related transactions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false Mail and telecommunications-related... Licenses, Authorizations, and Statements of Licensing Policy § 515.542 Mail and telecommunications-related..., incident to the provision of telecommunications services between the United States and Cuba, the provision...

TIM, a ray-tracing program for METATOY research and its dissemination

NASA Astrophysics Data System (ADS)

Lambert, Dean; Hamilton, Alasdair C.; Constable, George; Snehanshu, Harsh; Talati, Sharvil; Courtial, Johannes

2012-03-01

TIM (The Interactive METATOY) is a ray-tracing program specifically tailored towards our research in METATOYs, which are optical components that appear to be able to create wave-optically forbidden light-ray fields. For this reason, TIM possesses features not found in other ray-tracing programs. TIM can either be used interactively or by modifying the openly available source code; in both cases, it can easily be run as an applet embedded in a web page. Here we describe the basic structure of TIM's source code and how to extend it, and we give examples of how we have used TIM in our own research. Program summaryProgram title: TIM Catalogue identifier: AEKY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKY_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.: 124 478 No. of bytes in distributed program, including test data, etc.: 4 120 052 Distribution format: tar.gz Programming language: Java Computer: Any computer capable of running the Java Virtual Machine (JVM) 1.6 Operating system: Any; developed under Mac OS X Version 10.6 RAM: Typically 145 MB (interactive version running under Mac OS X Version 10.6) Classification: 14, 18 External routines: JAMA [1] (source code included) Nature of problem: Visualisation of scenes that include scene objects that create wave-optically forbidden light-ray fields. Solution method: Ray tracing. Unusual features: Specifically designed to visualise wave-optically forbidden light-ray fields; can visualise ray trajectories; can visualise geometric optic transformations; can create anaglyphs (for viewing with coloured "3D glasses") and random-dot autostereograms of the scene; integrable into web pages. Running time: Problem-dependent; typically seconds for a simple scene.

Linearized self-consistent quasiparticle GW method: Application to semiconductors and simple metals

NASA Astrophysics Data System (ADS)

Kutepov, A. L.; Oudovenko, V. S.; Kotliar, G.

2017-10-01

We present a code implementing the linearized quasiparticle self-consistent GW method (LQSGW) in the LAPW basis. Our approach is based on the linearization of the self-energy around zero frequency which differs it from the existing implementations of the QSGW method. The linearization allows us to use Matsubara frequencies instead of working on the real axis. This results in efficiency gains by switching to the imaginary time representation in the same way as in the space time method. The all electron LAPW basis set eliminates the need for pseudopotentials. We discuss the advantages of our approach, such as its N3 scaling with the system size N, as well as its shortcomings. We apply our approach to study the electronic properties of selected semiconductors, insulators, and simple metals and show that our code produces the results very close to the previously published QSGW data. Our implementation is a good platform for further many body diagrammatic resummations such as the vertex-corrected GW approach and the GW+DMFT method. Program Files doi:http://dx.doi.org/10.17632/cpchkfty4w.1 Licensing provisions: GNU General Public License Programming language: Fortran 90 External routines/libraries: BLAS, LAPACK, MPI (optional) Nature of problem: Direct implementation of the GW method scales as N4 with the system size, which quickly becomes prohibitively time consuming even in the modern computers. Solution method: We implemented the GW approach using a method that switches between real space and momentum space representations. Some operations are faster in real space, whereas others are more computationally efficient in the reciprocal space. This makes our approach scale as N3. Restrictions: The limiting factor is usually the memory available in a computer. Using 10 GB/core of memory allows us to study the systems up to 15 atoms per unit cell.

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

PubMed

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

Resource sharing of online teaching materials: The lon-capa project

NASA Astrophysics Data System (ADS)

Bauer, Wolfgang

2004-03-01

The use of information technology resources in conventional lecture-based courses, in distance-learning offerings, as well as hybrid courses, is increasing. But this may put additional burden on faculty, who are now asked to deliver this new content. Additionally, it may require the installation of commercial courseware systems, putting the colleges and universities in new financial licensing dependencies. To address exactly these two problems, the lon-capa system was invented to provide an open-source, gnu public license based, courseware system that allows for sharing of educational resources across institutional and disciplinary boundaries. This presentation will focus on both aspects of the system, the courseware capabilities that allow for customized environments for individual students, and the educational resources library that enables teachers to take full advantages of the work of their colleagues. Research results on learning effectiveness, resource and system usage patterns, and customization for different learning styles will be shown. Institutional perceptions of and responses to open source courseware systems will be discussed.

Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

PubMed Central

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A.; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available. PMID:25569628

Association between New Jersey's Graduated Driver Licensing decal provision and crash rates of young drivers with learners' permits.

PubMed

Curry, Allison E; Pfeiffer, Melissa R; Elliott, Michael R; Durbin, Dennis R

2015-12-01

New Jersey (NJ) implemented the first-in-the-US Graduated Driver Licensing (GDL) decal provision in May 2010 for young drivers with learner's permits or intermediate licenses. Previous analyses found an association between the provision and crash reduction among intermediate drivers. The aim of this study is to examine the association between NJ's provision and GDL citation and crash rates among drivers aged <21 years with learner's permits. We estimated monthly per-driver rates from January 2006 through June 2012. Negative binomial modeling compared pre and post decal crash rates adjusted for gender, age, calendar month, and gas price. The monthly GDL citation rate was two per 10,000 drivers in the predecal and postdecal periods. Crashes were rare and rates declined similarly pre and post decal (adjusted rate ratio of postdecal vs predecal slope: 1.04 (0.97 to 1.12)). NJ's GDL decal provision was not associated with a change in citation or crash rates among young NJ drivers with learner's permits. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

78 FR 63365 - Determination With Respect to the Child Soldiers Prevention Act of 2008

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-23

... provision of International Military Education and Training (IMET) and nonlethal Excess Defense Articles, and the issuance of licenses for direct commercial sales of nonlethal defense articles; and to waive in... for the issuance of licenses for direct commercial sales of nonlethal defense articles, provision of...

31 CFR 510.506 - Provision of certain legal services authorized.

Code of Federal Regulations, 2011 CFR

2011-07-01

... authorized. 510.506 Section 510.506 Money and Finance: Treasury Regulations Relating to Money and Finance... Licenses, Authorizations, and Statements of Licensing Policy § 510.506 Provision of certain legal services... interests in property are blocked pursuant to § 510.201(b) is authorized, provided that all receipts of...

31 CFR 510.506 - Provision of certain legal services authorized.

Code of Federal Regulations, 2014 CFR

2014-07-01

... authorized. 510.506 Section 510.506 Money and Finance: Treasury Regulations Relating to Money and Finance... Licenses, Authorizations, and Statements of Licensing Policy § 510.506 Provision of certain legal services... interests in property are blocked pursuant to § 510.201(b) is authorized, provided that all receipts of...

31 CFR 510.506 - Provision of certain legal services authorized.

Code of Federal Regulations, 2013 CFR

2013-07-01

... authorized. 510.506 Section 510.506 Money and Finance: Treasury Regulations Relating to Money and Finance... Licenses, Authorizations, and Statements of Licensing Policy § 510.506 Provision of certain legal services... interests in property are blocked pursuant to § 510.201(b) is authorized, provided that all receipts of...

47 CFR 25.136 - Licensing provisions for user transceivers in the 1.6/2.4 GHz, 1.5/1.6 GHz, and 2 GHz Mobile...

Code of Federal Regulations, 2011 CFR

2011-10-01

... Applications and Licenses Earth Stations § 25.136 Licensing provisions for user transceivers in the 1.6/2.4 GHz... specified in § 25.213, earth stations operating in the 1.6/2.4 GHz and 1.5/1.6 GHz Mobile Satellite Services... aircraft unless the earth station has a direct physical connection to the aircraft cabin or cockpit...

47 CFR 25.136 - Licensing provisions for user transceivers in the 1.6/2.4 GHz, 1.5/1.6 GHz, and 2 GHz Mobile...

Code of Federal Regulations, 2012 CFR

2012-10-01

... Applications and Licenses Earth Stations § 25.136 Licensing provisions for user transceivers in the 1.6/2.4 GHz... specified in § 25.213, earth stations operating in the 1.6/2.4 GHz and 1.5/1.6 GHz Mobile Satellite Services... aircraft unless the earth station has a direct physical connection to the aircraft cabin or cockpit...

47 CFR 25.136 - Licensing provisions for user transceivers in the 1.6/2.4 GHz, 1.5/1.6 GHz, and 2 GHz Mobile...

Code of Federal Regulations, 2013 CFR

2013-10-01

... Applications and Licenses Earth Stations § 25.136 Licensing provisions for user transceivers in the 1.6/2.4 GHz... specified in § 25.213, earth stations operating in the 1.6/2.4 GHz and 1.5/1.6 GHz Mobile-Satellite Services... aircraft unless the earth station has a direct physical connection to the aircraft cabin or cockpit...

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.

31 CFR 552.501 - General and specific licensing procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... provisions relating to licensing procedures, see part 501, subpart E of this chapter. Licensing actions taken... actions taken pursuant to this part. General licenses and statements of licensing policy relating to this part also may be available through the Yemen sanctions page on OFAC's Web site: www.treasury.gov/ofac. ...

31 CFR 552.501 - General and specific licensing procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... provisions relating to licensing procedures, see part 501, subpart E of this chapter. Licensing actions taken... actions taken pursuant to this part. General licenses and statements of licensing policy relating to this part also may be available through the Yemen sanctions page on OFAC's Web site: www.treasury.gov/ofac. ...

48 CFR 252.227-7007 - License term-running royalty.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 3 2011-10-01 2011-10-01 false License term-running... of Provisions And Clauses 252.227-7007 License term—running royalty. As prescribed at 227.7009-4(b), insert the following clause in patent releases, license agreements, and assignments: License Term—Running...

10 CFR 55.3 - License requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 2 2014-01-01 2014-01-01 false License requirements. 55.3 Section 55.3 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) OPERATORS' LICENSES General Provisions § 55.3 License requirements. A person must be authorized by a license issued by the Commission to perform the function of an operator or...

48 CFR 252.227-7007 - License term-running royalty.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false License term-running... of Provisions And Clauses 252.227-7007 License term—running royalty. As prescribed at 227.7009-4(b), insert the following clause in patent releases, license agreements, and assignments: License Term—Running...

10 CFR 55.3 - License requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false License requirements. 55.3 Section 55.3 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) OPERATORS' LICENSES General Provisions § 55.3 License requirements. A person must be authorized by a license issued by the Commission to perform the function of an operator or...

C++QEDv2: The multi-array concept and compile-time algorithms in the definition of composite quantum systems

NASA Astrophysics Data System (ADS)

Vukics, András

2012-06-01

C++QED is a versatile framework for simulating open quantum dynamics. It allows to build arbitrarily complex quantum systems from elementary free subsystems and interactions, and simulate their time evolution with the available time-evolution drivers. Through this framework, we introduce a design which should be generic for high-level representations of composite quantum systems. It relies heavily on the object-oriented and generic programming paradigms on one hand, and on the other hand, compile-time algorithms, in particular C++ template-metaprogramming techniques. The core of the design is the data structure which represents the state vectors of composite quantum systems. This data structure models the multi-array concept. The use of template metaprogramming is not only crucial to the design, but with its use all computations pertaining to the layout of the simulated system can be shifted to compile time, hence cutting on runtime. Program summaryProgram title: C++QED Catalogue identifier: AELU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:http://cpc.cs.qub.ac.uk/licence/aelu_v1_0.html. The C++QED package contains other software packages, Blitz, Boost and FLENS, all of which may be distributed freely but have individual license requirements. Please see individual packages for license conditions. No. of lines in distributed program, including test data, etc.: 597 974 No. of bytes in distributed program, including test data, etc.: 4 874 839 Distribution format: tar.gz Programming language: C++ Computer: i386-i686, x86_64 Operating system: In principle cross-platform, as yet tested only on UNIX-like systems (including Mac OS X). RAM: The framework itself takes about 60 MB, which is fully shared. The additional memory taken by the program which defines the actual physical system (script) is typically less than 1 MB. The memory storing the actual data scales with the system dimension for state-vector manipulations, and the square of the dimension for density-operator manipulations. This might easily be GBs, and often the memory of the machine limits the size of the simulated system. Classification: 4.3, 4.13, 6.2, 20 External routines: Boost C++ libraries (http://www.boost.org/), GNU Scientific Library (http://www.gnu.org/software/gsl/), Blitz++ (http://www.oonumerics.org/blitz/), Linear Algebra Package - Flexible Library for Efficient Numerical Solutions (http://flens.sourceforge.net/). Nature of problem: Definition of (open) composite quantum systems out of elementary building blocks [1]. Manipulation of such systems, with emphasis on dynamical simulations such as Master-equation evolution [2] and Monte Carlo wave-function simulation [3]. Solution method: Master equation, Monte Carlo wave-function method. Restrictions: Total dimensionality of the system. Master equation - few thousands. Monte Carlo wave-function trajectory - several millions. Unusual features: Because of the heavy use of compile-time algorithms, compilation of programs written in the framework may take a long time and much memory (up to several GBs). Additional comments: The framework is not a program, but provides and implements an application-programming interface for developing simulations in the indicated problem domain. Supplementary information: http://cppqed.sourceforge.net/. Running time: Depending on the magnitude of the problem, can vary from a few seconds to weeks.

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

HangOut: generating clean PSI-BLAST profiles for domains with long insertions.

PubMed

Kim, Bong-Hyun; Cong, Qian; Grishin, Nick V

2010-06-15

Profile-based similarity search is an essential step in structure-function studies of proteins. However, inclusion of non-homologous sequence segments into a profile causes its corruption and results in false positives. Profile corruption is common in multidomain proteins, and single domains with long insertions are a significant source of errors. We developed a procedure (HangOut) that, for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles. HangOut is implemented in Python 2.3 and runs on all Unix-compatible platforms. The source code is available under the GNU GPL license at http://prodata.swmed.edu/HangOut/. Supplementary data are available at Bioinformatics online.

NanoPack: visualizing and processing long read sequencing data.

PubMed

De Coster, Wouter; D'Hert, Svenn; Schultz, Darrin T; Cruts, Marc; Van Broeckhoven, Christine

2018-03-14

Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools. wouter.decoster@molgen.vib-ua.be. Supplementary tables and figures are available at Bioinformatics online.

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

MPI-Defrost: Extension of Defrost to MPI-based Cluster Environment

NASA Astrophysics Data System (ADS)

Amin, Mustafa A.; Easther, Richard; Finkel, Hal

2011-06-01

MPI-Defrost extends Frolov’s Defrost to an MPI-based cluster environment. This version has been restricted to a single field. Restoring two-field support should be straightforward, but will require some code changes. Some output options may also not be fully supported under MPI. This code was produced to support our own work, and has been made available for the benefit of anyone interested in either oscillon simulations or an MPI capable version of Defrost, and it is provided on an "as-is" basis. Andrei Frolov is the primary developer of Defrost and we thank him for placing his work under the GPL (GNU Public License), and thus allowing us to distribute this modified version.

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.

77 FR 8880 - Agency Information Collection Activities; Proposed Collection; Comment Request; General Licensing...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-15

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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).

10 CFR 71.5 - Transportation of licensed material.

Code of Federal Regulations, 2010 CFR

2010-01-01

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48 CFR 52.227-19 - Commercial Computer Software License.

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... software-Licensing. 1852.227-86 Section 1852.227-86 Federal Acquisition Regulations System NATIONAL... Provisions and Clauses 1852.227-86 Commercial computer software—Licensing. As prescribed in 1827.409-70, insert the following clause: Commercial Computer Software—Licensing (DEC 1987) (a) Any delivered...

48 CFR 52.227-19 - Commercial Computer Software License.

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... Software License. 52.227-19 Section 52.227-19 Federal Acquisition Regulations System FEDERAL ACQUISITION... Clauses 52.227-19 Commercial Computer Software License. As prescribed in 27.409(g), insert the following clause: Commercial Computer Software License (DEC 2007) (a) Notwithstanding any contrary provisions...

48 CFR 1852.227-86 - Commercial computer software-Licensing.

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48 CFR 52.227-19 - Commercial Computer Software License.

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2012-10-01

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48 CFR 1852.227-86 - Commercial computer software-Licensing.

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... software-Licensing. 1852.227-86 Section 1852.227-86 Federal Acquisition Regulations System NATIONAL... Provisions and Clauses 1852.227-86 Commercial computer software—Licensing. As prescribed in 1827.409-70, insert the following clause: Commercial Computer Software—Licensing (DEC 1987) (a) Any delivered...

48 CFR 1852.227-86 - Commercial computer software-Licensing.

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... software-Licensing. 1852.227-86 Section 1852.227-86 Federal Acquisition Regulations System NATIONAL... Provisions and Clauses 1852.227-86 Commercial computer software—Licensing. As prescribed in 1827.409-70, insert the following clause: Commercial Computer Software—Licensing (DEC 1987) (a) Any delivered...

10 CFR 71.5 - Transportation of licensed material.

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10 CFR 71.5 - Transportation of licensed material.

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10 CFR 71.5 - Transportation of licensed material.

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2010-10-01

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2010-10-01

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Code of Federal Regulations, 2014 CFR

2014-10-01

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Interference Cancellation System Design Using GNU Radio

DTIC Science & Technology

2015-12-01

ARL-TR-7546 ● DEC 2015 US Army Research Laboratory Interference Cancellation System Design Using GNU Radio by Jan Paolo...Interference Cancellation System Design Using GNU Radio by Jan Paolo Acosta Sensors and Electron Devices Directorate, ARL...REPORT DATE (DD-MM-YYYY) December 2015 2. REPORT TYPE Final 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE Interference Cancellation System

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.

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

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).

47 CFR 97.21 - Application for a modified or renewed license grant.

Code of Federal Regulations, 2011 CFR

2011-10-01

... SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE General Provisions § 97.21 Application for a modified or... name, club name, license trustee name, or license custodian name in accordance with § 1.913 of this chapter. For a club or military recreation station license grant, the application must be presented in...

47 CFR 97.21 - Application for a modified or renewed license grant.

Code of Federal Regulations, 2013 CFR

2013-10-01

... SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE General Provisions § 97.21 Application for a modified or... name, club name, license trustee name, or license custodian name in accordance with § 1.913 of this chapter. For a club or military recreation station license grant, the application must be presented in...

47 CFR 97.21 - Application for a modified or renewed license grant.

Code of Federal Regulations, 2012 CFR

2012-10-01

... SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE General Provisions § 97.21 Application for a modified or... name, club name, license trustee name, or license custodian name in accordance with § 1.913 of this chapter. For a club or military recreation station license grant, the application must be presented in...

47 CFR 97.21 - Application for a modified or renewed license grant.

Code of Federal Regulations, 2010 CFR

2010-10-01

... SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE General Provisions § 97.21 Application for a modified or... name, club name, license trustee name or license custodian name in accordance with § 1.913 of this chapter. For a club, military recreation or RACES station license grant, it must be presented in document...

47 CFR 97.21 - Application for a modified or renewed license grant.

Code of Federal Regulations, 2014 CFR

2014-10-01

... SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE General Provisions § 97.21 Application for a modified or... name, club name, license trustee name, or license custodian name in accordance with § 1.913 of this chapter. For a club or military recreation station license grant, the application must be presented in...

Collegiate Licensing in Canada and the Statutory Advantage.

ERIC Educational Resources Information Center

Burshtein, Sheldon

1985-01-01

Discusses a specific provision in a Canadian statute enabling universities and other educational institutions to obtain protection and financial gain in a collegiate licensing program, an advantage not held in other countries or by other trademark licensers in Canada. (MSE)

9 CFR 166.10 - Licensing.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE SWINE HEALTH PROTECTION SWINE HEALTH PROTECTION General Provisions § 166.10 Licensing. (a) Application. Any... swine shall apply for a license on a form which will be furnished, upon request, by the Area...

9 CFR 166.10 - Licensing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE SWINE HEALTH PROTECTION SWINE HEALTH PROTECTION General Provisions § 166.10 Licensing. (a) Application. Any... swine shall apply for a license on a form which will be furnished, upon request, by the Area...

9 CFR 166.10 - Licensing.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE SWINE HEALTH PROTECTION SWINE HEALTH PROTECTION General Provisions § 166.10 Licensing. (a) Application. Any... swine shall apply for a license on a form which will be furnished, upon request, by the Area...

9 CFR 166.10 - Licensing.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE SWINE HEALTH PROTECTION SWINE HEALTH PROTECTION General Provisions § 166.10 Licensing. (a) Application. Any... swine shall apply for a license on a form which will be furnished, upon request, by the Area...

9 CFR 166.10 - Licensing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE SWINE HEALTH PROTECTION SWINE HEALTH PROTECTION General Provisions § 166.10 Licensing. (a) Application. Any... swine shall apply for a license on a form which will be furnished, upon request, by the Area...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2011 CFR

2011-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2012 CFR

2012-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2013 CFR

2013-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2014 CFR

2014-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 31.12 - General license for certain items and self-luminous products containing radium-226.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false General license for certain items and self-luminous... LICENSES FOR BYPRODUCT MATERIAL § 31.12 General license for certain items and self-luminous products..., or transfer, in accordance with the provisions of paragraphs (b), (c), and (d) of this section...

10 CFR 31.12 - General license for certain items and self-luminous products containing radium-226.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General license for certain items and self-luminous... LICENSES FOR BYPRODUCT MATERIAL § 31.12 General license for certain items and self-luminous products..., or transfer, in accordance with the provisions of paragraphs (b), (c), and (d) of this section...

Generating and using truly random quantum states in Mathematica

NASA Astrophysics Data System (ADS)

Miszczak, Jarosław Adam

2012-01-01

The problem of generating random quantum states is of a great interest from the quantum information theory point of view. In this paper we present a package for Mathematica computing system harnessing a specific piece of hardware, namely Quantis quantum random number generator (QRNG), for investigating statistical properties of quantum states. The described package implements a number of functions for generating random states, which use Quantis QRNG as a source of randomness. It also provides procedures which can be used in simulations not related directly to quantum information processing. Program summaryProgram title: TRQS Catalogue identifier: AEKA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKA_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.: 7924 No. of bytes in distributed program, including test data, etc.: 88 651 Distribution format: tar.gz Programming language: Mathematica, C Computer: Requires a Quantis quantum random number generator (QRNG, http://www.idquantique.com/true-random-number-generator/products-overview.html) and supporting a recent version of Mathematica Operating system: Any platform supporting Mathematica; tested with GNU/Linux (32 and 64 bit) RAM: Case dependent Classification: 4.15 Nature of problem: Generation of random density matrices. Solution method: Use of a physical quantum random number generator. Running time: Generating 100 random numbers takes about 1 second, generating 1000 random density matrices takes more than a minute.

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

48 CFR 1852.225-70 - Export Licenses.

Code of Federal Regulations, 2010 CFR

2010-10-01

... writing, that the Contracting Officer authorizes it to export ITAR-controlled technical data (including... licenses or other approvals, if required, for exports of hardware, technical data, and software, or for the provision of technical assistance. (b) The Contractor shall be responsible for obtaining export licenses, if...

47 CFR 25.222 - Blanket Licensing provisions for Earth Stations on Vessels (ESVs) receiving in the 10.95-11.2 GHz...

Code of Federal Regulations, 2012 CFR

2012-10-01

... on Vessels (ESVs) receiving in the 10.95-11.2 GHz (space-to-Earth), 11.45-11.7 GHz (space-to-Earth), 11.7-12.2 GHz (space-to-Earth) frequency bands and transmitting in the 14.0-14.5 GHz (Earth-to-space... SATELLITE COMMUNICATIONS Technical Standards § 25.222 Blanket Licensing provisions for Earth Stations on...

47 CFR 25.227 - Blanket licensing provisions for Earth Stations Aboard Aircraft (ESAAs) receiving in the 10.95-11...

Code of Federal Regulations, 2013 CFR

2013-10-01

... Aboard Aircraft (ESAAs) receiving in the 10.95-11.2 GHz (space-to-Earth), 11.45-11.7 GHz (space-to-Earth), and 11.7-12.2 GHz (space-to-Earth) frequency bands and transmitting in the 14.0-14.5 GHz (Earth-to... SATELLITE COMMUNICATIONS Technical Standards § 25.227 Blanket licensing provisions for Earth Stations Aboard...

47 CFR 25.222 - Blanket Licensing provisions for Earth Stations on Vessels (ESVs) receiving in the 10.95-11.2 GHz...

Code of Federal Regulations, 2010 CFR

2010-10-01

... on Vessels (ESVs) receiving in the 10.95-11.2 GHz (space-to-Earth), 11.45-11.7 GHz (space-to-Earth), 11.7-12.2 GHz (space-to-Earth) frequency bands and transmitting in the 14.0-14.5 GHz (Earth-to-space... SATELLITE COMMUNICATIONS Technical Standards § 25.222 Blanket Licensing provisions for Earth Stations on...

47 CFR 25.227 - Blanket licensing provisions for Earth Stations Aboard Aircraft (ESAAs) receiving in the 10.95-11...

Code of Federal Regulations, 2014 CFR

2014-10-01

... Aboard Aircraft (ESAAs) receiving in the 10.95-11.2 GHz (space-to-Earth), 11.45-11.7 GHz (space-to-Earth), and 11.7-12.2 GHz (space-to-Earth) frequency bands and transmitting in the 14.0-14.5 GHz (Earth-to... SATELLITE COMMUNICATIONS Technical Standards § 25.227 Blanket licensing provisions for Earth Stations Aboard...

47 CFR 25.222 - Blanket Licensing provisions for Earth Stations on Vessels (ESVs) receiving in the 10.95-11.2 GHz...

Code of Federal Regulations, 2011 CFR

2011-10-01

... on Vessels (ESVs) receiving in the 10.95-11.2 GHz (space-to-Earth), 11.45-11.7 GHz (space-to-Earth), 11.7-12.2 GHz (space-to-Earth) frequency bands and transmitting in the 14.0-14.5 GHz (Earth-to-space... SATELLITE COMMUNICATIONS Technical Standards § 25.222 Blanket Licensing provisions for Earth Stations on...

State Licensing of Health Occupations.

ERIC Educational Resources Information Center

National Center for Health Statistics (DHEW/PHS), Hyattsville, MD.

About 25 health professions and occupations are licensed by one or more states according to the survey of state licensing provisions by the National Center for Health Statistics. Data is presented in 22 chapters on the licensure of administrators, chiropractors, clinical laboratory personnel, dental hygienists, dentists, professional engineers,…

10 CFR 60.3 - License required.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 2 2011-01-01 2011-01-01 false License required. 60.3 Section 60.3 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.3 License required. (a) DOE shall not receive or possess source, special nuclear, or...

10 CFR 60.3 - License required.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 2 2014-01-01 2014-01-01 false License required. 60.3 Section 60.3 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.3 License required. (a) DOE shall not receive or possess source, special nuclear, or...

10 CFR 60.3 - License required.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 2 2013-01-01 2013-01-01 false License required. 60.3 Section 60.3 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.3 License required. (a) DOE shall not receive or possess source, special nuclear, or...

31 CFR 536.100 - Licensing procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false Licensing procedures. 536.100 Section 536.100 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF... This Part to Other Laws and Regulations § 536.100 Licensing procedures. For provisions relating to...

31 CFR 536.100 - Licensing procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Licensing procedures. 536.100 Section 536.100 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF... This Part to Other Laws and Regulations § 536.100 Licensing procedures. For provisions relating to...

31 CFR 536.100 - Licensing procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false Licensing procedures. 536.100 Section 536.100 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF... This Part to Other Laws and Regulations § 536.100 Licensing procedures. For provisions relating to...

31 CFR 536.100 - Licensing procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false Licensing procedures. 536.100 Section 536.100 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF... This Part to Other Laws and Regulations § 536.100 Licensing procedures. For provisions relating to...

31 CFR 536.100 - Licensing procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false Licensing procedures. 536.100 Section 536.100 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF... This Part to Other Laws and Regulations § 536.100 Licensing procedures. For provisions relating to...

Structuring the Multimedia Deal: Legal Issues--Part 1: Licensing in the Multimedia Arena.

ERIC Educational Resources Information Center

Gersh, David L.; Jeffrey, Sheri

1993-01-01

Provides an overview of legal issues related to licensing entertainment rights for multimedia source materials, including the grant of rights clause, copyright ownership, territory and languages, term provision, specifications, approvals/controls, royalties, guilds, bankruptcies, termination of the license, and confidentiality. Common mistakes…

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.

19 CFR 111.2 - License and district permit required.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 19 Customs Duties 1 2011-04-01 2011-04-01 false License and district permit required. 111.2 Section 111.2 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CUSTOMS BROKERS General Provisions § 111.2 License and district permit required...

19 CFR 111.2 - License and district permit required.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false License and district permit required. 111.2 Section 111.2 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CUSTOMS BROKERS General Provisions § 111.2 License and district permit required...

19 CFR 111.2 - License and district permit required.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false License and district permit required. 111.2 Section 111.2 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CUSTOMS BROKERS General Provisions § 111.2 License and district permit required...

19 CFR 111.2 - License and district permit required.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 1 2012-04-01 2012-04-01 false License and district permit required. 111.2 Section 111.2 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CUSTOMS BROKERS General Provisions § 111.2 License and district permit required...

19 CFR 111.2 - License and district permit required.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false License and district permit required. 111.2 Section 111.2 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CUSTOMS BROKERS General Provisions § 111.2 License and district permit required...

10 CFR 60.7 - License not required for certain preliminary activities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 2 2014-01-01 2014-01-01 false License not required for certain preliminary activities. 60.7 Section 60.7 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.7 License not required for certain preliminary...

10 CFR 60.7 - License not required for certain preliminary activities.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 2 2013-01-01 2013-01-01 false License not required for certain preliminary activities. 60.7 Section 60.7 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.7 License not required for certain preliminary...

Museums in the Commercial Marketplace: The Need for Licensing Agreements.

ERIC Educational Resources Information Center

Hodes, Scott; Gross, Karen

1978-01-01

Discussed are the major features of a Model Licensing Agreement to be used by museums in any commercial reproduction venture. They include rights and obligations of the respective parties, maintenance of quality control, payment of royalties, arbitration, and termination provisions. The Model Licensing Agreement is appended. (JMD)

Negotiating Terms and Conditions: An Overview of the Federal Energy Regulatory Commission Hydropower Settlement Agreement Process

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

Levine, Aaron L; Curtis, Taylor L; Shields, Laura

The process for obtaining, transferring, or surrendering a Federal Energy Regulatory Commission (FERC) hydropower license or exemption from licensing can be a series of complex negotiations. In many instances, the process may include stakeholders with different and/or competing perspectives or objectives related to the original license, new license (i.e., relicense), transfer of a license, or surrender of a license. Divergent perspectives and objectives can lead to disputes among project participants, which may impact the development of FERC license terms and conditions. One mechanism to resolve disputes between project participants involving a FERC authorization is informal and formal settlement agreement conferences,more » which often result in settlement agreements addressing the disputed issues. This report provides hydropower stakeholders with a better understanding of the FERC settlement agreement process, including information on: How to initiate a settlement agreement. The procedural steps associated with the settlement agreement process. The legal standards the Commission must adhere to when determining whether settlement agreement provisions can become lawful and enforceable terms or conditions of a FERC authorization. Examples of settlement agreement provisions included as license terms and conditions or in off-license agreements from a collection of settlement agreements and Commission orders.« less

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.

A straightforward graphical user interface for basic and advanced signal processing of thermographic infrared sequences

NASA Astrophysics Data System (ADS)

Klein, Matthieu T.; Ibarra-Castanedo, Clemente; Maldague, Xavier P.; Bendada, Abdelhakim

2008-03-01

IR-View, is a free and open source Matlab software that was released in 1998 at the Computer Vision and Systems Laboratory (CVSL) at Université Laval, Canada, as an answer to many common and recurrent needs in Infrared thermography. IR-View has proven to be a useful tool at CVSL for the past 10 years. The software by itself and/or its concept and functions may be of interest for other laboratories and companies working in research in the IR NDT field. This article describes the functions and processing techniques integrated to IR-View, freely downloadable under the GNU license at http://mivim.gel.ulaval.ca. Demonstration of IR-View functionalities will also be done during the DSS08 SPIE Defense and Security Symposium.

A-Track: A New Approach for Detection of Moving Objects in FITS Images

NASA Astrophysics Data System (ADS)

Kılıç, Yücel; Karapınar, Nurdan; Atay, Tolga; Kaplan, Murat

2016-07-01

Small planet and asteroid observations are important for understanding the origin and evolution of the Solar System. In this work, we have developed a fast and robust pipeline, called A-Track, for detecting asteroids and comets in sequential telescope images. The moving objects are detected using a modified line detection algorithm, called ILDA. We have coded the pipeline in Python 3, where we have made use of various scientific modules in Python to process the FITS images. We tested the code on photometrical data taken by an SI-1100 CCD with a 1-meter telescope at TUBITAK National Observatory, Antalya. The pipeline can be used to analyze large data archives or daily sequential data. The code is hosted on GitHub under the GNU GPL v3 license.

Space Missions: Long Term Preservation of IDL-based Software using GDL

NASA Astrophysics Data System (ADS)

Coulais, A.; Schellens, M.; Arabas, S.; Lenoir, M.; Noreskal, L.; Erard, S.

2012-09-01

GNU Data Language (GDL) is a free software clone of IDL, an interactive language widely used in Astronomy and space missions since decades. Proprietary status, license restrictions, price, sustainability and continuity of support for particular platforms are recurrent concerns in the Astronomy community, especially concerning space missions, which require long-term support. In this paper, we describe the key features of GDL and the main achievements from recent development work. We illustrate the maturity of GDL by presenting two examples of application: reading spectral cubes in PDS format and use of the HEALPix library. These examples support the main argument of the paper: that GDL has reached a level of maturity and usability ensuring long term preservation of analysis capabilities for numerous ground experiments and spaces missions based on IDL.

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.

GenomeDiagram: a python package for the visualization of large-scale genomic data.

PubMed

Pritchard, Leighton; White, Jennifer A; Birch, Paul R J; Toth, Ian K

2006-03-01

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

Fast computation of close-coupling exchange integrals using polynomials in a tree representation

NASA Astrophysics Data System (ADS)

Wallerberger, Markus; Igenbergs, Katharina; Schweinzer, Josef; Aumayr, Friedrich

2011-03-01

The semi-classical atomic-orbital close-coupling method is a well-known approach for the calculation of cross sections in ion-atom collisions. It strongly relies on the fast and stable computation of exchange integrals. We present an upgrade to earlier implementations of the Fourier-transform method. For this purpose, we implement an extensive library for symbolic storage of polynomials, relying on sophisticated tree structures to allow fast manipulation and numerically stable evaluation. Using this library, we considerably speed up creation and computation of exchange integrals. This enables us to compute cross sections for more complex collision systems. Program summaryProgram title: TXINT Catalogue identifier: AEHS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHS_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.: 12 332 No. of bytes in distributed program, including test data, etc.: 157 086 Distribution format: tar.gz Programming language: Fortran 95 Computer: All with a Fortran 95 compiler Operating system: All with a Fortran 95 compiler RAM: Depends heavily on input, usually less than 100 MiB Classification: 16.10 Nature of problem: Analytical calculation of one- and two-center exchange matrix elements for the close-coupling method in the impact parameter model. Solution method: Similar to the code of Hansen and Dubois [1], we use the Fourier-transform method suggested by Shakeshaft [2] to compute the integrals. However, we heavily speed up the calculation using a library for symbolic manipulation of polynomials. Restrictions: We restrict ourselves to a defined collision system in the impact parameter model. Unusual features: A library for symbolic manipulation of polynomials, where polynomials are stored in a space-saving left-child right-sibling binary tree. This provides stable numerical evaluation and fast mutation while maintaining full compatibility with the original code. Additional comments: This program makes heavy use of the new features provided by the Fortran 90 standard, most prominently pointers, derived types and allocatable structures and a small portion of Fortran 95. Only newer compilers support these features. Following compilers support all features needed by the program. GNU Fortran Compiler "gfortran" from version 4.3.0 GNU Fortran 95 Compiler "g95" from version 4.2.0 Intel Fortran Compiler "ifort" from version 11.0

Runwien: a text-based interface for the WIEN package

NASA Astrophysics Data System (ADS)

Otero de la Roza, A.; Luaña, Víctor

2009-05-01

A new text-based interface for WIEN2k, the full-potential linearized augmented plane-waves (FPLAPW) program, is presented. This code provides an easy to use, yet powerful way of generating arbitrarily large sets of calculations. Thus, properties over a potential energy surface and WIEN2k parameter exploration can be calculated using a simple input text file. This interface also provides new capabilities to the WIEN2k package, such as the calculation of elastic constants on hexagonal systems or the automatic gathering of relevant information. Additionally, runwien is modular, flexible and intuitive. Program summaryProgram title: runwien Catalogue identifier: AECM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL version 3 No. of lines in distributed program, including test data, etc.: 62 567 No. of bytes in distributed program, including test data, etc.: 610 973 Distribution format: tar.gz Programming language: gawk (with locale POSIX or similar) Computer: All running Unix, Linux Operating system: Unix, GNU/Linux Classification: 7.3 External routines: WIEN2k ( http://www.wien2k.at/), GAWK ( http://www.gnu.org/software/gawk/), rename by L. Wall, a Perl script which renames files, modified by R. Barker to check for the existence of target files, gnuplot ( http://www.gnuplot.info/) Subprograms used:Cat Id: ADSY_v1_0/AECB_v1_0, Title: GIBBS/CRITIC, Reference: CPC 158 (2004) 57/CPC 999 (2009) 999 Nature of problem: Creation of a text-based, batch-oriented interface for the WIEN2k package. Solution method: WIEN2k solves the Kohn-Sham equations of a solid using the FPLAPW formalism. Runwien interprets an input file containing the description of the geometry and structure of the solid and drives the execution of the WIEN2k programs. The input is simplified thanks to the default values of the WIEN2k parameters known to runwien. Additional comments: Designed for WIEN2k versions 06.4, 07.2, 08.2, and 08.3. Running time: For the test case (TiC), a single geometry takes 5 to 10 minutes on a typical desktop PC (Intel Pentium 4, 3.4 GHz, 1 GB RAM). The full example including the calculation of the elastic constants and the equation of state, takes 9 hours and 32 minutes.

76 FR 16627 - Statutory Provisions Affecting State Appraiser Regulatory Programs

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-24

... following provisions: Reciprocity. Qualification requirements for State licensed appraisers. Minimum...' efforts to implement the requirements. Reciprocity: Provisions of the Dodd-Frank Act require States to... related transaction unless the State wherein the appraiser is credentialed has such a reciprocity policy...

18 CFR 12.2 - Rules of construction.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT SAFETY OF WATER POWER PROJECTS AND PROJECT WORKS... Licensing determines that compliance with the relevant provision of the license will better protect life...

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.

Evaluating Intellectual Property and Data Rights in Competition Source Selections - Leveraging the Assertions Process to a New Level to Foster Open Systems Architecture

DTIC Science & Technology

2015-04-30

itself. This is the traditional methodology (combined with attaching commercial software licenses to the contract and citing patent royalty ... Royalties It helps to visualize the Intellectual Property Volume approach so the following notional tables with example deliverable technical data...attorney’s fees  Automatic renewal provisions that violate the Anti-Deficiency Act  Provisions that prohibit disclosure of license terms/conditions

47 CFR 25.138 - Blanket Licensing provisions of GSO FSS Earth Stations in the 18.3-18.8 GHz (space-to-Earth), 19...

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 2 2012-10-01 2012-10-01 false Blanket Licensing provisions of GSO FSS Earth Stations in the 18.3-18.8 GHz (space-to-Earth), 19.7-20.2 GHz (space-to-Earth), 28.35-28.6 GHz (Earth-to-space), and 29.25-30.0 GHz (Earth-to-space) bands. 25.138 Section 25.138 Telecommunication FEDERAL...

47 CFR 25.138 - Blanket Licensing provisions of GSO FSS Earth Stations in the 18.3-18.8 GHz (space-to-Earth), 19...

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 2 2011-10-01 2011-10-01 false Blanket Licensing provisions of GSO FSS Earth Stations in the 18.3-18.8 GHz (space-to-Earth), 19.7-20.2 GHz (space-to-Earth), 28.35-28.6 GHz (Earth-to-space), and 29.25-30.0 GHz (Earth-to-space) bands. 25.138 Section 25.138 Telecommunication FEDERAL...

47 CFR 25.138 - Blanket Licensing provisions of GSO FSS Earth Stations in the 18.3-18.8 GHz (space-to-Earth), 19...

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Blanket Licensing provisions of GSO FSS Earth Stations in the 18.3-18.8 GHz (space-to-Earth), 19.7-20.2 GHz (space-to-Earth), 28.35-28.6 GHz (Earth-to-space), and 29.25-30.0 GHz (Earth-to-space) bands. 25.138 Section 25.138 Telecommunication FEDERAL...

47 CFR 25.138 - Blanket Licensing provisions of GSO FSS Earth Stations in the 18.3-18.8 GHz (space-to-Earth), 19...

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2013-10-01

... 47 Telecommunication 2 2013-10-01 2013-10-01 false Blanket Licensing provisions of GSO FSS Earth Stations in the 18.3-18.8 GHz (space-to-Earth), 19.7-20.2 GHz (space-to-Earth), 28.35-28.6 GHz (Earth-to-space), and 29.25-30.0 GHz (Earth-to-space) bands. 25.138 Section 25.138 Telecommunication FEDERAL...

10 CFR 60.7 - License not required for certain preliminary activities.

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2010-01-01

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10 CFR 54.30 - Matters not subject to a renewal review.

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2011-01-01

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48 CFR 252.227-7006 - License grant-running royalty.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 3 2011-10-01 2011-10-01 false License grant-running... of Provisions And Clauses 252.227-7006 License grant—running royalty. As prescribed at 227.7009-4(a...—Running Royalty (AUG 1984) (a) The Contractor hereby grants to the Government, as represented by the...

77 FR 29617 - Intent to Grant a Partially Exclusive Patent License

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-18

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10 CFR 110.9 - List of Nuclear Material under NRC export licensing authority.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false List of Nuclear Material under NRC export licensing authority. 110.9 Section 110.9 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL General Provisions § 110.9 List of Nuclear Material under NRC export licensing...

10 CFR 110.9 - List of Nuclear Material under NRC export licensing authority.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 2 2013-01-01 2013-01-01 false List of Nuclear Material under NRC export licensing authority. 110.9 Section 110.9 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL General Provisions § 110.9 List of Nuclear Material under NRC export licensing...

10 CFR 110.9 - List of Nuclear Material under NRC export licensing authority.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 2 2012-01-01 2012-01-01 false List of Nuclear Material under NRC export licensing authority. 110.9 Section 110.9 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL General Provisions § 110.9 List of Nuclear Material under NRC export licensing...

10 CFR 110.9 - List of Nuclear Material under NRC export licensing authority.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 2 2014-01-01 2014-01-01 false List of Nuclear Material under NRC export licensing authority. 110.9 Section 110.9 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL General Provisions § 110.9 List of Nuclear Material under NRC export licensing...

10 CFR 110.9 - List of Nuclear Material under NRC export licensing authority.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 2 2011-01-01 2011-01-01 false List of Nuclear Material under NRC export licensing authority. 110.9 Section 110.9 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL General Provisions § 110.9 List of Nuclear Material under NRC export licensing...

34 CFR 395.7 - The issuance and conditions of licenses.

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2010-07-01

... licensing qualified applicants, including a provision for giving preference to blind persons who are in need... United States; and (3) Certified by the State vocational rehabilitation agency as qualified to operate a...

26 CFR 301.7231-1 - Failure to obtain license for collection of foreign items.

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2010-04-01

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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...

Deep-HiTS: Rotation Invariant Convolutional Neural Network for Transient Detection

NASA Astrophysics Data System (ADS)

Cabrera-Vives, Guillermo; Reyes, Ignacio; Förster, Francisco; Estévez, Pablo A.; Maureira, Juan-Carlos

2017-02-01

We introduce Deep-HiTS, a rotation-invariant convolutional neural network (CNN) model for classifying images of transient candidates into artifacts or real sources for the High cadence Transient Survey (HiTS). CNNs have the advantage of learning the features automatically from the data while achieving high performance. We compare our CNN model against a feature engineering approach using random forests (RFs). We show that our CNN significantly outperforms the RF model, reducing the error by almost half. Furthermore, for a fixed number of approximately 2000 allowed false transient candidates per night, we are able to reduce the misclassified real transients by approximately one-fifth. To the best of our knowledge, this is the first time CNNs have been used to detect astronomical transient events. Our approach will be very useful when processing images from next generation instruments such as the Large Synoptic Survey Telescope. We have made all our code and data available to the community for the sake of allowing further developments and comparisons at https://github.com/guille-c/Deep-HiTS. Deep-HiTS is licensed under the terms of the GNU General Public License v3.0.

ICT: isotope correction toolbox.

PubMed

Jungreuthmayer, Christian; Neubauer, Stefan; Mairinger, Teresa; Zanghellini, Jürgen; Hann, Stephan

2016-01-01

Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Digital beacon receiver for ionospheric TEC measurement developed with GNU Radio

NASA Astrophysics Data System (ADS)

Yamamoto, M.

2008-11-01

A simple digital receiver named GNU Radio Beacon Receiver (GRBR) was developed for the satellite-ground beacon experiment to measure the ionospheric total electron content (TEC). The open-source software toolkit for the software defined radio, GNU Radio, is utilized to realize the basic function of the receiver and perform fast signal processing. The software is written in Python for a LINUX PC. The open-source hardware called Universal Software Radio Peripheral (USRP), which best matches the GNU Radio, is used as a front-end to acquire the satellite beacon signals of 150 and 400 MHz. The first experiment was successful as results from GRBR showed very good agreement to those from the co-located analog beacon receiver. Detailed design information and software codes are open at the URL http://www.rish.kyoto-u.ac.jp/digitalbeacon/.

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...

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.

Gnuastro: GNU Astronomy Utilities

NASA Astrophysics Data System (ADS)

Akhlaghi, Mohammad

2018-01-01

Gnuastro (GNU Astronomy Utilities) manipulates and analyzes astronomical data. It is an official GNU package of a large collection of programs and C/C++ library functions. Command-line programs perform arithmetic operations on images, convert FITS images to common types like JPG or PDF, convolve an image with a given kernel or matching of kernels, perform cosmological calculations, crop parts of large images (possibly in multiple files), manipulate FITS extensions and keywords, and perform statistical operations. In addition, it contains programs to make catalogs from detection maps, add noise, make mock profiles with a variety of radial functions using monte-carlo integration for their centers, match catalogs, and detect objects in an image among many other operations. The command-line programs share the same basic command-line user interface for the comfort of both the users and developers. Gnuastro is written to comply fully with the GNU coding standards and integrates well with all Unix-like operating systems. This enables astronomers to expect a fully familiar experience in the source code, building, installing and command-line user interaction that they have seen in all the other GNU software that they use. Gnuastro's extensive library is included for users who want to build their own unique programs.

libdrdc: software standards library

NASA Astrophysics Data System (ADS)

Erickson, David; Peng, Tie

2008-04-01

This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

STOP-IT: Windows executable software for the stop-signal paradigm.

PubMed

Verbruggen, Frederick; Logan, Gordon D; Stevens, Michaël A

2008-05-01

The stop-signal paradigm is a useful tool for the investigation of response inhibition. In this paradigm, subjects are instructed to respond as fast as possible to a stimulus unless a stop signal is presented after a variable delay. However, programming the stop-signal task is typically considered to be difficult. To overcome this issue, we present software called STOP-IT, for running the stop-signal task, as well as an additional analyzing program called ANALYZE-IT. The main advantage of both programs is that they are a precompiled executable, and for basic use there is no need for additional programming. STOP-IT and ANALYZE-IT are completely based on free software, are distributed under the GNU General Public License, and are available at the personal Web sites of the first two authors or at expsy.ugent.be/tscope/stop.html.

FOAM: the modular adaptive optics framework

NASA Astrophysics Data System (ADS)

van Werkhoven, T. I. M.; Homs, L.; Sliepen, G.; Rodenhuis, M.; Keller, C. U.

2012-07-01

Control software for adaptive optics systems is mostly custom built and very specific in nature. We have developed FOAM, a modular adaptive optics framework for controlling and simulating adaptive optics systems in various environments. Portability is provided both for different control hardware and adaptive optics setups. To achieve this, FOAM is written in C++ and runs on standard CPUs. Furthermore we use standard Unix libraries and compilation procedures and implemented a hardware abstraction layer in FOAM. We have successfully implemented FOAM on the adaptive optics system of ExPo - a high-contrast imaging polarimeter developed at our institute - in the lab and will test it on-sky late June 2012. We also plan to implement FOAM on adaptive optics systems for microscopy and solar adaptive optics. FOAM is available* under the GNU GPL license and is free to be used by anyone.

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees.

PubMed

Huang, Wen; Zhou, Guifang; Marchand, Melissa; Ash, Jeremy R; Morris, David; Van Dooren, Paul; Brown, Jeremy M; Gallivan, Kyle A; Wilgenbusch, Jim C

2016-12-01

Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty in individual gene trees, variation across genes, or both. Extracting phylogenetic signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some of these challenges, we have developed TreeScaper, an application for tree set visualization as well as the identification of distinct phylogenetic signals. GUI and command-line versions of TreeScaper and a manual with tutorials can be downloaded from https://github.com/whuang08/TreeScaper/releases TreeScaper is distributed under the GNU General Public License. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

VQone MATLAB toolbox: A graphical experiment builder for image and video quality evaluations: VQone MATLAB toolbox.

PubMed

Nuutinen, Mikko; Virtanen, Toni; Rummukainen, Olli; Häkkinen, Jukka

2016-03-01

This article presents VQone, a graphical experiment builder, written as a MATLAB toolbox, developed for image and video quality ratings. VQone contains the main elements needed for the subjective image and video quality rating process. This includes building and conducting experiments and data analysis. All functions can be controlled through graphical user interfaces. The experiment builder includes many standardized image and video quality rating methods. Moreover, it enables the creation of new methods or modified versions from standard methods. VQone is distributed free of charge under the terms of the GNU general public license and allows code modifications to be made so that the program's functions can be adjusted according to a user's requirements. VQone is available for download from the project page (http://www.helsinki.fi/psychology/groups/visualcognition/).

Biological effects and equivalent doses in radiotherapy: A software solution

PubMed Central

Voyant, Cyril; Julian, Daniel; Roustit, Rudy; Biffi, Katia; Lantieri, Céline

2013-01-01

Background The limits of TDF (time, dose, and fractionation) and linear quadratic models have been known for a long time. Medical physicists and physicians are required to provide fast and reliable interpretations regarding delivered doses or any future prescriptions relating to treatment changes. Aim We, therefore, propose a calculation interface under the GNU license to be used for equivalent doses, biological doses, and normal tumor complication probability (Lyman model). Materials and methods The methodology used draws from several sources: the linear-quadratic-linear model of Astrahan, the repopulation effects of Dale, and the prediction of multi-fractionated treatments of Thames. Results and conclusions The results are obtained from an algorithm that minimizes an ad-hoc cost function, and then compared to an equivalent dose computed using standard calculators in seven French radiotherapy centers. PMID:24936319

ProtoMD: A prototyping toolkit for multiscale molecular dynamics

NASA Astrophysics Data System (ADS)

Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.

2016-05-01

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.

Nuclear Regulatory Commission activities to prepare for reviewing license applications and issuing licenses

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

Uleck, R.B.; DeFino, C.V.

1991-12-31

The Low-Level Radioactive Waste Policy Amendments Act of 1985 (LLRWPAA) assigned States the responsibility to provide for disposal of commercial low-level radioactive waste (LLRW) by 1993. The LLRWPAA also required the US Nuclear Regulatory Commission (NRC) to establish procedures and develop the technical review capability to process license applications for new LLRW disposal facilities. Under the LLRWPAA, NRC is required, to the extent practicable, to complete its review of an LLRW disposal facility license application within 15 months of its submittal by a State. This provision of the LLRWPAA helps ensure that NRC, in addition to protecting public health andmore » safety and the environment, facilitates States` achievement of LLRWPAA milestones for new facility development. A timely NRC review is needed for States to accomplish their objective of having new disposal facilities in operation on the dates prescribed in the LLRWPAA. To help assure NRC and States` compliance with the provisions of the LLRWPAA, NRC has developed a licensing review strategy that includes: (1) the further development of regulatory guidance, (2) enhancement of licensing review capability, and (3) prelicensing regulatory consultation with potential applicants.« less

10 CFR 35.6 - Provisions for the protection of human research subjects.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Provisions for the protection of human research subjects... Information § 35.6 Provisions for the protection of human research subjects. (a) A licensee may conduct research involving human research subjects only if it uses the byproduct materials specified on its license...

10 CFR 35.6 - Provisions for the protection of human research subjects.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Provisions for the protection of human research subjects... Information § 35.6 Provisions for the protection of human research subjects. (a) A licensee may conduct research involving human research subjects only if it uses the byproduct materials specified on its license...

10 CFR 35.6 - Provisions for the protection of human research subjects.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Provisions for the protection of human research subjects... Information § 35.6 Provisions for the protection of human research subjects. (a) A licensee may conduct research involving human research subjects only if it uses the byproduct materials specified on its license...

- XSUMMER- Transcendental functions and symbolic summation in FORM

NASA Astrophysics Data System (ADS)

Moch, S.; Uwer, P.

2006-05-01

Harmonic sums and their generalizations are extremely useful in the evaluation of higher-order perturbative corrections in quantum field theory. Of particular interest have been the so-called nested sums, where the harmonic sums and their generalizations appear as building blocks, originating for example, from the expansion of generalized hypergeometric functions around integer values of the parameters. In this paper we discuss the implementation of several algorithms to solve these sums by algebraic means, using the computer algebra system FORM. Program summaryTitle of program:XSUMMER Catalogue identifier:ADXQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXQ_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland License:GNU Public License and FORM License Computers:all Operating system:all Program language:FORM Memory required to execute:Depending on the complexity of the problem, recommended at least 64 MB RAM No. of lines in distributed program, including test data, etc.:9854 No. of bytes in distributed program, including test data, etc.:126 551 Distribution format:tar.gz Other programs called:none External files needed:none Nature of the physical problem:Systematic expansion of higher transcendental functions in a small parameter. The expansions arise in the calculation of loop integrals in perturbative quantum field theory. Method of solution:Algebraic manipulations of nested sums. Restrictions on complexity of the problem:Usually limited only by the available disk space. Typical running time:Dependent on the complexity of the problem.

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2013 CFR

2013-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2011 CFR

2011-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2012 CFR

2012-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2014 CFR

2014-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 781.4 - Communications.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Communications. 781.4 Section 781.4 Energy DEPARTMENT OF ENERGY DOE PATENT LICENSING REGULATIONS General Provisions § 781.4 Communications. All communications concerning the regulations in this part, including applications for licenses, should be addressed or...

10 CFR 781.4 - Communications.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Communications. 781.4 Section 781.4 Energy DEPARTMENT OF ENERGY DOE PATENT LICENSING REGULATIONS General Provisions § 781.4 Communications. All communications concerning the regulations in this part, including applications for licenses, should be addressed or...

10 CFR 781.4 - Communications.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Communications. 781.4 Section 781.4 Energy DEPARTMENT OF ENERGY DOE PATENT LICENSING REGULATIONS General Provisions § 781.4 Communications. All communications concerning the regulations in this part, including applications for licenses, should be addressed or...

10 CFR 781.4 - Communications.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Communications. 781.4 Section 781.4 Energy DEPARTMENT OF ENERGY DOE PATENT LICENSING REGULATIONS General Provisions § 781.4 Communications. All communications concerning the regulations in this part, including applications for licenses, should be addressed or...

14 CFR 1274.942 - Export licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... writing, that the Agreement Officer authorize it to export ITAR-controlled technical data (including... appropriate licenses or other approvals, if required, for exports of hardware, technical data, and software, or for the provision of technical assistance. (b) The Recipient shall be responsible for obtaining...

10 CFR 781.4 - Communications.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Communications. 781.4 Section 781.4 Energy DEPARTMENT OF ENERGY DOE PATENT LICENSING REGULATIONS General Provisions § 781.4 Communications. All communications concerning the regulations in this part, including applications for licenses, should be addressed or...

45 CFR 400.117 - Provision of care and services.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 2 2010-10-01 2010-10-01 false Provision of care and services. 400.117 Section... Child Welfare Services § 400.117 Provision of care and services. (a) A State may provide care and... agency approved or licensed under State law. (b) If a State arranges for the care and services through a...

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.

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).