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.

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 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.

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.

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

NASA Astrophysics Data System (ADS)

Lonie, David C.; Zurek, Eva

2011-02-01

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

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.

RANGER-DTL 2.0: Rigorous Reconstruction of Gene-Family Evolution by Duplication, Transfer, and Loss.

PubMed

Bansal, Mukul S; Kellis, Manolis; Kordi, Misagh; Kundu, Soumya

2018-04-24

RANGER-DTL 2.0 is a software program for inferring gene family evolution using Duplication-Transfer-Loss reconciliation. This new software is highly scalable and easy to use, and offers many new features not currently available in any other reconciliation program. RANGER-DTL 2.0 has a particular focus on reconciliation accuracy and can account for many sources of reconciliation uncertainty including uncertain gene tree rooting, gene tree topological uncertainty, multiple optimal reconciliations, and alternative event cost assignments. RANGER-DTL 2.0 is open-source and written in C ++ and Python. Pre-compiled executables, source code (open-source under GNU GPL), and a detailed manual are freely available from http://compbio.engr.uconn.edu/software/RANGER-DTL/. mukul.bansal@uconn.edu.

BnmrOffice: A Free Software for β-nmr Data Analysis

NASA Astrophysics Data System (ADS)

Saadaoui, Hassan

A data-analysis framework with a graphical user interface (GUI) is developed to analyze β-nmr spectra in an automated and intuitive way. This program, named BnmrOffice is written in C++ and employs the QT libraries and tools for designing the GUI, and the CERN's Minuit optimization routines for minimization. The program runs under multiple platforms, and is available for free under the terms of the GNU GPL standards. The GUI is structured in tabs to search, plot and analyze data, along other functionalities. The user can tweak the minimization options; and fit multiple data files (or runs) using single or global fitting routines with pre-defined or new models. Currently, BnmrOffice reads TRIUMF's MUD data and ASCII files, and can be extended to other formats.

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.

FORM version 4.0

NASA Astrophysics Data System (ADS)

Kuipers, J.; Ueda, T.; Vermaseren, J. A. M.; Vollinga, J.

2013-05-01

We present version 4.0 of the symbolic manipulation system FORM. The most important new features are manipulation of rational polynomials and the factorization of expressions. Many other new functions and commands are also added; some of them are very general, while others are designed for building specific high level packages, such as one for Gröbner bases. New is also the checkpoint facility, that allows for periodic backups during long calculations. Finally, FORM 4.0 has become available as open source under the GNU General Public License version 3. Program summaryProgram title: FORM. Catalogue identifier: AEOT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOT_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.: 151599 No. of bytes in distributed program, including test data, etc.: 1 078 748 Distribution format: tar.gz Programming language: The FORM language. FORM itself is programmed in a mixture of C and C++. Computer: All. Operating system: UNIX, LINUX, Mac OS, Windows. Classification: 5. Nature of problem: FORM defines a symbolic manipulation language in which the emphasis lies on fast processing of very large formulas. It has been used successfully for many calculations in Quantum Field Theory and mathematics. In speed and size of formulas that can be handled it outperforms other systems typically by an order of magnitude. Special in this version: The version 4.0 contains many new features. Most important are factorization and rational arithmetic. The program has also become open source under the GPL. The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes. Solution method: See "Nature of Problem", above. Additional comments: NOTE: The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes.

MendelianRandomization: an R package for performing Mendelian randomization analyses using summarized data.

PubMed

Yavorska, Olena O; Burgess, Stephen

2017-12-01

MendelianRandomization is a software package for the R open-source software environment that performs Mendelian randomization analyses using summarized data. The core functionality is to implement the inverse-variance weighted, MR-Egger and weighted median methods for multiple genetic variants. Several options are available to the user, such as the use of robust regression, fixed- or random-effects models and the penalization of weights for genetic variants with heterogeneous causal estimates. Extensions to these methods, such as allowing for variants to be correlated, can be chosen if appropriate. Graphical commands allow summarized data to be displayed in an interactive graph, or the plotting of causal estimates from multiple methods, for comparison. Although the main method of data entry is directly by the user, there is also an option for allowing summarized data to be incorporated from the PhenoScanner database of genotype-phenotype associations. We hope to develop this feature in future versions of the package. The R software environment is available for download from [https://www.r-project.org/]. The MendelianRandomization package can be downloaded from the Comprehensive R Archive Network (CRAN) within R, or directly from [https://cran.r-project.org/web/packages/MendelianRandomization/]. Both R and the MendelianRandomization package are released under GNU General Public Licenses (GPL-2|GPL-3). © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

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.

Self- and Air-Broadened Line Shape Parameters of (12)CH(4) : 4500-4620 cm(-1)

NASA Astrophysics Data System (ADS)

Devi, V. Malathy; Benner, D. Chris; Sung, K.; Brown, L. R.; Crawford, T. J.; Smith, M. A. H.; Mantz, A. W.; Predoi-Cross, A.

2014-06-01

Accurate knowledge of spectral line shape parameters is important for infrared transmission and radiance calculations in the terrestrial atmosphere. We report the self and air-broadened Lorentz widths, shifts and line mixing coefficients along with their temperature dependencies for methane absorption lines in the 2.2 µm spectral region. For this, we obtained a series of high-resolution, high S/N spectra of 99.99% 12C-enriched samples of pure methane and its dilute mixtures in dry air at cold temperatures down to 150 K using the Bruker IFS 125HR Fourier transform spectrometer at JPL. The coolable absorption cell had an optical path of 20.38 cm and was specially built to reside inside the sample compartment of the Bruker FTS1. The 13 spectra used in the analysis consisted of seven pure 12CH4 spectra at pressures from 4.5 to 169 Torr and six air-broadened spectra with total sample pressures of 113-300 Torr and methane volume mixing ratios between 4 and 9.7%. These 13 spectra were fit simultaneously using the multispectrum least-squares fitting technique2. The results will be compared to existing values reported in the literature3. as part of the GNU EPrints system , and is freely redistributable under the GPL .

Jflow: a workflow management system for web applications.

PubMed

Mariette, Jérôme; Escudié, Frédéric; Bardou, Philippe; Nabihoudine, Ibouniyamine; Noirot, Céline; Trotard, Marie-Stéphane; Gaspin, Christine; Klopp, Christophe

2016-02-01

Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a Python library providing all requested features to setup, run and monitor workflows. Jflow is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/jflow. The package is coming with full documentation, quick start and a running test portal. Jerome.Mariette@toulouse.inra.fr. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

PTools: an opensource molecular docking library

PubMed Central

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-01-01

Background Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. Results We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. Conclusion The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation. PMID:19409097

PTools: an opensource molecular docking library.

PubMed

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-05-01

Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.

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

Open source system OpenVPN in a function of Virtual Private Network

NASA Astrophysics Data System (ADS)

Skendzic, A.; Kovacic, B.

2017-05-01

Using of Virtual Private Networks (VPN) can establish high security level in network communication. VPN technology enables high security networking using distributed or public network infrastructure. VPN uses different security and managing rules inside networks. It can be set up using different communication channels like Internet or separate ISP communication infrastructure. VPN private network makes security communication channel over public network between two endpoints (computers). OpenVPN is an open source software product under GNU General Public License (GPL) that can be used to establish VPN communication between two computers inside business local network over public communication infrastructure. It uses special security protocols and 256-bit Encryption and it is capable of traversing network address translators (NATs) and firewalls. It allows computers to authenticate each other using a pre-shared secret key, certificates or username and password. This work gives review of VPN technology with a special accent on OpenVPN. This paper will also give comparison and financial benefits of using open source VPN software in business environment.

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

PubMed

Diaz-Uriarte, Ramon

2017-06-15

OncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes. Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul. ramon.diaz@iib.uam.es. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Libpsht - algorithms for efficient spherical harmonic transforms

NASA Astrophysics Data System (ADS)

Reinecke, M.

2011-02-01

Libpsht (or "library for performant spherical harmonic transforms") is a collection of algorithms for efficient conversion between spatial-domain and spectral-domain representations of data defined on the sphere. The package supports both transforms of scalars and spin-1 and spin-2 quantities, and can be used for a wide range of pixelisations (including HEALPix, GLESP, and ECP). It will take advantage of hardware features such as multiple processor cores and floating-point vector operations, if available. Even without this additional acceleration, the employed algorithms are among the most efficient (in terms of CPU time, as well as memory consumption) currently being used in the astronomical community. The library is written in strictly standard-conforming C90, ensuring portability to many different hard- and software platforms, and allowing straightforward integration with codes written in various programming languages like C, C++, Fortran, Python etc. Libpsht is distributed under the terms of the GNU General Public License (GPL) version 2 and can be downloaded from .

Astrometry with A-Track Using Gaia DR1 Catalogue

NASA Astrophysics Data System (ADS)

Kılıç, Yücel; Erece, Orhan; Kaplan, Murat

2018-04-01

In this work, we built all sky index files from Gaia DR1 catalogue for the high-precision astrometric field solution and the precise WCS coordinates of the moving objects. For this, we used build-astrometry-index program as a part of astrometry.net code suit. Additionally, we added astrometry.net's WCS solution tool to our previously developed software which is a fast and robust pipeline for detecting moving objects such as asteroids and comets in sequential FITS images, called A-Track. Moreover, MPC module was added to A-Track. This module is linked to an asteroid database to name the found objects and prepare the MPC file to report the results. After these innovations, we tested a new version of the A-Track code on photometrical data taken by the SI-1100 CCD with 1-meter telescope at TÜBİTAK National Observatory, Antalya. The pipeline can be used to analyse large data archives or daily sequential data. The code is hosted on GitHub under the GNU GPL v3 license.

Libpsht: Algorithms for Efficient Spherical Harmonic Transforms

NASA Astrophysics Data System (ADS)

Reinecke, Martin

2010-10-01

Libpsht (or "library for Performing Spherical Harmonic Transforms") is a collection of algorithms for efficient conversion between spatial-domain and spectral-domain representations of data defined on the sphere. The package supports transforms of scalars as well as spin-1 and spin-2 quantities, and can be used for a wide range of pixelisations (including HEALPix, GLESP and ECP). It will take advantage of hardware features like multiple processor cores and floating-point vector operations, if available. Even without this additional acceleration, the employed algorithms are among the most efficient (in terms of CPU time as well as memory consumption) currently being used in the astronomical community. The library is written in strictly standard-conforming C90, ensuring portability to many different hard- and software platforms, and allowing straightforward integration with codes written in various programming languages like C, C++, Fortran, Python etc. Libpsht is distributed under the terms of the GNU General Public License (GPL) version 2. Development on this project has ended; its successor is libsharp (ascl:1402.033).

A basic analysis toolkit for biological sequences

PubMed Central

Giancarlo, Raffaele; Siragusa, Alessandro; Siragusa, Enrico; Utro, Filippo

2007-01-01

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL. PMID:17877802

DOGMA: domain-based transcriptome and proteome quality assessment.

PubMed

Dohmen, Elias; Kremer, Lukas P M; Bornberg-Bauer, Erich; Kemena, Carsten

2016-09-01

Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines. We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds. DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ CONTACTS: e.dohmen@wwu.de or c.kemena@wwu.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

Rovibrational Line Lists for Nine Isotopologues of CO Suitable for Modeling and Interpreting Spectra at Very High Temperatures and Diverse Environments

NASA Astrophysics Data System (ADS)

Li, G.; Gordon, I. E.; Rothman, L. S.; Tan, Y.; Hu, S.-M.; Kassi, S.; Campargue, A.

2014-06-01

In order to improve and extend the existing HITRAN database1 and HITEMP2data for carbon monoxide, the ro-vibrational line lists were computed for all transitions of nine isotopologues of the CO molecule, namely 12C16O, 12C17O, 12C18O, 13C16O, 13C17O, 13C18O, 14C16O, 14C17O, and 14C18O in the electronic ground state up to v = 41 and J = 150. Line positions and intensity calculations were carried out using a newly-determined piece-wise dipole moment function (DMF) in conjunction with the wavefunctions calculated from a previous experimentally-determined potential energy function of Coxon and Hajigeorgiou3. Ab initio calculations and a direct-fit method which simultaneously fits all the reliable experimental ro-vibrational matrix elements has been used to construct the piecewise dipole moment function. To provide additional input parameters into the fit, new Cavity Ring Down Spectroscopy experiments were carried out to enable measurements of the lines in the 4-0 band with low uncertainty (Grenoble) as well as the first measurements of lines in the 6-0 band (Hefei). Accurate partition sums have been derived through direct summation for a temperature range from 1 to 9000 Kelvin. A complete set of broadening and shift parameters is also provided and now include parameters induced by CO2 and H2 in order to aid planetary applications. as part of the GNU EPrints system , and is freely redistributable under the GPL .

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

Ditzler, Gregory; Morrison, J. Calvin; Lan, Yemin

Background: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field of machine learning – can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate betweenmore » age groups in the human gut microbiome. Results: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. Conclusions: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.« less

Fizzy: feature subset selection for metagenomics.

PubMed

Ditzler, Gregory; Morrison, J Calvin; Lan, Yemin; Rosen, Gail L

2015-11-04

Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α- & β-diversity. Feature subset selection--a sub-field of machine learning--can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate between age groups in the human gut microbiome. We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.

Fizzy. Feature subset selection for metagenomics

DOE PAGES

Ditzler, Gregory; Morrison, J. Calvin; Lan, Yemin; ...

2015-11-04

Background: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field of machine learning – can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate betweenmore » age groups in the human gut microbiome. Results: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. Conclusions: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.« less

High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software

PubMed Central

Fabregat-Traver, Diego; Sharapov, Sodbo Zh.; Hayward, Caroline; Rudan, Igor; Campbell, Harry; Aulchenko, Yurii; Bientinesi, Paolo

2014-01-01

To raise the power of genome-wide association studies (GWAS) and avoid false-positive results in structured populations, one can rely on mixed model based tests. When large samples are used, and when multiple traits are to be studied in the ’omics’ context, this approach becomes computationally challenging. Here we consider the problem of mixed-model based GWAS for arbitrary number of traits, and demonstrate that for the analysis of single-trait and multiple-trait scenarios different computational algorithms are optimal. We implement these optimal algorithms in a high-performance computing framework that uses state-of-the-art linear algebra kernels, incorporates optimizations, and avoids redundant computations, increasing throughput while reducing memory usage and energy consumption. We show that, compared to existing libraries, our algorithms and software achieve considerable speed-ups. The OmicABEL software described in this manuscript is available under the GNU GPL v. 3 license as part of the GenABEL project for statistical genomics at http: //www.genabel.org/packages/OmicABEL. PMID:25717363

High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software.

PubMed

Fabregat-Traver, Diego; Sharapov, Sodbo Zh; Hayward, Caroline; Rudan, Igor; Campbell, Harry; Aulchenko, Yurii; Bientinesi, Paolo

2014-01-01

To raise the power of genome-wide association studies (GWAS) and avoid false-positive results in structured populations, one can rely on mixed model based tests. When large samples are used, and when multiple traits are to be studied in the 'omics' context, this approach becomes computationally challenging. Here we consider the problem of mixed-model based GWAS for arbitrary number of traits, and demonstrate that for the analysis of single-trait and multiple-trait scenarios different computational algorithms are optimal. We implement these optimal algorithms in a high-performance computing framework that uses state-of-the-art linear algebra kernels, incorporates optimizations, and avoids redundant computations, increasing throughput while reducing memory usage and energy consumption. We show that, compared to existing libraries, our algorithms and software achieve considerable speed-ups. The OmicABEL software described in this manuscript is available under the GNU GPL v. 3 license as part of the GenABEL project for statistical genomics at http: //www.genabel.org/packages/OmicABEL.

BiDiBlast: comparative genomics pipeline for the PC.

PubMed

de Almeida, João M G C F

2010-06-01

Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http://moodle.fct.unl.pt/course/view.php?id=2079 or https://sourceforge.net/projects/bidiblast/ under the GNU GPL license. Copyright 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

Measurement of Ether Phospholipids in Human Plasma with HPLC-ELSD and LC/ESI-MS After Hydrolysis of Plasma with Phospholipase A1.

PubMed

Mawatari, Shiro; Hazeyama, Seira; Fujino, Takehiko

2016-08-01

Ethanolamine ether phospholipid (eEtnGpl) and choline ether phospholipid (eChoGpl) are present in human plasma or serum, but the relative concentration of the ether phospholipids in plasma is very low as compared to those in other tissues. Nowadays, measurement of ether phospholipids in plasma depends on tandem mass spectrometry (LC/MS/MS), but a system for LC/MS/MS is generally too expensive for usual clinical laboratories. Treatment of plasma with phospholipase A1 (PLA1) causes complete hydrolysis of diacylphospholipids, but ether phospholipids remain intact. After the treatment of plasma with PLA1, both eEtnGpl and eChoGpl are detected as independent peaks by high-performance liquid chromatography with evaporative light scattering detection (HPLC-ELSD). The same sample used for HPLC-ELSD can be applied to detect eEtnGpl and eChoGpl with electrospray ionization mass spectrometry. Presence of alkylacylphospholipids in both eChoGpl and eEtnGpl in human plasma was indicated by sequential hydrolysis of plasma with PLA1 and hydrochloric acid.

Critic: a new program for the topological analysis of solid-state electron densities

NASA Astrophysics Data System (ADS)

Otero-de-la-Roza, A.; Blanco, M. A.; Pendás, A. Martín; Luaña, Víctor

2009-01-01

In this paper we introduce CRITIC, a new program for the topological analysis of the electron densities of crystalline solids. Two different versions of the code are provided, one adapted to the LAPW (Linear Augmented Plane Wave) density calculated by the WIEN2K package and the other to the ab initio Perturbed Ion ( aiPI) density calculated with the PI7 code. Using the converged ground state densities, CRITIC can locate their critical points, determine atomic basins and integrate properties within them, and generate several graphical representations which include topological atomic basins and primary bundles, contour maps of ρ and ∇ρ, vector maps of ∇ρ, chemical graphs, etc. Program summaryProgram title: CRITIC Catalogue identifier: AECB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_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.: 1 206 843 No. of bytes in distributed program, including test data, etc.: 12 648 065 Distribution format: tar.gz Programming language: FORTRAN 77 and 90 Computer: Any computer capable of compiling Fortran Operating system: Unix, GNU/Linux Classification: 7.3 Nature of problem: Topological analysis of the electron density in periodic solids. Solution method: The automatic localization of the electron density critical points is based on a recursive partitioning of the Wigner-Seitz cell into tetrahedra followed by a Newton search from significant points on each tetrahedra. Plotting of and integration on the atomic basins is currently based on a new implementation of Keith's promega algorithm. Running time: Variable, depending on the task. From seconds to a few minutes for the localization of critical points. Hours to days for the determination of the atomic basins shape and properties. Times correspond to a typical 2007 PC.

ACPYPE - AnteChamber PYthon Parser interfacE.

PubMed

Sousa da Silva, Alan W; Vranken, Wim F

2012-07-23

ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein-ligand complexes from the PDB. ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.

NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

PubMed

Hu, Jialu; Kehr, Birte; Reinert, Knut

2014-02-15

Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

lpNet: a linear programming approach to reconstruct signal transduction networks.

PubMed

Matos, Marta R A; Knapp, Bettina; Kaderali, Lars

2015-10-01

With the widespread availability of high-throughput experimental technologies it has become possible to study hundreds to thousands of cellular factors simultaneously, such as coding- or non-coding mRNA or protein concentrations. Still, extracting information about the underlying regulatory or signaling interactions from these data remains a difficult challenge. We present a flexible approach towards network inference based on linear programming. Our method reconstructs the interactions of factors from a combination of perturbation/non-perturbation and steady-state/time-series data. We show both on simulated and real data that our methods are able to reconstruct the underlying networks fast and efficiently, thus shedding new light on biological processes and, in particular, into disease's mechanisms of action. We have implemented the approach as an R package available through bioconductor. This R package is freely available under the Gnu Public License (GPL-3) from bioconductor.org (http://bioconductor.org/packages/release/bioc/html/lpNet.html) and is compatible with most operating systems (Windows, Linux, Mac OS) and hardware architectures. bettina.knapp@helmholtz-muenchen.de 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.

Two C++ Libraries for Counting Trees on a Phylogenetic Terrace.

PubMed

Biczok, R; Bozsoky, P; Eisenmann, P; Ernst, J; Ribizel, T; Scholz, F; Trefzer, A; Weber, F; Hamann, M; Stamatakis, A

2018-05-08

The presence of terraces in phylogenetic tree space, that is, a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al. (2011). However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the lack of an efficient library to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace, and (iii) enumerate all trees on a terrace. In our bioinformatics practical that is set up as a programming contest we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating trees on a terrace. Both implementations yield exactly the same results, are more than one order of magnitude faster, and require one order of magnitude less memory than a previous 3rd party python implementation. The source codes are available under GNU GPL at https://github.com/terraphast. Alexandros.Stamatakis@h-its.org. Supplementary data are available at Bioinformatics online.

Pathogenic Nontuberculous Mycobacteria Resist and Inactivate Cathelicidin: Implication of a Novel Role for Polar Mycobacterial Lipids

PubMed Central

Honda, Jennifer R.; Hess, Tamara; Malcolm, Kenneth C.; Ovrutsky, Alida R.; Bai, Xiyuan; Irani, Vida R.; Dobos, Karen M.; Chan, Edward D.; Flores, Sonia C.

2015-01-01

Nontuberculous mycobacteria (NTM) are a large group of environmental organisms with worldwide distribution, but only a relatively few are known to be pathogenic. Chronic, debilitating lung disease is the most common manifestation of NTM infection, which is often refractory to treatment. The incidence and prevalence of NTM lung disease are increasing in the United States and in many parts of the world. Hence, a more complete understanding of NTM pathogenesis will provide the foundation to develop innovative approaches to treat this recalcitrant disease. Herein, we demonstrate that several species of NTM show broad resistance to the antimicrobial peptide, cathelicidin (LL-37). Resistance to LL-37 was not significantly different between M. avium that contain serovar-specific glycopeptidolipid (GPL, M. avium ssGPL) and M. avium that do not (M. avium ΔssGPL). Similarly, M. abscessus containing non-specific GPL (M. abscessus nsGPL(+)) or lacking nsGPL (M. abscessus nsGPL(-)) remained equally resistant to LL-37. These findings would support the notion that GPL are not the components responsible for NTM resistance to LL-37. Unexpectedly, the growth of M. abscessus nsGPL(-) increased with LL-37 or scrambled LL-37 peptide in a dose-dependent fashion. We also discovered that LL-37 exposed to NTM had reduced antimicrobial activity, and initial work indicates that this is likely due to inactivation of LL-37 by lipid component(s) of the NTM cell envelope. We conclude that pathogenic NTM resist and inactivate LL-37. The mechanism by which NTM circumvent the antimicrobial activity of LL-37 remains to be determined. PMID:25993058

Effects of differentiation on the phospholipid and phospholipid fatty acid composition of N1E-115 neuroblastoma cells.

PubMed

Murphy, E J; Horrocks, L A

1993-04-07

The effects of differentiation on the phospholipid and phospholipid fatty acid composition of N1E-115 neuroblastoma cells were determined. The cellular lipids were extracted on days 0, 3 and 7, following the addition of 1.2% dimethylsulfoxide to induce cellular differentiation. Proportions of ethanolamine glycerophospholipids (EtnGpl), phosphatidylinositol (PtdIns) and sphingomyelin (CerPCho) were significantly elevated following differentiation. The mole percentage of choline glycerophospholipids (ChoGpl) decreased with differentiation. The plasmalogens, both choline and ethanolamine, increased by 1.3- and 2.3-fold, respectively, during differentiation. The fatty acid composition of the phospholipid classes was also altered. PtdIns and ChoGpl had decreased proportions of polyenoic fatty acids, while these proportions were increased in EtnGpl. Both ChoGpl and EtnGpl had increased n-3/n-6 series fatty acid ratios, but this ratio was decreased in PtdIns. The mole percentage of arachidonic acid was significantly decreased in both PtdIns and ChoGpl, but elevated in EtnGpl and may be a result of the increase in ethanolamine plasmalogen. Thus, differentiation did not increase the overall mole percentage of polyenoic FA in the cells nor increase the n-6 series fatty acid proportions. We speculate plasmalogens may have a role in the differentiation process or in maintaining the cell in the differentiated state.

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

PubMed

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

2010-06-30

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

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

PubMed Central

2010-01-01

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

GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

PubMed

Lajugie, Julien; Fourel, Nicolas; Bouhassira, Eric E

2015-01-01

Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Non-invasive Fetal ECG Signal Quality Assessment for Multichannel Heart Rate Estimation.

PubMed

Andreotti, Fernando; Graser, Felix; Malberg, Hagen; Zaunseder, Sebastian

2017-12-01

The noninvasive fetal ECG (NI-FECG) from abdominal recordings offers novel prospects for prenatal monitoring. However, NI-FECG signals are corrupted by various nonstationary noise sources, making the processing of abdominal recordings a challenging task. In this paper, we present an online approach that dynamically assess the quality of NI-FECG to improve fetal heart rate (FHR) estimation. Using a naive Bayes classifier, state-of-the-art and novel signal quality indices (SQIs), and an existing adaptive Kalman filter, FHR estimation was improved. For the purpose of training and validating the proposed methods, a large annotated private clinical dataset was used. The suggested classification scheme demonstrated an accuracy of Krippendorff's alpha in determining the overall quality of NI-FECG signals. The proposed Kalman filter outperformed alternative methods for FHR estimation achieving accuracy. The proposed algorithm was able to reliably reflect changes of signal quality and can be used in improving FHR estimation. NI-ECG signal quality estimation and multichannel information fusion are largely unexplored topics. Based on previous works, multichannel FHR estimation is a field that could strongly benefit from such methods. The developed SQI algorithms as well as resulting classifier were made available under a GNU GPL open-source license and contributed to the FECGSYN toolbox.

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids.

PubMed

Dorier, Julien; Goundaroulis, Dimos; Benedetti, Fabrizio; Stasiak, Andrzej

2018-05-02

The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluating the entanglement of open curves without the need to close them, using the recent concept of knotoids which is a generalization of the classical knot theory to open curves. Knoto-ID can analyse the global topology of the full chain as well as the local topology by exhaustively studying all subchains or only determining the knotted core. Knoto-ID permits to localize topologically non-trivial protein folds that are not detected by informatics tools detecting knotted protein folds. Knoto-ID is written in C ++ and includes R (www.R-project.org) scripts to generate plots of projections maps, fingerprint matrices and disk matrices. Knoto-ID is distributed under the GNU General Public License (GPL), version 2 or any later version and is available at https://github.com/sib-swiss/Knoto-ID. A binary distribution for Mac OS X, Linux and Windows with detailed user guide and examples can be obtained from https://www.vital-it.ch/software/Knoto-ID. julien.dorier@sib.swiss.

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

PubMed

Laird, Matthew R; Langille, Morgan G I; Brinkman, Fiona S L

2015-10-15

A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations. GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general. GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/. brinkman@sfu.ca. © The Author 2015. Published by Oxford University Press.

Astrochem: Abundances of chemical species in the interstellar medium

NASA Astrophysics Data System (ADS)

Maret, Sébastien; Bergin, Edwin A.

2015-07-01

Astrochem computes the abundances of chemical species in the interstellar medium, as function of time. It studies the chemistry in a variety of astronomical objects, including diffuse clouds, dense clouds, photodissociation regions, prestellar cores, protostars, and protostellar disks. Astrochem reads a network of chemical reactions from a text file, builds up a system of kinetic rates equations, and solves it using a state-of-the-art stiff ordinary differential equation (ODE) solver. The Jacobian matrix of the system is computed implicitly, so the resolution of the system is extremely fast: large networks containing several thousands of reactions are usually solved in a few seconds. A variety of gas phase process are considered, as well as simple gas-grain interactions, such as the freeze-out and the desorption via several mechanisms (thermal desorption, cosmic-ray desorption and photo-desorption). The computed abundances are written in a HDF5 file, and can be plotted in different ways with the tools provided with Astrochem. Chemical reactions and their rates are written in a format which is meant to be easy to read and to edit. A tool to convert the chemical networks from the OSU and KIDA databases into this format is also provided. Astrochem is written in C, and its source code is distributed under the terms of the GNU General Public License (GPL).

MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data

PubMed Central

Loher, Phillipe; Telonis, Aristeidis G.; Rigoutsos, Isidore

2017-01-01

Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs. Furthermore, to ensure specificity, MINTmap identifies the subset of discovered tRFs that could be originating outside of tRNA space and flags them as candidate false positives. Our comparative analysis shows that MINTmap exhibits superior sensitivity and specificity to other available methods while also being exceptionally fast. The MINTmap codes are available through https://github.com/TJU-CMC-Org/MINTmap/ under an open source GNU GPL v3.0 license. PMID:28220888

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

PubMed

Murray, Kevin D; Webers, Christfried; Ong, Cheng Soon; Borevitz, Justin; Warthmann, Norman

2017-09-01

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

CVT/GPL phase 3 integrated testing

NASA Technical Reports Server (NTRS)

Shurney, R. E.; Cantrell, E.; Maybee, G.; Schmitt, S.

1975-01-01

The hardware for 20 candidate shuttle program life sciences experiments was installed in the GPL and experiments were conducted during a 5-day simulated mission. The experiments involved humans, primates, rats, chickens, and marigold plants. All experiments were completed to the satisfaction of the experimenters. In addition to the scientific data gathered for each experiment, information was obtained concerning experiment hardware design and integration, experiment procedures, GPL support systems, and test operations. The results of the integrated tests are presented.

Utilization of a ts-sacB selection system for the generation of a Mycobacterium avium serovar-8 specific glycopeptidolipid allelic exchange mutant

PubMed Central

Irani, Vida R; Lee, Sun-Hwa; Eckstein, Torsten M; Inamine, Julia M; Belisle, John T; Maslow, Joel N

2004-01-01

Background Mycobacterium avium are ubiquitous environmental organisms and a cause of disseminated infection in patients with end-stage AIDS. The glycopeptidolipids (GPL) of M. avium are proposed to participate in the pathogenesis of this organism, however, establishment of a clear role for GPL in disease production has been limited by the inability to genetically manipulate M. avium. Methods To be able to study the role of the GPL in M. avium pathogenesis, a ts-sacB selection system, not previously used in M. avium, was employed as a means to achieve homologous recombination for the rhamnosyltransferase (rtfA) gene of a pathogenic serovar 8 strain of M. avium to prevent addition of serovar-specific sugars to rhamnose of the fatty acyl-peptide backbone of GPL. The genotype of the resultant rtfA mutant was confirmed by polymerase chain reaction and southern hybridization. Disruption in the proximal sugar of the haptenic oligosaccharide resulted in the loss of serovar specific GPL with no change in the pattern of non-serovar specific GPL moieties as shown by thin layer chromatography and gas chromatography/mass spectrometry. Complementation of wild type (wt) rtfA in trans through an integrative plasmid restored serovar-8 specific GPL expression identical to wt serovar 8 parent strain. Results In this study, we affirm our results that rtfA encodes an enzyme responsible for the transfer of Rha to 6d-Tal and provide evidence of a second allelic exchange mutagenesis system suitable for M. avium. Conclusion We report the second allelic exchange system for M. avium utilizing ts-sacB as double-negative and xylE as positive counter-selection markers, respectively. This system of allelic exchange would be especially useful for M. avium strains that demonstrate significant isoniazid (INH) resistance despite transformation with katG. Through the construction of mutants in GPL or other mycobacterial components, their roles in M. avium pathogenesis, biosynthesis, or drug resistance can be studied in a consistent manner. PMID:15458565

An inexpensive Arduino-based LED stimulator system for vision research.

PubMed

Teikari, Petteri; Najjar, Raymond P; Malkki, Hemi; Knoblauch, Kenneth; Dumortier, Dominique; Gronfier, Claude; Cooper, Howard M

2012-11-15

Light emitting diodes (LEDs) are being used increasingly as light sources in life sciences applications such as in vision research, fluorescence microscopy and in brain-computer interfacing. Here we present an inexpensive but effective visual stimulator based on light emitting diodes (LEDs) and open-source Arduino microcontroller prototyping platform. The main design goal of our system was to use off-the-shelf and open-source components as much as possible, and to reduce design complexity allowing use of the system to end-users without advanced electronics skills. The main core of the system is a USB-connected Arduino microcontroller platform designed initially with a specific emphasis on the ease-of-use creating interactive physical computing environments. The pulse-width modulation (PWM) signal of Arduino was used to drive LEDs allowing linear light intensity control. The visual stimulator was demonstrated in applications such as murine pupillometry, rodent models for cognitive research, and heterochromatic flicker photometry in human psychophysics. These examples illustrate some of the possible applications that can be easily implemented and that are advantageous for students, educational purposes and universities with limited resources. The LED stimulator system was developed as an open-source project. Software interface was developed using Python with simplified examples provided for Matlab and LabVIEW. Source code and hardware information are distributed under the GNU General Public Licence (GPL, version 3). Copyright © 2012 Elsevier B.V. All rights reserved.

HyDe: a Python Package for Genome-Scale Hybridization Detection.

PubMed

Blischak, Paul D; Chifman, Julia; Wolfe, Andrea D; Kubatko, Laura S

2018-03-19

The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this paper we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python, and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde).

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements

PubMed Central

2013-01-01

Background The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistical models for predicting potential transcription factor binding sites (TFBS). The rapidly increasing number of genome sequence data requires sophisticated computational approaches to manage and query experimental and predicted TFBS data in the context of other epigenetic factors and across different organisms. Results We have developed D-Light, a novel client-server software package to store and query large amounts of TFBS data for any number of genomes. Users can add small-scale data to the server database and query them in a large scale, genome-wide promoter context. The client is implemented in Java and provides simple graphical user interfaces and data visualization. Here we also performed a statistical analysis showing what a user can expect for certain parameter settings and we illustrate the usage of D-Light with the help of a microarray data set. Conclusions D-Light is an easy to use software tool to integrate, store and query annotation data for promoters. A public D-Light server, the client and server software for local installation and the source code under GNU GPL license are available at http://biwww.che.sbg.ac.at/dlight. PMID:23617301

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.

PubMed

Benoit, Gaëtan; Lemaitre, Claire; Lavenier, Dominique; Drezen, Erwan; Dayris, Thibault; Uricaru, Raluca; Rizk, Guillaume

2015-09-14

Data volumes generated by next-generation sequencing (NGS) technologies is now a major concern for both data storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as the widely used gzip method. We present a novel reference-free method meant to compress data issued from high throughput sequencing technologies. Our approach, implemented in the software LEON, employs techniques derived from existing assembly principles. The method is based on a reference probabilistic de Bruijn Graph, built de novo from the set of reads and stored in a Bloom filter. Each read is encoded as a path in this graph, by memorizing an anchoring kmer and a list of bifurcations. The same probabilistic de Bruijn Graph is used to perform a lossy transformation of the quality scores, which allows to obtain higher compression rates without losing pertinent information for downstream analyses. LEON was run on various real sequencing datasets (whole genome, exome, RNA-seq or metagenomics). In all cases, LEON showed higher overall compression ratios than state-of-the-art compression software. On a C. elegans whole genome sequencing dataset, LEON divided the original file size by more than 20. LEON is an open source software, distributed under GNU affero GPL License, available for download at http://gatb.inria.fr/software/leon/.

mdFoam+: Advanced molecular dynamics in OpenFOAM

NASA Astrophysics Data System (ADS)

Longshaw, S. M.; Borg, M. K.; Ramisetti, S. B.; Zhang, J.; Lockerby, D. A.; Emerson, D. R.; Reese, J. M.

2018-03-01

This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.

DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets.

PubMed

Hendriks, Bart S; Espelin, Christopher W

2010-02-01

DataPflex is a MATLAB-based application that facilitates the manipulation and visualization of multidimensional datasets. The strength of DataPflex lies in the intuitive graphical user interface for the efficient incorporation, manipulation and visualization of high-dimensional data that can be generated by multiplexed protein measurement platforms including, but not limited to Luminex or Meso-Scale Discovery. Such data can generally be represented in the form of multidimensional datasets [for example (time x stimulation x inhibitor x inhibitor concentration x cell type x measurement)]. For cases where measurements are made in a combinational fashion across multiple dimensions, there is a need for a tool to efficiently manipulate and reorganize such data for visualization. DataPflex accepts data consisting of up to five arbitrary dimensions in addition to a measurement dimension. Data are imported from a simple .xls format and can be exported to MATLAB or .xls. Data dimensions can be reordered, subdivided, merged, normalized and visualized in the form of collections of line graphs, bar graphs, surface plots, heatmaps, IC50's and other custom plots. Open source implementation in MATLAB enables easy extension for custom plotting routines and integration with more sophisticated analysis tools. DataPflex is distributed under the GPL license (http://www.gnu.org/licenses/) together with documentation, source code and sample data files at: http://code.google.com/p/datapflex. Supplementary data available at Bioinformatics online.

Incubation of human sperm with micelles made from glycerophospholipid mixtures increases sperm motility and resistance to oxidative stress

PubMed Central

Costa, Carlos; Bassaizteguy, Verónica; Cardozo, Romina; Montes, José; Settineri, Robert; Nicolson, Garth L.

2018-01-01

Membrane integrity is essential in maintaining sperm viability, signaling, and motility, which are essential for fertilization. Sperm are highly susceptible to oxidative stress, as they are rich in sensitive polyunsaturated fatty acids (PUFA), and are unable to synthesize and repair many essential membrane constituents. Because of this, sperm cellular membranes are important targets of this process. Membrane Lipid Replacement (MLR) with glycerophospholipid mixtures (GPL) has been shown to ameliorate oxidative stress in cells, restore their cellular membranes, and prevent loss of function. Therefore, we tested the effects of MLR on sperm by tracking and monitoring GPL incorporation into their membrane systems and studying their effects on sperm motility and viability under different experimental conditions. Incubation of sperm with mixtures of exogenous, unoxidized GPL results in their incorporation into sperm membranes, as shown by the use of fluorescent dyes attached to GPL. The percent overall (total) sperm motility was increased from 52±2.5% to 68±1.34% after adding GPL to the incubation media, and overall sperm motility was recovered from 7±2% after H2O2 treatment to 58±2.5%)(n = 8, p<0.01) by the incorporation of GPL into sperm membranes. When sperm were exposed to H2O2, the mitochondrial inner membrane potential (MIMP), monitored using the MIMP tracker dye JC-1 in flow cytometry, diminished, whereas the addition of GPL prevented the decrease in MIMP. Confocal microscopy with Rhodamine-123 and JC-1 confirmed the mitochondrial localization of the dyes. We conclude that incubation of human sperm with glycerolphospholipids into the membranes of sperm improves sperm viability, motility, and resistance to oxidizing agents like H2O2. This suggests that human sperm might be useful to test innovative new treatments like MLR, since such treatments could improve fertility when it is adversely affected by increased oxidative stress. PMID:29856778

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.

Sero-Diagnosis of Mycobacterium avium Complex Lung Disease Using Serum Immunoglobulin A Antibody against Glycopeptidolipid Antigen in Taiwan

PubMed Central

Wang, Jann-Tay; Jou, Ruwen; Wang, Jann-Yuan; Kobayashi, Kazuo; Lai, Hsin-Chih; Yu, Chong-Jen; Lee, Li-Na; Luh, Kwen-Tay

2013-01-01

Background Lung disease (LD) due to non-tuberculous mycobacteria is an important clinical concern. Mycobacterium avium complex (MAC) is one of the most common causative agents but the diagnosis of MAC-LD remains challenging. Detection of serum IgA antibody against MAC glycopeptidolipid (GPL) has recently been shown to improve the diagnosis of MAC-LD, but has yet to be validated worldwide. Methods This prospective study was conducted in a tertiary referral center in northern Taiwan and enrolled patients with MAC-LD, MAC contamination, other lung diseases, and control subjects. Serum immunoglobulin A (IgA) antibody against MAC-GPL was detected in the participants and its specificity and sensitivity was assessed. Results There were 56 patients with MAC-LD, 11 with MAC contamination, 13 M. kansasii-LD, 26 LD due to rapidly-growing mycobacteria (RGM), 48 pulmonary tuberculosis, and 42 household contacts of patients with TB. Patients with MAC-LD were older and 32% of them had an underlying co-morbidity. By logistic regression, serum MAC-GPL IgA level was an independent predictor of MAC-LD among the study subjects and those with culture-positive specimens for MAC. By the receiver operating characteristic curve, serum MAC-GPL IgA had a good power to discriminate MAC-LD from MAC contamination. Under the optimal cut-off value of 0.73 U/mL, its sensitivity and specificity were 60% and 91%, respectively. Among MAC-LD patients, presence of co-morbidity was associated with MAC-GPL <0.73 U/ml in logistic regression analysis. Conclusions Measurement of serum anti-MAC-GPL IgA level is useful for the diagnosis of MAC-LD. However, its implement in clinical practice for immuno-compromised hosts needs careful consideration. PMID:24260398

Exploratory Characterization of a Perfluoropolyether Oil as a Possible Viscosity Standard at Deepwater Production Conditions of 533 K and 241 MPa

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

Baled, Hseen O.; Tapriyal, Deepak; Morreale, Bryan D.

2013-08-29

DuPont’s perfluoropolyether oil Krytox® GPL 102 is a promising candidate for the high-temperature, high-pressure Deepwater viscosity standard (DVS). The preferred DVS is a thermally stable liquid that exhibits a viscosity of roughly 20 mPa∙s at 533 K and 241 MPa; a viscosity value representative of light oils found in ultra-deep formations beneath the deep waters of the Gulf of Mexico. A windowed rolling-ball viscometer designed by our team is used to determine the Krytox® GPL 102 viscosity at pressures to 245 MPa and temperatures of 311 K, 372 K, and 533 K. At 533 K and 243 MPa, the Krytox®more » GPL 102 viscosity is (27.2±1.3)mPa∙s. The rolling-ball viscometer viscosity results for Krytox® GPL 102 are correlated with an empirical 10-parameter surface fitting function that yields an MAPD of 3.9 %. A Couette rheometer is also used to measure the Krytox® GPL 102 viscosity, yielding a value of (26.2±1)mPa∙s at 533 K and 241 MPa. The results of this exploratory study suggest that Krytox®GPL 102 is a promising candidate for the DVS, primarily because this fluoroether oil is thermally stable and exhibits a viscosity closer to the targeted value of 20 mPa ∙ s at 533 K and 241 MPa than any other fluid reported to date. Finally and nonetheless, further studies must be conducted by other researcher groups using various types of viscometers and rheometers on samples of Krytox GPL® 102 from the same lot to further establish the properties of Krytox GPL® 102.« less

SeedVicious: Analysis of microRNA target and near-target sites.

PubMed

Marco, Antonio

2018-01-01

Here I describe seedVicious, a versatile microRNA target site prediction software that can be easily fitted into annotation pipelines and run over custom datasets. SeedVicious finds microRNA canonical sites plus other, less efficient, target sites. Among other novel features, seedVicious can compute evolutionary gains/losses of target sites using maximum parsimony, and also detect near-target sites, which have one nucleotide different from a canonical site. Near-target sites are important to study population variation in microRNA regulation. Some analyses suggest that near-target sites may also be functional sites, although there is no conclusive evidence for that, and they may actually be target alleles segregating in a population. SeedVicious does not aim to outperform but to complement existing microRNA prediction tools. For instance, the precision of TargetScan is almost doubled (from 11% to ~20%) when we filter predictions by the distance between target sites using this program. Interestingly, two adjacent canonical target sites are more likely to be present in bona fide target transcripts than pairs of target sites at slightly longer distances. The software is written in Perl and runs on 64-bit Unix computers (Linux and MacOS X). Users with no computing experience can also run the program in a dedicated web-server by uploading custom data, or browse pre-computed predictions. SeedVicious and its associated web-server and database (SeedBank) are distributed under the GPL/GNU license.

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

PubMed Central

2010-01-01

Background Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2. Results A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms. Conclusions MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses. PMID:20650010

Ab Initio Computation of Dynamical Properties: Pressure Broadening

NASA Astrophysics Data System (ADS)

Wiesenfeld, Laurent; Drouin, Brian

2014-06-01

Rotational spectroscopy of polar molecules is the main observational tool in many areas of astrophysics, for gases of low densities (n ˜ 102 - 108 cm-3). Spectral line shapes in astrophysical media are largely dominated by turbulence-induced Doppler effects and natural line broadening are negligible. However line broadening remains an important tool for denser gases, like planetary high atmospheres. Understanding the excitation schemes of polar molecules requires the knowledge of excitation transfer rate due to collisional excitation, between the polar molecule and the ambient gas, usually H2. Transport properties in ionized media also require a precise knowledge of momentum transfer rates by elastic collisions. In order to assess the theoretically computed cross section and energy/momentum transfer rates, direct absolute experiments are scarce. The best way is to measure not individual scattering events but rather the global effect of the buffer gas, thanks to the pressure broadening cross sections, whose magnitude can be measured without any scaling parameters. At low temperatures, both elastic and inelastic scattering amplitudes are tested. At higher temperature, depending on the interaction strength, only inelastic scattering cross section are shown to play a significant role 1 ,2. Thanks to the advances of computer capabilities, it has become practical to compute spectral line parameters fromab initio quantum chemistry. In particular, the theory of rotational line broadening is readily incorporated into scattering quantum dynamical theory, like close-coupling schemes. The only approximations used in the computation are the isolated collision/isolated line approximations. We compute the non-binding interaction potential with high precision quantum chemistry and fit the resulting ab initio points onto a suitable functional. We have recently computed several such systems, for molecules in H2 buffer gas: H2O,3 H2CO,4 HCO+ .5 Detailed computations taking into account the ortho or para state of H2 were performed, at temperatures ranging from 10 K to 100K, typically. Reliable results are found, that compare favorably to experiments. In particular, the water-molecular hydrogen system has been thoroughly computed and successfully experimentally tested 6. New projects consider other simple molecules as well as heavier systems, relevant for cometary comae and planetary high atmospheres. as part of the GNU EPrints system , and is freely redistributable under the GPL .

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

Clinical efficacy of anti-glycopeptidolipid-core IgA test for diagnosing Mycobacterium avium complex infection in lung.

PubMed

Numata, Takanori; Araya, Jun; Yoshii, Yutaka; Shimizu, Kenichiro; Hara, Hiromichi; Nakayama, Katsutoshi; Kuwano, Kazuyoshi

2015-11-01

It is difficult to verify the bacteriological diagnosis of Mycobacterium avium complex (MAC) infection. The anti-glycopeptidolipid (GPL)-core IgA antibody test was recently developed as a diagnostic method for MAC pulmonary disease. Only a few studies evaluate its clinical efficacy. We conducted retrospective evaluations of clinical characteristics of patients suspected of MAC infection to explore the usefulness of the anti-GPL-core IgA antibody test. We retrospectively evaluated 296 patients who were suspected to have MAC infection and underwent anti-GPL-core IgA antibody test between March 2013 and July 2014 in Jikei University hospital. A total of 29 patients were diagnosed with 'definite MAC' based on the American Thoracic Society (ATS) criteria with multiple identifications of MAC. On the other hand, 106 patients were diagnosed with other pulmonary diseases than MAC. The sensitivity and specificity of anti-GPL-core IgA antibody test for MAC diagnosis were 58.6% and 98.1%, respectively. The definite MAC group showed no significant differences in strains, treatment history or number of segments involved. The duration of MAC disease in the positive-antibody group was significantly longer than in the negative-antibody group (P = 0.046). A significant increase in the false-negative rate was observed in patients with malignant disease (P = 0.029). The anti-GPL-core IgA antibody test demonstrated high sensitivity and specificity for the diagnosis of MAC infection especially in patients without malignant diseases. © 2015 Asian Pacific Society of Respirology.

Amphibian-killing chytrid in Brazil comprises both locally endemic and globally expanding populations.

PubMed

Jenkinson, T S; Betancourt Román, C M; Lambertini, C; Valencia-Aguilar, A; Rodriguez, D; Nunes-de-Almeida, C H L; Ruggeri, J; Belasen, A M; da Silva Leite, D; Zamudio, K R; Longcore, J E; Toledo, F L; James, T Y

2016-07-01

Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is the emerging infectious disease implicated in recent population declines and extinctions of amphibian species worldwide. Bd strains from regions of disease-associated amphibian decline to date have all belonged to a single, hypervirulent clonal genotype (Bd-GPL). However, earlier studies in the Atlantic Forest of southeastern Brazil detected a novel, putatively enzootic lineage (Bd-Brazil), and indicated hybridization between Bd-GPL and Bd-Brazil. Here, we characterize the spatial distribution and population history of these sympatric lineages in the Brazilian Atlantic Forest. To investigate the genetic structure of Bd in this region, we collected and genotyped Bd strains along a 2400-km transect of the Atlantic Forest. Bd-Brazil genotypes were restricted to a narrow geographic range in the southern Atlantic Forest, while Bd-GPL strains were widespread and largely geographically unstructured. Bd population genetics in this region support the hypothesis that the recently discovered Brazilian lineage is enzootic in the Atlantic Forest of Brazil and that Bd-GPL is a more recently expanded invasive. We collected additional hybrid isolates that demonstrate the recurrence of hybridization between panzootic and enzootic lineages, thereby confirming the existence of a hybrid zone in the Serra da Graciosa mountain range of Paraná State. Our field observations suggest that Bd-GPL may be more infective towards native Brazilian amphibians, and potentially more effective at dispersing across a fragmented landscape. We also provide further evidence of pathogen translocations mediated by the Brazilian ranaculture industry with implications for regulations and policies on global amphibian trade. © 2016 John Wiley & Sons Ltd.

Hydraulic Conductivity of Geosynthetic Clay Liners to Low-Level Radioactive Waste Leachate

DOE PAGES

Tian, Kuo; Benson, Craig H.; Likos, William J.

2016-04-25

Hydraulic conductivity was evaluated for eight commercially available geosynthetic clay liners (GCLs) permeated with leachate characteristic of low-level radioactive waste (LLW) disposal facilities operated by the U.S. Department of Energy (DOE). Two of the GCLs (CS and GS) contained conventional sodium bentonite (Na-B). The others contained a bentonite–polymer mixture (CPL, CPH, GPL1, GPL2, and GPH) or bentonite–polymer composite (BPC). All GCLs (except GPL2 and GPH) were permeated directly with two synthetic LLW leachates that are essentially identical, except one has no radionuclides (nonradioactive synthetic leachate, or NSL) and the other has radionuclides (radioactive synthetic leachate, or RSL). Hydraulic conductivities tomore » RSL and NSL were identical. For the CS and GS GCLs, the hydraulic conductivity gradually increased by a factor of 5–25 because divalent cations in the leachate replaced native sodium cations bound to the bentonite. The CPL, GPL1, and GPL2 GCLs with low polymer loading (1.2–3.3%) had hydraulic conductivities similar to the conventional GCLs. In contrast, hydraulic conductivity of the CPH, GPH, and BPC GCLs with high polymer loading (≥5%) to RSL or NSL was comparable to, or lower than, the hydraulic conductivity to deionized water. Permeation with leachate reduced the swell index of the bentonite in all of the GCLs. A conceptual model featuring pore blocking by polymer hydrogel is proposed to explain why the hydraulic conductivity of bentonite–polymer GCLs to LLW leachates remains low even though the leachate inhibits bentonite swelling.« less

Hydraulic Conductivity of Geosynthetic Clay Liners to Low-Level Radioactive Waste Leachate

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

Tian, Kuo; Benson, Craig H.; Likos, William J.

Hydraulic conductivity was evaluated for eight commercially available geosynthetic clay liners (GCLs) permeated with leachate characteristic of low-level radioactive waste (LLW) disposal facilities operated by the U.S. Department of Energy (DOE). Two of the GCLs (CS and GS) contained conventional sodium bentonite (Na-B). The others contained a bentonite–polymer mixture (CPL, CPH, GPL1, GPL2, and GPH) or bentonite–polymer composite (BPC). All GCLs (except GPL2 and GPH) were permeated directly with two synthetic LLW leachates that are essentially identical, except one has no radionuclides (nonradioactive synthetic leachate, or NSL) and the other has radionuclides (radioactive synthetic leachate, or RSL). Hydraulic conductivities tomore » RSL and NSL were identical. For the CS and GS GCLs, the hydraulic conductivity gradually increased by a factor of 5–25 because divalent cations in the leachate replaced native sodium cations bound to the bentonite. The CPL, GPL1, and GPL2 GCLs with low polymer loading (1.2–3.3%) had hydraulic conductivities similar to the conventional GCLs. In contrast, hydraulic conductivity of the CPH, GPH, and BPC GCLs with high polymer loading (≥5%) to RSL or NSL was comparable to, or lower than, the hydraulic conductivity to deionized water. Permeation with leachate reduced the swell index of the bentonite in all of the GCLs. A conceptual model featuring pore blocking by polymer hydrogel is proposed to explain why the hydraulic conductivity of bentonite–polymer GCLs to LLW leachates remains low even though the leachate inhibits bentonite swelling.« less

Glycerophospholipid Supplementation as a Potential Intervention for Supporting Cerebral Structure in Older Adults

PubMed Central

Reddan, Jeffery M.; White, David J.; Macpherson, Helen; Scholey, Andrew; Pipingas, Andrew

2018-01-01

Modifying nutritional intake through supplementation may be efficacious for altering the trajectory of cerebral structural decline evident with increasing age. To date, there have been a number of clinical trials in older adults whereby chronic supplementation with B vitamins, omega-3 fatty acids, or resveratrol, has been observed to either slow the rate of decline or repair cerebral tissue. There is also some evidence from animal studies indicating that supplementation with glycerophospholipids (GPL) may benefit cerebral structure, though these effects have not yet been investigated in adult humans. Despite this paucity of research, there are a number of factors predicting poorer cerebral structure in older humans, which GPL supplementation appears to beneficially modify or protect against. These include elevated concentrations of homocysteine, unbalanced activity of reactive oxygen species both increasing the risk of oxidative stress, increased concentrations of pro-inflammatory messengers, as well as poorer cardio- and cerebrovascular function. As such, it is hypothesized that GPL supplementation will support cerebral structure in older adults. These cerebral effects may influence cognitive function. The current review aims to provide a theoretical basis for future clinical trials investigating the effects of GPL supplementation on cerebral structural integrity in older adults. PMID:29563868

The orbifolder: A tool to study the low-energy effective theory of heterotic orbifolds

NASA Astrophysics Data System (ADS)

Nilles, H. P.; Ramos-Sánchez, S.; Vaudrevange, P. K. S.; Wingerter, A.

2012-06-01

The orbifolder is a program developed in C++ that computes and analyzes the low-energy effective theory of heterotic orbifold compactifications. The program includes routines to compute the massless spectrum, to identify the allowed couplings in the superpotential, to automatically generate large sets of orbifold models, to identify phenomenologically interesting models (e.g. MSSM-like models) and to analyze their vacuum configurations. Program summaryProgram title: orbifolder Catalogue identifier: AELR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELR_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.: 145 572 No. of bytes in distributed program, including test data, etc.: 930 517 Distribution format: tar.gz Programming language:C++ Computer: Personal computer Operating system: Tested on Linux (Fedora 15, Ubuntu 11, SuSE 11) Word size: 32 bits or 64 bits Classification: 11.1 External routines: Boost (http://www.boost.org/), GSL (http://www.gnu.org/software/gsl/) Nature of problem: Calculating the low-energy spectrum of heterotic orbifold compactifications. Solution method: Quadratic equations on a lattice; representation theory; polynomial algebra. Running time: Less than a second per model.

Biana: a software framework for compiling biological interactions and analyzing networks

PubMed Central

2010-01-01

Background The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. Results We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. Conclusions BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules. PMID:20105306

Biana: a software framework for compiling biological interactions and analyzing networks.

PubMed

Garcia-Garcia, Javier; Guney, Emre; Aragues, Ramon; Planas-Iglesias, Joan; Oliva, Baldo

2010-01-27

The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

EggLib: processing, analysis and simulation tools for population genetics and genomics

PubMed Central

2012-01-01

Background With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. Results In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. Conclusions EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded. PMID:22494792

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.

PubMed

Chevrette, Marc G; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R; Medema, Marnix H

2017-10-15

Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use. Here, we introduce prediCAT, a new phylogenetics-inspired algorithm, which quantitatively estimates the degree of predictability of each A-domain. We then systematically benchmarked all algorithms on a newly gathered, independent test set of 434 A-domain sequences, showing that active-site-motif-based algorithms outperform whole-domain-based methods. Subsequently, we developed SANDPUMA, a powerful ensemble algorithm, based on newly trained versions of all high-performing algorithms, which significantly outperforms individual methods. Finally, we deployed SANDPUMA in a systematic investigation of 7635 Actinobacteria genomes, suggesting that NRP chemical diversity is much higher than previously estimated. SANDPUMA has been integrated into the widely used antiSMASH biosynthetic gene cluster analysis pipeline and is also available as an open-source, standalone tool. SANDPUMA is freely available at https://bitbucket.org/chevrm/sandpuma and as a docker image at https://hub.docker.com/r/chevrm/sandpuma/ under the GNU Public License 3 (GPL3). chevrette@wisc.edu or marnix.medema@wur.nl. 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

The new version 2.12 of BKG Ntrip Client (BNC)

NASA Astrophysics Data System (ADS)

Stürze, Andrea; Mervart, Leos; Weber, Georg; Rülke, Axel; Wiesensarter, Erwin; Neumaier, Peter

2016-04-01

A new version of the BKG Ntrip Client (BNC) has been released. Originally developed in cooperation of the Federal Agency for Cartography and Geodesy (BKG) and the Czech Technical University (CTU) with a focus on multi-stream real-time access to GPS observations, the software has once again been substantially extended. Promoting Open Standards as recommended by the Radio Technical Commission for Maritime Services (RTCM) remains the prime subject. Beside its Graphical User Interface (GUI), the real-time software for Windows, Linux, Mac, and Linux platforms now comes with complete Command Line Interface (CLI) and considerable post processing functionality. RINEX Version 3 file editing & Quality Check (QC) with full support of Galileo, BeiDou, and SBAS - besides GPS and GLONASS - is part of the new features. Comparison of satellite orbit/clock files in SP3 format is another fresh ability of BNC. Simultaneous multi-station Precise Point Positioning (PPP) for real-time displacement-monitoring of entire reference station networks is one more recent addition to BNC. Implemented RTCM messages for PPP (under development) comprise satellite orbit and clock corrections, code and phase observation biases, and the Vertical Total Electron Content (VTEC) of the ionosphere. The well established, mature codebase is mostly written in C++ language. Its publication under GNU GPL is thought to be well-suited for test, validation and demonstration of new approaches in precise real-time satellite navigation when IP streaming is involved. The poster highlights BNC features which are new in version 2.12 and beneficial to IAG institutions and services such as IGS/RT-IGS and to the interested public in general.

UManSysProp v1.0: an online and open-source facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, David; Barley, Mark; Bane, Michael K.; Higham, Nicholas; Aumont, Bernard; Dingle, Nicholas; McFiggans, Gordon

2016-03-01

In this paper we describe the development and application of a new web-based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include pure component vapour pressures, critical properties, and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN (cloud condensation nuclei) activation potential of mixed inorganic-organic aerosol particles; and absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES (Simplified Molecular Input Line Entry System) strings and UManSysProp will automatically extract the relevant information for calculations. Built using open-source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web interface, or can be accessed using the user's own code via a JSON API (application program interface). We also provide the source code for all predictive techniques provided on the site, covered by the GNU GPL (General Public License) license to encourage development of a user community. We have released this via a Github repository (doi:10.5281/zenodo.45143). In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

EggLib: processing, analysis and simulation tools for population genetics and genomics.

PubMed

De Mita, Stéphane; Siol, Mathieu

2012-04-11

With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded.

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.

PubMed

Mahmud, Md Pavel; Wiedenhoeft, John; Schliep, Alexander

2012-09-15

Mapping billions of reads from next generation sequencing experiments to reference genomes is a crucial task, which can require hundreds of hours of running time on a single CPU even for the fastest known implementations. Traditional approaches have difficulties dealing with matches of large edit distance, particularly in the presence of frequent or large insertions and deletions (indels). This is a serious obstacle both in determining the spectrum and abundance of genetic variations and in personal genomics. For the first time, we adopt the approximate string matching paradigm of geometric embedding to read mapping, thus rephrasing it to nearest neighbor queries in a q-gram frequency vector space. Using the L(1) distance between frequency vectors has the benefit of providing lower bounds for an edit distance with affine gap costs. Using a cache-oblivious kd-tree, we realize running times, which match the state-of-the-art. Additionally, running time and memory requirements are about constant for read lengths between 100 and 1000 bp. We provide a first proof-of-concept that geometric embedding is a promising paradigm for read mapping and that L(1) distance might serve to detect structural variations. TreQ, our initial implementation of that concept, performs more accurate than many popular read mappers over a wide range of structural variants. TreQ will be released under the GNU Public License (GPL), and precomputed genome indices will be provided for download at http://treq.sf.net. pavelm@cs.rutgers.edu Supplementary data are available at Bioinformatics online.

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees

PubMed Central

Mahmud, Md Pavel; Wiedenhoeft, John; Schliep, Alexander

2012-01-01

Motivation: Mapping billions of reads from next generation sequencing experiments to reference genomes is a crucial task, which can require hundreds of hours of running time on a single CPU even for the fastest known implementations. Traditional approaches have difficulties dealing with matches of large edit distance, particularly in the presence of frequent or large insertions and deletions (indels). This is a serious obstacle both in determining the spectrum and abundance of genetic variations and in personal genomics. Results: For the first time, we adopt the approximate string matching paradigm of geometric embedding to read mapping, thus rephrasing it to nearest neighbor queries in a q-gram frequency vector space. Using the L1 distance between frequency vectors has the benefit of providing lower bounds for an edit distance with affine gap costs. Using a cache-oblivious kd-tree, we realize running times, which match the state-of-the-art. Additionally, running time and memory requirements are about constant for read lengths between 100 and 1000 bp. We provide a first proof-of-concept that geometric embedding is a promising paradigm for read mapping and that L1 distance might serve to detect structural variations. TreQ, our initial implementation of that concept, performs more accurate than many popular read mappers over a wide range of structural variants. Availability and implementation: TreQ will be released under the GNU Public License (GPL), and precomputed genome indices will be provided for download at http://treq.sf.net. Contact: pavelm@cs.rutgers.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22962448

Contribution of glycerophospholipids and sphingomyelin to the circulating NEFA.

PubMed

Maier, Felicitas; Demmelmair, Hans; Fugmann, Marina; Hellmuth, Christian; Lechner, Andreas; Koletzko, Berthold; Uhl, Olaf

2016-07-01

Serum nonesterified fatty acids (NEFA) are known to be associated with the development of insulin resistance. Recently, differences in the NEFA profile were found in subjects with history of gestational diabetes (postGDM) and healthy controls. Little is known about the NEFA sources in the postprandial state, which prevails most of the day in humans in modern societies. In the present study, we aimed to explore the potential contributions of glycerophospholipid (GPL) and sphingomyelin (SM) fatty acids to the circulating NEFA. Serum-samples of 19 postGDM women and 20 controls were obtained in fasting state (t0) and 90 minutes (t90) after an oral glucose tolerance test. Fatty acid composition of NEFA and SM were analyzed with liquid chromatography coupled to triple quadrupole mass spectrometry and GPL by gas chromatography. The ratio of individual NEFA at t90 vs. t0 (t90/0-ratio) showed no difference between the two groups but increased with chain-length (7% for C16:1, 82% for C26:3). Only NEFA 10:0 was found with lower concentration at t0 and t90 in postGDM. At t90, long-chain polyunsaturated fatty acid correlated closely between NEFA and GPL in postGDM (20:5, 22:4, 22:5 and 22:6) and controls (20:3, 20:4 and 20:5). Very long-chain fatty acid 24:0 correlated significantly between NEFA and SM in postGDM and controls. Saturated and monounsaturated fatty acids correlated less between NEFA and GPL or SM. The NEFA composition varied highly between fasting and fed state in both groups. GPL appeared to contribute long-chain polyunsaturated fatty acid, while SM appeared to contribute very long-chain fatty acids to the NEFA pool. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nonlinear Buckling Analysis of Functionally Graded Graphene Reinforced Composite Shallow Arches with Elastic Rotational Constraints under Uniform Radial Load.

PubMed

Huang, Yonghui; Yang, Zhicheng; Liu, Airong; Fu, Jiyang

2018-05-28

The buckling behavior of functionally graded graphene platelet-reinforced composite (FG-GPLRC) shallow arches with elastic rotational constraints under uniform radial load is investigated in this paper. The nonlinear equilibrium equation of the FG-GPLRC shallow arch with elastic rotational constraints under uniform radial load is established using the Halpin-Tsai micromechanics model and the principle of virtual work, from which the critical buckling load of FG-GPLRC shallow arches with elastic rotational constraints can be obtained. This paper gives special attention to the effect of the GPL distribution pattern, weight fraction, geometric parameters, and the constraint stiffness on the buckling load. The numerical results show that all of the FG-GPLRC shallow arches with elastic rotational constraints have a higher buckling load-carrying capacity compared to the pure epoxy arch, and arches of the distribution pattern X have the highest buckling load among four distribution patterns. When the GPL weight fraction is constant, the thinner and larger GPL can provide the better reinforcing effect to the FG-GPLRC shallow arch. However, when the value of the aspect ratio is greater than 4, the flakiness ratio is greater than 103, and the effect of GPL's dimensions on the buckling load of the FG-GPLRC shallow arch is less significant. In addition, the buckling model of FG-GPLRC shallow arch with elastic rotational constraints is changed as the GPL distribution patterns or the constraint stiffness changes. It is expected that the method and the results that are presented in this paper will be useful as a reference for the stability design of this type of arch in the future.

Effects of Reorientation of Graphene Platelets (GPLs) on Young's Modulus of Polymer Composites under Bi-Axial Stretching.

PubMed

Feng, Chuang; Wang, Yu; Yang, Jie

2018-01-07

Effects of bi-axial stretching induced reorientation of graphene platelets (GPLs) on the Young's modulus of GPL/polymer composites is studied by Mori-Tanaka micromechanics model. The dispersion state of the GPLs in polymer matrix is captured by an orientation distribution function (ODF), in which two Euler angles are used to identify the orientation of the GPLs. Compared to uni-axial stretching, the increase of the stretching strain in the second direction enhances the re-alignment of GPL fillers in this direction while it deteriorates the re-alignment of the fillers in the other two directions. Comprehensive parametric study on the effects of the out-of-plane Young's modulus, stretching strain, strain ratio, Poisson's ratio and weight fraction and GPL dimension on the effective Young's moduli of the composites in the three directions are conducted. It is found that the out-of-plane Young's modulus has limited effects on the overall Young's modulus of the composites. The second stretching enhances the Young's modulus in this direction while it decreases the Young's modulus in the other two directions. The results demonstrate the increase of Poisson's ratio is favorable in increasing the Young's modulus of the composites. GPLs with larger diameter-to-thickness ratio have better reinforcing effect on the Young's modulus of GPL/polymer nanocomposites.

Proliferative Glioblastoma Cancer Cells Exhibit Persisting Temporal Control of Metabolism and Display Differential Temporal Drug Susceptibility in Chemotherapy.

PubMed

Wagner, Paula M; Sosa Alderete, Lucas G; Gorné, Lucas D; Gaveglio, Virginia; Salvador, Gabriela; Pasquaré, Susana; Guido, Mario E

2018-06-07

Even in immortalized cell lines, circadian clocks regulate physiological processes in a time-dependent manner, driving transcriptional and metabolic rhythms, the latter being able to persist without transcription. Circadian rhythm disruptions in modern life (shiftwork, jetlag, etc.) may lead to higher cancer risk. Here, we investigated whether the human glioblastoma T98G cells maintained quiescent or under proliferation keep a functional clock and whether cells display differential time responses to bortezomib chemotherapy. In arrested cultures, mRNAs for clock (Per1, Rev-erbα) and glycerophospholipid (GPL)-synthesizing enzyme genes, 32 P-GPL labeling, and enzyme activities exhibited circadian rhythmicity; oscillations were also found in the redox state/peroxiredoxin oxidation. In proliferating cells, rhythms of gene expression were lost or their periodicity shortened whereas the redox and GPL metabolisms continued to fluctuate with a similar periodicity as under arrest. Cell viability significantly changed over time after bortezomib treatment; however, this rhythmicity and the redox cycles were altered after Bmal1 knock-down, indicating cross-talk between the transcriptional and the metabolic oscillators. An intrinsic metabolic clock continues to function in proliferating cells, controlling diverse metabolisms and highlighting differential states of tumor suitability for more efficient, time-dependent chemotherapy when the redox state is high and GPL metabolism low.

The mouse liver displays daily rhythms in the metabolism of phospholipids and in the activity of lipid synthesizing enzymes.

PubMed

Gorné, Lucas D; Acosta-Rodríguez, Victoria A; Pasquaré, Susana J; Salvador, Gabriela A; Giusto, Norma M; Guido, Mario Eduardo

2015-02-01

The circadian system involves central and peripheral oscillators regulating temporally biochemical processes including lipid metabolism; their disruption leads to severe metabolic diseases (obesity, diabetes, etc). Here, we investigated the temporal regulation of glycerophospholipid (GPL) synthesis in mouse liver, a well-known peripheral oscillator. Mice were synchronized to a 12:12 h light-dark (LD) cycle and then released to constant darkness with food ad libitum. Livers collected at different times exhibited a daily rhythmicity in some individual GPL content with highest levels during the subjective day. The activity of GPL-synthesizing/remodeling enzymes: phosphatidate phosphohydrolase 1 (PAP-1/lipin) and lysophospholipid acyltransferases (LPLATs) also displayed significant variations, with higher levels during the subjective day and at dusk. We evaluated the temporal regulation of expression and activity of phosphatidylcholine (PC) synthesizing enzymes. PC is mainly synthesized through the Kennedy pathway with Choline Kinase (ChoK) as a key regulatory enzyme or through the phosphatidylethanolamine (PE) N-methyltransferase (PEMT) pathway. The PC/PE content ratio exhibited a daily variation with lowest levels at night, while ChoKα and PEMT mRNA expression displayed maximal levels at nocturnal phases. Our results demonstrate that mouse liver GPL metabolism oscillates rhythmically with a precise temporal control in the expression and/or activity of specific enzymes.

Amphibian Symbiotic Bacteria Do Not Show a Universal Ability To Inhibit Growth of the Global Panzootic Lineage of Batrachochytrium dendrobatidis.

PubMed

Antwis, Rachael E; Preziosi, Richard F; Harrison, Xavier A; Garner, Trenton W J

2015-06-01

Microbiomes associated with multicellular organisms influence the disease susceptibility of hosts. The potential exists for such bacteria to protect wildlife from infectious diseases, particularly in the case of the globally distributed and highly virulent fungal pathogen Batrachochytrium dendrobatidis of the global panzootic lineage (B. dendrobatidis GPL), responsible for mass extinctions and population declines of amphibians. B. dendrobatidis GPL exhibits wide genotypic and virulence variation, and the ability of candidate probiotics to restrict growth across B. dendrobatidis isolates has not previously been considered. Here we show that only a small proportion of candidate probiotics exhibited broad-spectrum inhibition across B. dendrobatidis GPL isolates. Moreover, some bacterial genera showed significantly greater inhibition than others, but overall, genus and species were not particularly reliable predictors of inhibitory capabilities. These findings indicate that bacterial consortia are likely to offer a more stable and effective approach to probiotics, particularly if related bacteria are selected from genera with greater antimicrobial capabilities. Together these results highlight a complex interaction between pathogens and host-associated symbiotic bacteria that will require consideration in the development of bacterial probiotics for wildlife conservation. Future efforts to construct protective microbiomes should incorporate bacteria that exhibit broad-spectrum inhibition of B. dendrobatidis GPL isolates. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Genomic epidemiology of the emerging pathogen Batrachochytrium dendrobatidis from native and invasive amphibian species in Chile.

PubMed

Valenzuela-Sánchez, A; O'Hanlon, S J; Alvarado-Rybak, M; Uribe-Rivera, D E; Cunningham, A A; Fisher, M C; Soto-Azat, C

2018-04-01

Emerging fungal diseases represent a threat to food security, animal and human health worldwide. Amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has been associated with catastrophic and well-documented amphibian population declines and extinctions. For the first time, Bd was cultured from native and non-native wild amphibians in Chile. Phylogenomic analyses revealed that Chilean isolates AVS2, AVS4 and AVS7 group within the global panzootic lineage of Bd (BdGPL) in a single highly supported clade that includes a genotype previously isolated from the United Kingdom. Our results extend the known distribution of BdGPL in South America and suggest a single and relatively recent introduction of BdGPL into the country, providing additional support to the role of anthropogenic activity in the global spread of this panzootic lineage. © 2017 Blackwell Verlag GmbH.

CIF2Cell: Generating geometries for electronic structure programs

NASA Astrophysics Data System (ADS)

Björkman, Torbjörn

2011-05-01

The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP. Program summaryProgram title: CIF2Cell Catalogue identifier: AEIM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL version 3 No. of lines in distributed program, including test data, etc.: 12 691 No. of bytes in distributed program, including test data, etc.: 74 933 Distribution format: tar.gz Programming language: Python (versions 2.4-2.7) Computer: Any computer that can run Python (versions 2.4-2.7) Operating system: Any operating system that can run Python (versions 2.4-2.7) Classification: 7.3, 7.8, 8 External routines: PyCIFRW [1] Nature of problem: Generate the geometrical setup of a crystallographic cell for a variety of electronic structure programs from data contained in a CIF file. Solution method: The CIF file is parsed using routines contained in the library PyCIFRW [1], and crystallographic as well as bibliographic information is extracted. The program then generates the principal cell from symmetry information, crystal parameters, space group number and Wyckoff sites. Reduction to a primitive cell is then performed, and the resulting cell is output to suitably named files along with documentation of the information source generated from any bibliographic information contained in the CIF file. If the space group symmetries is not present in the CIF file the program will fall back on internal tables, so only the minimal input of space group, crystal parameters and Wyckoff positions are required. Additional key features are handling of alloys and supercell generation. Additional comments: Currently implements support for the following general purpose electronic structure programs: ABINIT [2,3], CASTEP [4], CPMD [5], Crystal [6], Elk [7], exciting [8], EMTO [9], Fleur [10], RSPt [11], Siesta [12] and VASP [13-16]. Running time: The examples provided in the distribution take only seconds to run.

Effects of Reorientation of Graphene Platelets (GPLs) on Young’s Modulus of Polymer Composites under Bi-Axial Stretching

PubMed Central

Yang, Jie

2018-01-01

Effects of bi-axial stretching induced reorientation of graphene platelets (GPLs) on the Young’s modulus of GPL/polymer composites is studied by Mori-Tanaka micromechanics model. The dispersion state of the GPLs in polymer matrix is captured by an orientation distribution function (ODF), in which two Euler angles are used to identify the orientation of the GPLs. Compared to uni-axial stretching, the increase of the stretching strain in the second direction enhances the re-alignment of GPL fillers in this direction while it deteriorates the re-alignment of the fillers in the other two directions. Comprehensive parametric study on the effects of the out-of-plane Young’s modulus, stretching strain, strain ratio, Poisson’s ratio and weight fraction and GPL dimension on the effective Young’s moduli of the composites in the three directions are conducted. It is found that the out-of-plane Young’s modulus has limited effects on the overall Young’s modulus of the composites. The second stretching enhances the Young’s modulus in this direction while it decreases the Young’s modulus in the other two directions. The results demonstrate the increase of Poisson’s ratio is favorable in increasing the Young’s modulus of the composites. GPLs with larger diameter-to-thickness ratio have better reinforcing effect on the Young’s modulus of GPL/polymer nanocomposites. PMID:29316669

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences.

PubMed

Gupta, Parth Sarthi Sen; Banerjee, Shyamashree; Islam, Rifat Nawaz Ul; Mondal, Sudipta; Mondal, Buddhadev; Bandyopadhyay, Amal K

2014-01-01

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in.

PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences

PubMed Central

Gupta, Parth Sarthi Sen; Banerjee, Shyamashree; Islam, Rifat Nawaz Ul; Mondal, Sudipta; Mondal, Buddhadev; Bandyopadhyay, Amal K

2014-01-01

In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. Availability PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in PMID:24616564

Resolution of singularities for multi-loop integrals

NASA Astrophysics Data System (ADS)

Bogner, Christian; Weinzierl, Stefan

2008-04-01

We report on a program for the numerical evaluation of divergent multi-loop integrals. The program is based on iterated sector decomposition. We improve the original algorithm of Binoth and Heinrich such that the program is guaranteed to terminate. The program can be used to compute numerically the Laurent expansion of divergent multi-loop integrals regulated by dimensional regularisation. The symbolic and the numerical steps of the algorithm are combined into one program. Program summaryProgram title: sector_decomposition Catalogue identifier: AEAG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAG_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.: 47 506 No. of bytes in distributed program, including test data, etc.: 328 485 Distribution format: tar.gz Programming language: C++ Computer: all Operating system: Unix RAM: Depending on the complexity of the problem Classification: 4.4 External routines: GiNaC, available from http://www.ginac.de, GNU scientific library, available from http://www.gnu.org/software/gsl Nature of problem: Computation of divergent multi-loop integrals. Solution method: Sector decomposition. Restrictions: Only limited by the available memory and CPU time. Running time: Depending on the complexity of the problem.

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/.

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.

CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.

PubMed

Fidaner, Işık Barış; Cankorur-Cetinkaya, Ayca; Dikicioglu, Duygu; Kirdar, Betul; Cemgil, Ali Taylan; Oliver, Stephen G

2016-02-01

Simple bioinformatic tools are frequently used to analyse time-series datasets regardless of their ability to deal with transient phenomena, limiting the meaningful information that may be extracted from them. This situation requires the development and exploitation of tailor-made, easy-to-use and flexible tools designed specifically for the analysis of time-series datasets. We present a novel statistical application called CLUSTERnGO, which uses a model-based clustering algorithm that fulfils this need. This algorithm involves two components of operation. Component 1 constructs a Bayesian non-parametric model (Infinite Mixture of Piecewise Linear Sequences) and Component 2, which applies a novel clustering methodology (Two-Stage Clustering). The software can also assign biological meaning to the identified clusters using an appropriate ontology. It applies multiple hypothesis testing to report the significance of these enrichments. The algorithm has a four-phase pipeline. The application can be executed using either command-line tools or a user-friendly Graphical User Interface. The latter has been developed to address the needs of both specialist and non-specialist users. We use three diverse test cases to demonstrate the flexibility of the proposed strategy. In all cases, CLUSTERnGO not only outperformed existing algorithms in assigning unique GO term enrichments to the identified clusters, but also revealed novel insights regarding the biological systems examined, which were not uncovered in the original publications. The C++ and QT source codes, the GUI applications for Windows, OS X and Linux operating systems and user manual are freely available for download under the GNU GPL v3 license at http://www.cmpe.boun.edu.tr/content/CnG. sgo24@cam.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Open Source Software Openfoam as a New Aerodynamical Simulation Tool for Rocket-Borne Measurements

NASA Astrophysics Data System (ADS)

Staszak, T.; Brede, M.; Strelnikov, B.

2015-09-01

The only way to do in-situ measurements, which are very important experimental studies for atmospheric science, in the mesoshere/lower thermosphere (MLT) is to use sounding rockets. The drawback of using rockets is the shock wave appearing because of the very high speed of the rocket motion (typically about 1000 mIs). This shock wave disturbs the density, the temperature and the velocity fields in the vicinity of the rocket, compared to undisturbed values of the atmosphere. This effect, however, can be quantified and the measured data has to be corrected not just to make it more precise but simply usable. The commonly accepted and widely used tool for this calculations is the Direct Simulation Monte Carlo (DSMC) technique developed by GA. Bird which is available as stand-alone program limited to use a single processor. Apart from complications with simulations of flows around bodies related to different flow regimes in the altitude range of MLT, that rise due to exponential density change by several orders of magnitude, a particular hardware configuration introduces significant difficulty for aerodynamical calculations due to choice of the grid sizes mainly depending on the demands on adequate DSMCs and good resolution of geometries with scale differences of factor of iO~. This makes either the calculation time unreasonably long or even prevents the calculation algorithm from converging. In this paper we apply the free open source software OpenFOAM (licensed under GNU GPL) for a three-dimensional CFD-Simulation of a flow around a sounding rocket instrumentation. An advantage of this software package, among other things, is that it can run on high performance clusters, which are easily scalable. We present the first results and discuss the potential of the new tool in applications for sounding rockets.

Domain similarity based orthology detection.

PubMed

Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

2015-05-13

Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in MATLAB.

PubMed

Sinha, Shriprakash

2016-12-01

Simulation study in systems biology involving computational experiments dealing with Wnt signaling pathways abound in literature but often lack a pedagogical perspective that might ease the understanding of beginner students and researchers in transition, who intend to work on the modeling of the pathway. This paucity might happen due to restrictive business policies which enforce an unwanted embargo on the sharing of important scientific knowledge. A tutorial introduction to computational modeling of Wnt signaling pathway in a human colorectal cancer dataset using static Bayesian network models is provided. The walkthrough might aid biologists/informaticians in understanding the design of computational experiments that is interleaved with exposition of the Matlab code and causal models from Bayesian network toolbox. The manuscript elucidates the coding contents of the advance article by Sinha (Integr. Biol. 6:1034-1048, 2014) and takes the reader in a step-by-step process of how (a) the collection and the transformation of the available biological information from literature is done, (b) the integration of the heterogeneous data and prior biological knowledge in the network is achieved, (c) the simulation study is designed, (d) the hypothesis regarding a biological phenomena is transformed into computational framework, and (e) results and inferences drawn using d -connectivity/separability are reported. The manuscript finally ends with a programming assignment to help the readers get hands-on experience of a perturbation project. Description of Matlab files is made available under GNU GPL v3 license at the Google code project on https://code.google.com/p/static-bn-for-wnt-signaling-pathway and https: //sites.google.com/site/shriprakashsinha/shriprakashsinha/projects/static-bn-for-wnt-signaling-pathway. Latest updates can be found in the latter website.

BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs

PubMed Central

Eklund, Anders; Dufort, Paul; Villani, Mattias; LaConte, Stephen

2014-01-01

Analysis of functional magnetic resonance imaging (fMRI) data is becoming ever more computationally demanding as temporal and spatial resolutions improve, and large, publicly available data sets proliferate. Moreover, methodological improvements in the neuroimaging pipeline, such as non-linear spatial normalization, non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approaches, can dramatically increase the computational burden. Despite these challenges, there do not yet exist any fMRI software packages which leverage inexpensive and powerful graphics processing units (GPUs) to perform these analyses. Here, we therefore present BROCCOLI, a free software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. BROCCOLI has, for example, been tested with an Intel CPU, an Nvidia GPU, and an AMD GPU. These tests show that parallel processing of fMRI data can lead to significantly faster analysis pipelines. This speedup can be achieved on relatively standard hardware, but further, dramatic speed improvements require only a modest investment in GPU hardware. BROCCOLI (running on a GPU) can perform non-linear spatial normalization to a 1 mm3 brain template in 4–6 s, and run a second level permutation test with 10,000 permutations in about a minute. These non-parametric tests are generally more robust than their parametric counterparts, and can also enable more sophisticated analyses by estimating complicated null distributions. Additionally, BROCCOLI includes support for Bayesian first-level fMRI analysis using a Gibbs sampler. The new software is freely available under GNU GPL3 and can be downloaded from github (https://github.com/wanderine/BROCCOLI/). PMID:24672471

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

PubMed

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

2005-06-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

The Role of a Platelet Lysate-Based Compartmentalized System as a Carrier of Cells and Platelet-Origin Cytokines for Periodontal Tissue Regeneration.

PubMed

Babo, Pedro S; Cai, Xinjie; Plachokova, Adelina S; Reis, Rui L; Jansen, John A; Gomes, Manuela E; Walboomers, X Frank

2016-10-01

Currently available clinical therapies are not capable to regenerate tissues that are lost by periodontitis. Tissue engineering can be applied as a strategy to regenerate reliably the tissues and function of damaged periodontium. A prerequisite for this regeneration is the colonization of the defect with the adequate cell populations. In this study, we proposed a bilayered system composed of (1) a platelet lysate (PL)-based construct produced by crosslinking of PL proteins with genipin (gPL) for the delivery of rat periodontal ligament cells (rat-PDLCs); combined with (2) an injectable composite consisting of calcium phosphate cement incorporated with PL-loaded poly(d, l-lactic-co-glycolic acid) microspheres. This system was expected to promote periodontal regeneration by the delivery of adequate progenitor cells and providing a stable system enriched with adequate cytokines and growth factors for the orchestration of tissue regrowth in periodontal defects. The bilayered system was tested in a three-wall intrabony defect in rats and the healing of periodontal tissue was assessed 6 weeks after surgery. Results showed that the bilayered system was able to promote the regrowth of functional periodontal tissues, both with (cells + gPL) and without the loading of PDLCs (gPL). Significant connective tissue attachment (45.0 ± 15.0% and 64.0 ± 15.0% for gPL and cells + gPL group, respectively) and new bone area (33.8 ± 21% and 21.3 ± 3% for gPL and cells + gPL group, respectively) were observed. Nevertheless, rat PDLCs delivered with gPL construct in the defect area were hardly visible 6 weeks after surgery and did not contribute for the regeneration of new periodontal tissue. Overall, our findings show that the bilayered system promotes the stabilization of PL proteins on the root surface and has a positive effect in the repair of periodontal tissues both in quality and in quantity.

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

NASA Technical Reports Server (NTRS)

Reyes, Miguel A. De Jesus

2014-01-01

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

A Comparison of DESI-MS and LC-MS for the Lipidomic Profiling of Human Cancer Tissue

NASA Astrophysics Data System (ADS)

Abbassi-Ghadi, Nima; Jones, Emrys A.; Gomez-Romero, Maria; Golf, Ottmar; Kumar, Sacheen; Huang, Juzheng; Kudo, Hiromi; Goldin, Rob D.; Hanna, George B.; Takats, Zoltan

2016-02-01

In this study, we make a direct comparison between desorption electrospray ionization-mass spectrometry (DESI-MS) and ultraperformance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS) platforms for the profiling of glycerophospholipid (GPL) species in esophageal cancer tissue. In particular, we studied the similarities and differences in the range of GPLs detected and the congruency of their relative abundances as detected by each analytical platform. The main differences between mass spectra of the two modalities were found to be associated with the variance in adduct formation of common GPLs, rather than the presence of different GPL species. Phosphatidylcholines as formate adducts in UPLC-ESI-MS accounted for the majority of differences in negative ion mode and alkali metal adducts of phosphatidylcholines in DESI-MS for positive ion mode. Comparison of the relative abundance of GPLs, normalized to a common peak, revealed a correlation coefficient of 0.70 ( P < 0.001). The GPL profile detected by DESI-MS is congruent to UPLC-ESI-MS, which reaffirms the role of DESI-MS for lipidomic profiling and a potential premise for quantification.

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/

Effet des Plastifiants sur la Temperature de Transition Vitreuse, Tg, du Butadiene a Terminaison Hydroxy et du Polyazoture de Glycidyle - Simulations et Experiences (Effect of the Plasticizers on the Vitreous Transition Temperature, Tg, of the Butadiene to Termination Hydroxy and the Polyazoture of Glycidyle - Simulations and Experiences)

DTIC Science & Technology

2008-09-01

diverses temperatures 26 a) HTPB pur b) HTPB-DOA (polymere et plastifiant) c) GAP pur d) Gpl pur e)Gap-Gpl Liste des tableaux Tableau 1...Composition des mailles amorphes construites 11 Tableau 2. Proprietes des polymeres et plastifiants utilises 11 Tableau 3. Comparaisons entre les Tt...obtenues experimentalement, les T% publiees dans les ecrits scientifiques et celles predites a partir des 7"gdes composes purs 19 Tableau 4. Comparaison

Effects of scan rate on the corrosion behavior SS 304 stainless steel in the nanofluid measured by Tafel polarization methods

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

Prajitno, Djoko Hadi

The Effects of scan rate on the Tafel polarization curve that is obtained to determine corrosion rate are conducted. The tafel polarization curves are obtained at different scan rates for Stainless Steel 304 in nanofluids contain 0.01 gpl nano particle ZrO{sub 2}. The corrosion stainless steel in nanofluid contains adm+0.01 gpl ZrO{sub 2} nanoparticles at different scan rate was performed by Tafel polarization. The results show that according corrosion potential examination of the stainless steel in nanofluid media 0.01gpl ZrO{sub 2} nanoparticle was actively corroded. The value of cathodic Tafel slope stainless steel in nanofluid at different scan rate relativelymore » unchanged after polarization testing. Mean while the value of anodic Tafel slope stainless steel in nanofluid increase at different scan rate. The results of Tafel polarization technique show that corrosion rate of stainless steel in nanofluid increase with increasing scan rate. X ray diffraction examination of stainless steel after Tafel polarization depict that γ Fe phase is major phase in the surface of alloy.« less

WIRGO in TIC's? [What (on Earth) is Really Going On in Terrestrial Impact Craters?

NASA Astrophysics Data System (ADS)

Dence, Michael R.

2003-02-01

Canada is well endowed with impact craters formed in crystalline rocks with relatively homogeneous physical properties. They exhibit all the main morphological-structural variations with crater size seen in craters on other rocky planets, from small simple bowl to large peak and ring forms. Lacking stratigraphy, analysis is based on the imprint of shock melting and metamorphism, the position of the GPL (limit of initial Grady-Kipp fracturing due to shock wave reverberations) relative to shock level, the geometry of late stage shears and breccias and the volume of shocked material beyond the GPL. Simple craters, exemplified by Brent (D = 3.7 km) allow direct comparison with models and experimental data. Results of interest include: 1. The central pool of impact melt and underlying breccia at the base of the crater fill is interpreted as the remnant of the transient crater lining; 2. The overlying main mass of breccias filling the final apparent crater results from latestage slumping of large slabs bounded by a primary shear surface that conforms to a sphere segment of radius, rs approx. = 2dtc, where dtc is the transient crater depth; 3. The foot of the primary shear intersects above the GPL at the centre of the melt pool and the rapid emplacement of slumped slabs produces further brecciation while suppressing any tendency for the centre to rise. In the autochthonous breccias below the melt and in the underlying para-allochthone below the GPL, shock metamorphism weakens with depth. The apparent attenuation of the shock pulse can be compared with experimentally derived rates of attenuation to give a measure of displacements down axis and estimates of the size of a nominal bolide of given velocity, the volume of impact melt and the energy released on impact. In larger complex craters (e.g. Charlevoix, D = 52 km) apparent shock attenuation is low near the centre but is higher towards the margin. The inflection point marks the change from uplift of deep material in the centre to subsidence of near-surface material at the margins. From the observed general relationship PGPL = 3.5 D0.5, where PGPL (in GPa) is the estimated level of shock metamorphism at the Grady-Kipp fracture limit, it is apparent that the differential stress due to shock wave reflections weakens at about twice the attenuation rate of the initial shock pulse. Thus, with increasing size, compression of the para-authochthone below the GPL plays an increasingly larger role in controlling the depth of the transient crater and hence the radius of the primary shear. It follows that, where the rate of relaxation of the para-authochthone is more rapid than the propagation of the primary shear from the rim towards the centre, the shear surface intersects below the GPL and central uplift occurs.

A Constant Envelope OFDM Implementation on GNU Radio

DTIC Science & Technology

2015-02-02

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

MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics.

PubMed

Hunter, Adam; Dayalan, Saravanan; De Souza, David; Power, Brad; Lorrimar, Rodney; Szabo, Tamas; Nguyen, Thu; O'Callaghan, Sean; Hack, Jeremy; Pyke, James; Nahid, Amsha; Barrero, Roberto; Roessner, Ute; Likic, Vladimir; Tull, Dedreia; Bacic, Antony; McConville, Malcolm; Bellgard, Matthew

2017-01-01

An increasing number of research laboratories and core analytical facilities around the world are developing high throughput metabolomic analytical and data processing pipelines that are capable of handling hundreds to thousands of individual samples per year, often over multiple projects, collaborations and sample types. At present, there are no Laboratory Information Management Systems (LIMS) that are specifically tailored for metabolomics laboratories that are capable of tracking samples and associated metadata from the beginning to the end of an experiment, including data processing and archiving, and which are also suitable for use in large institutional core facilities or multi-laboratory consortia as well as single laboratory environments. Here we present MASTR-MS, a downloadable and installable LIMS solution that can be deployed either within a single laboratory or used to link workflows across a multisite network. It comprises a Node Management System that can be used to link and manage projects across one or multiple collaborating laboratories; a User Management System which defines different user groups and privileges of users; a Quote Management System where client quotes are managed; a Project Management System in which metadata is stored and all aspects of project management, including experimental setup, sample tracking and instrument analysis, are defined, and a Data Management System that allows the automatic capture and storage of raw and processed data from the analytical instruments to the LIMS. MASTR-MS is a comprehensive LIMS solution specifically designed for metabolomics. It captures the entire lifecycle of a sample starting from project and experiment design to sample analysis, data capture and storage. It acts as an electronic notebook, facilitating project management within a single laboratory or a multi-node collaborative environment. This software is being developed in close consultation with members of the metabolomics research community. It is freely available under the GNU GPL v3 licence and can be accessed from, https://muccg.github.io/mastr-ms/.

Repeat-aware modeling and correction of short read errors.

PubMed

Yang, Xiao; Aluru, Srinivas; Dorman, Karin S

2011-02-15

High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of kmers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous kmer may be frequently observed if it has few nucleotide differences with valid kmers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content. We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of kmers from their observed frequencies by analyzing the misread relationships among observed kmers. We also propose a method to estimate the threshold useful for validating kmers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at "http://aluru-sun.ece.iastate.edu/doku.php?id = redeem". We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors for genomes with high repeat content.

OPM: The Open Porous Media Initiative

NASA Astrophysics Data System (ADS)

Flemisch, B.; Flornes, K. M.; Lie, K.; Rasmussen, A.

2011-12-01

The principal objective of the Open Porous Media (OPM) initiative is to develop a simulation suite that is capable of modeling industrially and scientifically relevant flow and transport processes in porous media and bridge the gap between the different application areas of porous media modeling, including reservoir mechanics, CO2 sequestration, biological systems, and product development of engineered media. The OPM initiative will provide a long-lasting, efficient, and well-maintained open-source software for flow and transport in porous media built on modern software principles. The suite is released under the GNU General Public License (GPL). Our motivation is to provide a means to unite industry and public research on simulation of flow and transport in porous media. For academic users, we seek to provide a software infrastructure that facilitates testing of new ideas on models with industry-standard complexity, while at the same time giving the researcher control over discretization and solvers. Similarly, we aim to accelerate the technology transfer from academic institutions to professional companies by making new research results available as free software of professional standard. The OPM initiative is currently supported by six research groups in Norway and Germany and funded by existing grants from public research agencies as well as from Statoil Petroleum and Total E&P Norge. However, a full-scale development of the OPM initiative requires substantially more funding and involvement of more research groups and potential end users. In this talk, we will provide an overview of the current activities in the OPM initiative. Special emphasis will be given to the demonstration of the synergies achieved by combining the strengths of individual open-source software components. In particular, a new fully implicit solver developed within the DUNE-based simulator DuMux could be enhanced by the ability to read industry-standard Eclipse input files and to run on grids given in corner-point format. Examples taken from the SPE comparative solution projects and CO2 sequestration benchmarks illustrate the current capabilities of the simulation suite.

sedFlow - a tool for simulating fractional bedload transport and longitudinal profile evolution in mountain streams

NASA Astrophysics Data System (ADS)

Heimann, F. U. M.; Rickenmann, D.; Turowski, J. M.; Kirchner, J. W.

2015-01-01

Especially in mountainous environments, the prediction of sediment dynamics is important for managing natural hazards, assessing in-stream habitats and understanding geomorphic evolution. We present the new modelling tool {sedFlow} for simulating fractional bedload transport dynamics in mountain streams. sedFlow is a one-dimensional model that aims to realistically reproduce the total transport volumes and overall morphodynamic changes resulting from sediment transport events such as major floods. The model is intended for temporal scales from the individual event (several hours to few days) up to longer-term evolution of stream channels (several years). The envisaged spatial scale covers complete catchments at a spatial discretisation of several tens of metres to a few hundreds of metres. sedFlow can deal with the effects of streambeds that slope uphill in a downstream direction and uses recently proposed and tested approaches for quantifying macro-roughness effects in steep channels. sedFlow offers different options for bedload transport equations, flow-resistance relationships and other elements which can be selected to fit the current application in a particular catchment. Local grain-size distributions are dynamically adjusted according to the transport dynamics of each grain-size fraction. sedFlow features fast calculations and straightforward pre- and postprocessing of simulation data. The high simulation speed allows for simulations of several years, which can be used, e.g., to assess the long-term impact of river engineering works or climate change effects. In combination with the straightforward pre- and postprocessing, the fast calculations facilitate efficient workflows for the simulation of individual flood events, because the modeller gets the immediate results as direct feedback to the selected parameter inputs. The model is provided together with its complete source code free of charge under the terms of the GNU General Public License (GPL) (www.wsl.ch/sedFlow). Examples of the application of sedFlow are given in a companion article by Heimann et al. (2015).

Inexpensive Open-Source Data Logging in the Field

NASA Astrophysics Data System (ADS)

Wickert, A. D.

2013-12-01

I present a general-purpose open-source field-capable data logger, which provides a mechanism to develop dense networks of inexpensive environmental sensors. This data logger was developed as a low-power variant of the Arduino open-source development system, and is named the ALog ("Arduino Logger") BottleLogger (it is slim enough to fit inside a Nalgene water bottle) version 1.0. It features an integrated high-precision real-time clock, SD card slot for high-volume data storage, and integrated power switching. The ALog can interface with sensors via six analog/digital pins, two digital pins, and one digital interrupt pin that can read event-based inputs, such as those from a tipping-bucket rain gauge. We have successfully tested the ALog BottleLogger with ultrasonic rangefinders (for water stage and snow accumulation and melt), temperature sensors, tipping-bucket rain gauges, soil moisture and water potential sensors, resistance-based tools to measure frost heave, and cameras that it triggers based on events. The source code for the ALog, including functions to interface with a a range of commercially-available sensors, is provided as an Arduino C++ library with example implementations. All schematics, circuit board layouts, and source code files are open-source and freely available under GNU GPL v3.0 and Creative Commons Attribution-ShareAlike 3.0 Unported licenses. Through this work, we hope to foster a community-driven movement to collect field environmental data on a budget that permits citizen-scientists and researchers from low-income countries to collect the same high-quality data as researchers in wealthy countries. These data can provide information about global change to managers, governments, scientists, and interested citizens worldwide. Watertight box with ALog BottleLogger data logger on the left and battery pack with 3 D cells on the right. Data can be collected for 3-5 years on one set of batteries.

CH5M3D: an HTML5 program for creating 3D molecular structures.

PubMed

Earley, Clarke W

2013-11-18

While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user's computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/.

CH5M3D: an HTML5 program for creating 3D molecular structures

PubMed Central

2013-01-01

Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

Technical Note: FreeCT_wFBP: A robust, efficient, open-source implementation of weighted filtered backprojection for helical, fan-beam CT.

PubMed

Hoffman, John; Young, Stefano; Noo, Frédéric; McNitt-Gray, Michael

2016-03-01

With growing interest in quantitative imaging, radiomics, and CAD using CT imaging, the need to explore the impacts of acquisition and reconstruction parameters has grown. This usually requires extensive access to the scanner on which the data were acquired and its workflow is not designed for large-scale reconstruction projects. Therefore, the authors have developed a freely available, open-source software package implementing a common reconstruction method, weighted filtered backprojection (wFBP), for helical fan-beam CT applications. FreeCT_wFBP is a low-dependency, GPU-based reconstruction program utilizing c for the host code and Nvidia CUDA C for GPU code. The software is capable of reconstructing helical scans acquired with arbitrary pitch-values, and sampling techniques such as flying focal spots and a quarter-detector offset. In this work, the software has been described and evaluated for reconstruction speed, image quality, and accuracy. Speed was evaluated based on acquisitions of the ACR CT accreditation phantom under four different flying focal spot configurations. Image quality was assessed using the same phantom by evaluating CT number accuracy, uniformity, and contrast to noise ratio (CNR). Finally, reconstructed mass-attenuation coefficient accuracy was evaluated using a simulated scan of a FORBILD thorax phantom and comparing reconstructed values to the known phantom values. The average reconstruction time evaluated under all flying focal spot configurations was found to be 17.4 ± 1.0 s for a 512 row × 512 column × 32 slice volume. Reconstructions of the ACR phantom were found to meet all CT Accreditation Program criteria including CT number, CNR, and uniformity tests. Finally, reconstructed mass-attenuation coefficient values of water within the FORBILD thorax phantom agreed with original phantom values to within 0.0001 mm(2)/g (0.01%). FreeCT_wFBP is a fast, highly configurable reconstruction package for third-generation CT available under the GNU GPL. It shows good performance with both clinical and simulated data.

GNU Radio Sandia Utilities v. 1.0

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

Gilbert, Jacob; Knee, Peter

This software adds a data handling module to the GNU Radio (GR) software defined radio (SDR) framework as well as some general-purpose function blocks (filters, metadata control, etc). This software is useful for processing bursty RF transmissions with GR, and serves as a base for applying SDR signal processing techniques to a whole burst of data at a time, as opposed to streaming data which GR has been primarily focused around.

Concept Verification Test - Evaluation of Spacelab/Payload operation concepts

NASA Technical Reports Server (NTRS)

Mcbrayer, R. O.; Watters, H. H.

1977-01-01

The Concept Verification Test (CVT) procedure is used to study Spacelab operational concepts by conducting mission simulations in a General Purpose Laboratory (GPL) which represents a possible design of Spacelab. In conjunction with the laboratory a Mission Development Simulator, a Data Management System Simulator, a Spacelab Simulator, and Shuttle Interface Simulator have been designed. (The Spacelab Simulator is more functionally and physically representative of the Spacelab than the GPL.) Four simulations of Spacelab mission experimentation were performed, two involving several scientific disciplines, one involving life sciences, and the last involving material sciences. The purpose of the CVT project is to support the pre-design and development of payload carriers and payloads, and to coordinate hardware, software, and operational concepts of different developers and users.

Rapid Prototyping of Application Specific Signal Processors (RASSP)

DTIC Science & Technology

1993-12-23

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

Continuous-time quantum Monte Carlo impurity solvers

NASA Astrophysics Data System (ADS)

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

2011-04-01

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

MinFinder v2.0: An improved version of MinFinder

NASA Astrophysics Data System (ADS)

Tsoulos, Ioannis G.; Lagaris, Isaac E.

2008-10-01

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

Stochastic hyperfine interactions modeling library

NASA Astrophysics Data System (ADS)

Zacate, Matthew O.; Evenson, William E.

2011-04-01

The stochastic hyperfine interactions modeling library (SHIML) provides a set of routines to assist in the development and application of stochastic models of hyperfine interactions. The library provides routines written in the C programming language that (1) read a text description of a model for fluctuating hyperfine fields, (2) set up the Blume matrix, upon which the evolution operator of the system depends, and (3) find the eigenvalues and eigenvectors of the Blume matrix so that theoretical spectra of experimental techniques that measure hyperfine interactions can be calculated. The optimized vector and matrix operations of the BLAS and LAPACK libraries are utilized; however, there was a need to develop supplementary code to find an orthonormal set of (left and right) eigenvectors of complex, non-Hermitian matrices. In addition, example code is provided to illustrate the use of SHIML to generate perturbed angular correlation spectra for the special case of polycrystalline samples when anisotropy terms of higher order than A can be neglected. Program summaryProgram title: SHIML Catalogue identifier: AEIF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL 3 No. of lines in distributed program, including test data, etc.: 8224 No. of bytes in distributed program, including test data, etc.: 312 348 Distribution format: tar.gz Programming language: C Computer: Any Operating system: LINUX, OS X RAM: Varies Classification: 7.4 External routines: TAPP [1], BLAS [2], a C-interface to BLAS [3], and LAPACK [4] Nature of problem: In condensed matter systems, hyperfine methods such as nuclear magnetic resonance (NMR), Mössbauer effect (ME), muon spin rotation (μSR), and perturbed angular correlation spectroscopy (PAC) measure electronic and magnetic structure within Angstroms of nuclear probes through the hyperfine interaction. When interactions fluctuate at rates comparable to the time scale of a hyperfine method, there is a loss in signal coherence, and spectra are damped. The degree of damping can be used to determine fluctuation rates, provided that theoretical expressions for spectra can be derived for relevant physical models of the fluctuations. SHIML provides routines to help researchers quickly develop code to incorporate stochastic models of fluctuating hyperfine interactions in calculations of hyperfine spectra. Solution method: Calculations are based on the method for modeling stochastic hyperfine interactions for PAC by Winkler and Gerdau [5]. The method is extended to include other hyperfine methods following the work of Dattagupta [6]. The code provides routines for reading model information from text files, allowing researchers to develop new models quickly without the need to modify computer code for each new model to be considered. Restrictions: In the present version of the code, only methods that measure the hyperfine interaction on one probe spin state, such as PAC, μSR, and NMR, are supported. Running time: Varies

Status of GDL - GNU Data Language

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Porting the Starlink Software Collection to GNU Autotools

NASA Astrophysics Data System (ADS)

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

2005-12-01

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

Application of the GNU Radio platform in the multistatic radar

NASA Astrophysics Data System (ADS)

Szlachetko, Boguslaw; Lewandowski, Andrzej

2009-06-01

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

Rapid identification of serotypes of Mycobacterium avium-M. intracellulare complex by using infected swine sera and reference antigenic glycolipids.

PubMed

Ikawa, H; Oka, S; Murakami, H; Hayashi, A; Yano, I

1989-11-01

The species of 136 strains of acid-fast bacteria isolated from swine with mycobacteriosis were identified by numerical taxonomy and chemotaxonomy on the basis of mycolic acid subclass composition as members of the Mycobacterium avium-M. intracellulare (MAI) complex. The isolates were further classified by using both thin-layer chromatography of the antigenic glycopeptidolipids (GPL) obtained from the bacteria by the method of Tsang et al. (A. Y. Tsang, I. Drupa, M. Goldberg, J. K. McClatchy, and P. J. Brennan, Int. J. Syst. Bacteriol. 33:285-292, 1983) and the seroagglutination test devised by W. B. Schaefer (Am. Rev. Respir. Dis. 92[Suppl.]:85-93, 1965). For the reference standard, purified antigenic GPL of serotypes 4, 8, and 9 were isolated and their structures were analyzed by negative fast-atom bombardment-mass spectrometry. The fast-atom bombardment-mass spectrometric spectra of the intact GPL antigens of serotypes 4, 8, and 9 agreed with the structures reported earlier by Brennan et al. (P. J. Brennan and M. B. Goren, J. Biol. Chem. 254:4205-4211, 1979; P. J. Brennan, G. O. Aspinall, and J. E. Nam Shin, J. Biol. Chem. 256:6817-6822, 1981). With these antigenic GPL, the thin-layer chromatographic behaviors of the alkali-stable lipids of the above-described isolates were examined. These MAI complex isolates fell into the serotype 8 (85 strains), 4 (33 strains), and 9 (7 strains) and untypeable (11 strains) categories. Furthermore, an enzyme-linked immunosorbent assay (ELISA) based on type-specific glycolipid antigens and infected swine sera was used to diagnose the serological types of the MAI complex isolates. Of 14 cases typed by both the seroagglutination reaction and thin-layer chromatography, 13 showed clear agreement with the ELISA results. The results demonstrated that ELISA using infected sera was especially useful, and it can be recommended on the basis of simplicity, sensitivity, and specificity as an adjunct to the seroaggulutination test and thin-layer chromatography for identification of mycobacteria belonging to the MAI complex.

The glycerol backbone of phospholipids derives from noncarbohydrate precursors in starved lung cancer cells.

PubMed

Leithner, Katharina; Triebl, Alexander; Trötzmüller, Martin; Hinteregger, Barbara; Leko, Petra; Wieser, Beatrix I; Grasmann, Gabriele; Bertsch, Alexandra L; Züllig, Thomas; Stacher, Elvira; Valli, Alessandro; Prassl, Ruth; Olschewski, Andrea; Harris, Adrian L; Köfeler, Harald C; Olschewski, Horst; Hrzenjak, Andelko

2018-06-12

Cancer cells are reprogrammed to consume large amounts of glucose to support anabolic biosynthetic pathways. However, blood perfusion and consequently the supply with glucose are frequently inadequate in solid cancers. PEPCK-M ( PCK2 ), the mitochondrial isoform of phosphoenolpyruvate carboxykinase (PEPCK), has been shown by us and others to be functionally expressed and to mediate gluconeogenesis, the reverse pathway of glycolysis, in different cancer cells. Serine and ribose synthesis have been identified as downstream pathways fed by PEPCK in cancer cells. Here, we report that PEPCK-M-dependent glycerol phosphate formation from noncarbohydrate precursors (glyceroneogenesis) occurs in starved lung cancer cells and supports de novo glycerophospholipid synthesis. Using stable isotope-labeled glutamine and lactate, we show that PEPCK-M generates phosphoenolpyruvate and 3-phosphoglycerate, which are at least partially converted to glycerol phosphate and incorporated into glycerophospholipids (GPL) under glucose and serum starvation. This pathway is required to maintain levels of GPL, especially phosphatidylethanolamine (PE), as shown by stable shRNA-mediated silencing of PEPCK-M in H23 lung cancer cells. PEPCK-M shRNA led to reduced colony formation after starvation, and the effect was partially reversed by the addition of dioleyl-PE. Furthermore, PEPCK-M silencing abrogated cancer growth in a lung cancer cell xenograft model. In conclusion, glycerol phosphate formation for de novo GPL synthesis via glyceroneogenesis is a newly characterized anabolic pathway in cancer cells mediated by PEPCK-M under conditions of severe nutrient deprivation. Copyright © 2018 the Author(s). Published by PNAS.

Identification of a novel tetrapeptide structure of the Mycobacterium avium glycopeptidolipid that functions as a specific target for the host antibody response.

PubMed

Matsunaga, Isamu; Komori, Takaya; Mori, Naoki; Sugita, Masahiko

2012-03-23

Mycobacterium avium complex (MAC) is a group of non-tuberculous mycobacteria that cause tuberculosis-like diseases in humans. Unlike Mycobacterium tuberculosis, MAC expresses high levels of glycopeptidolipids (GPLs) containing a well-defined tetrapeptide-amino alcohol core, composed of D-phenylalanine, D-allo-threonine, D-alanine, and L-alaninol, that is modified with a fatty acid and sugar residues. Surprisingly, however, a careful scrutiny of the mass spectrum of MAC GPLs revealed the presence of ions that could not readily accountable for the known GPL structure. The magnitude of the ions was increased prominently when GPLs were isolated from the valine-supplemented culture, and the ions representing the authentic GPL species were diminished, suggesting the possibility that the basic structure of the peptide backbone might be altered in response to the exogenously added valine. Indeed, further mass spectrometry (MS)/MS and gas chromatography-MS analysis indicated a substitution of D-valine for the N-terminal D-phenylalanine of the tetrapeptide core, and the presence of D-valine and the absence of D-phenylalanine was confirmed by high-performance liquid chromatography, using the derivatized amino acid residues that were released from the tetrapeptide. Finally, specific antibodies to the purified valine-containing GPL species were detected in the serum of a MAC-infected guinea pig. Therefore, these results identify a new molecular species of MAC GPLs with immunogenic potential. Copyright © 2012 Elsevier Inc. All rights reserved.

The glycerol backbone of phospholipids derives from noncarbohydrate precursors in starved lung cancer cells

PubMed Central

Trötzmüller, Martin; Hinteregger, Barbara; Leko, Petra; Wieser, Beatrix I.; Grasmann, Gabriele; Bertsch, Alexandra L.; Züllig, Thomas; Stacher, Elvira; Valli, Alessandro; Prassl, Ruth; Olschewski, Andrea; Harris, Adrian L.; Köfeler, Harald C.; Olschewski, Horst; Hrzenjak, Andelko

2018-01-01

Cancer cells are reprogrammed to consume large amounts of glucose to support anabolic biosynthetic pathways. However, blood perfusion and consequently the supply with glucose are frequently inadequate in solid cancers. PEPCK-M (PCK2), the mitochondrial isoform of phosphoenolpyruvate carboxykinase (PEPCK), has been shown by us and others to be functionally expressed and to mediate gluconeogenesis, the reverse pathway of glycolysis, in different cancer cells. Serine and ribose synthesis have been identified as downstream pathways fed by PEPCK in cancer cells. Here, we report that PEPCK-M–dependent glycerol phosphate formation from noncarbohydrate precursors (glyceroneogenesis) occurs in starved lung cancer cells and supports de novo glycerophospholipid synthesis. Using stable isotope-labeled glutamine and lactate, we show that PEPCK-M generates phosphoenolpyruvate and 3-phosphoglycerate, which are at least partially converted to glycerol phosphate and incorporated into glycerophospholipids (GPL) under glucose and serum starvation. This pathway is required to maintain levels of GPL, especially phosphatidylethanolamine (PE), as shown by stable shRNA-mediated silencing of PEPCK-M in H23 lung cancer cells. PEPCK-M shRNA led to reduced colony formation after starvation, and the effect was partially reversed by the addition of dioleyl-PE. Furthermore, PEPCK-M silencing abrogated cancer growth in a lung cancer cell xenograft model. In conclusion, glycerol phosphate formation for de novo GPL synthesis via glyceroneogenesis is a newly characterized anabolic pathway in cancer cells mediated by PEPCK-M under conditions of severe nutrient deprivation. PMID:29844165

GPL Report: The Broad Federal Investment in Educational R&D.

ERIC Educational Resources Information Center

Florio, David H.

1979-01-01

This article describes the breadth of federal support for educational knowledge production and application. Support from the Education Division of the Department of Health, Education, and Welfare is discussed in detail. (Author/MC)

LabData database sub-systems for post-processing and quality control of stable isotope and gas chromatography measurements

NASA Astrophysics Data System (ADS)

Suckow, A. O.

2013-12-01

Measurements need post-processing to obtain results that are comparable between laboratories. Raw data may need to be corrected for blank, memory, drift (change of reference values with time), linearity (dependence of reference on signal height) and normalized to international reference materials. Post-processing parameters need to be stored for traceability of results. State of the art stable isotope correction schemes are available based on MS Excel (Geldern and Barth, 2012; Gröning, 2011) or MS Access (Coplen, 1998). These are specialized to stable isotope measurements only, often only to the post-processing of a special run. Embedding of algorithms into a multipurpose database system was missing. This is necessary to combine results of different tracers (3H, 3He, 2H, 18O, CFCs, SF6...) or geochronological tools (Sediment dating e.g. with 210Pb, 137Cs), to relate to attribute data (submitter, batch, project, geographical origin, depth in core, well information etc.) and for further interpretation tools (e.g. lumped parameter modelling). Database sub-systems to the LabData laboratory management system (Suckow and Dumke, 2001) are presented for stable isotopes and for gas chromatographic CFC and SF6 measurements. The sub-system for stable isotopes allows the following post-processing: 1. automated import from measurement software (Isodat, Picarro, LGR), 2. correction for sample-to sample memory, linearity, drift, and renormalization of the raw data. The sub-system for gas chromatography covers: 1. storage of all raw data 2. storage of peak integration parameters 3. correction for blank, efficiency and linearity The user interface allows interactive and graphical control of the post-processing and all corrections by export to and plot in MS Excel and is a valuable tool for quality control. The sub-databases are integrated into LabData, a multi-user client server architecture using MS SQL server as back-end and an MS Access front-end and installed in four laboratories to date. Attribute data storage (unique ID for each subsample, origin, project context etc.) and laboratory management features are included. Export routines to Excel (depth profiles, time series, all possible tracer-versus tracer plots...) and modelling capabilities are add-ons. The source code is public domain and available under the GNU general public licence agreement (GNU-GPL). References Coplen, T.B., 1998. A manual for a laboratory information management system (LIMS) for light stable isotopes. Version 7.0. USGS open file report 98-284. Geldern, R.v., Barth, J.A.C., 2012. Optimization of instrument setup and post-run corrections for oxygen and hydrogen stable isotope measurements of water by isotope ratio infrared spectroscopy (IRIS). Limnology and Oceanography: Methods 10, 1024-1036. Gröning, M., 2011. Improved water δ2H and δ18O calibration and calculation of measurement uncertainty using a simple software tool. Rapid Communications in Mass Spectrometry 25, 2711-2720. Suckow, A., Dumke, I., 2001. A database system for geochemical, isotope hydrological and geochronological laboratories. Radiocarbon 43, 325-337.

Vibration and bending behavior of functionally graded nanocomposite doubly-curved shallow shells reinforced by graphene nanoplatelets

NASA Astrophysics Data System (ADS)

Wang, Aiwen; Chen, Hongyan; Hao, Yuxin; Zhang, Wei

2018-06-01

Free vibration and static bending of functionally graded (FG) graphene nanoplatelet (GPL) reinforced composite doubly-curved shallow shells with three distinguished distributions are analyzed. Material properties with gradient variation in the thickness aspect are evaluated by the modified Halpin-Tsai model. Mathematical model of the simply supported doubly-curved shallow shells rests upon Hamilton Principle and a higher order shear deformation theory (HSDT). The free vibration frequencies and bending deflections are gained by taking into account Navier technique. The agreement between the obtained results and ANSYS as well as the prior results in the open literature verifies the accuracy of the theory in this article. Further, parametric studies are accomplished to highlight the significant influence of GPL distribution patterns and weight fraction, stratification number, dimensions of GPLs and shells on the mechanical behavior of the system.

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

PubMed

Thomson, Robert C

2009-07-30

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

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

PubMed Central

Thomson, Robert C.

2009-01-01

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

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

DTIC Science & Technology

2004-03-01

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

Metabolism and phospholipid assembly of polyunsaturated fatty acids in human bone marrow mesenchymal stromal cells.

PubMed

Tigistu-Sahle, Feven; Lampinen, Milla; Kilpinen, Lotta; Holopainen, Minna; Lehenkari, Petri; Laitinen, Saara; Käkelä, Reijo

2017-01-01

High arachidonic acid (20:4n-6) and low n-3 PUFA levels impair the capacity of cultured human bone marrow mesenchymal stromal cells (hBMSCs) to modulate immune functions. The capacity of the hBMSCs to modify PUFA structures was found to be limited. Therefore, different PUFA supplements given to the cells resulted in very different glycerophospholipid (GPL) species profiles and substrate availability for phospholipases, which have preferences for polar head group and acyl chains when liberating PUFA precursors for production of lipid mediators. When supplemented with 20:4n-6, the cells increased prostaglandin E2 secretion. However, they elongated 20:4n-6 to the less active precursor, 22:4n-6, and also incorporated it into triacylglycerols, which may have limited the proinflammatory signaling. The n-3 PUFA precursor, 18:3n-3, had little potency to reduce the GPL 20:4n-6 content, while the eicosapentaenoic (20:5n-3) and docosahexaenoic (22:6n-3) acid supplements efficiently displaced the 20:4n-6 acyls, and created diverse GPL species substrate pools allowing attenuation of inflammatory signaling. The results emphasize the importance of choosing appropriate PUFA supplements for in vitro hBMSC expansion and suggests that for optimal function they require an exogenous fatty acid source providing 20:5n-3 and 22:6n-3 sufficiently, but 20:4n-6 moderately, which calls for specifically designed optimal PUFA supplements for the cultures. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

Elegent—An elastic event generator

NASA Astrophysics Data System (ADS)

Kašpar, J.

2014-03-01

Although elastic scattering of nucleons may look like a simple process, it presents a long-lasting challenge for theory. Due to missing hard energy scale, the perturbative QCD cannot be applied. Instead, many phenomenological/theoretical models have emerged. In this paper we present a unified implementation of some of the most prominent models in a C++ library, moreover extended to account for effects of the electromagnetic interaction. The library is complemented with a number of utilities. For instance, programs to sample many distributions of interest in four-momentum transfer squared, t, impact parameter, b, and collision energy √{s}. These distributions at ISR, Spp¯S, RHIC, Tevatron and LHC energies are available for download from the project web site. Both in the form of ROOT files and PDF figures providing comparisons among the models. The package includes also a tool for Monte-Carlo generation of elastic scattering events, which can easily be embedded in any other program framework. Catalogue identifier: AERT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERT_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.: 10551 No. of bytes in distributed program, including test data, etc.: 126316 Distribution format: tar.gz Programming language: C++. Computer: Any in principle, tested on x86-64 architecture. Operating system: Any in principle, tested on GNU/Linux. RAM: Strongly depends on the task, but typically below 20MB Classification: 11.6. External routines: ROOT, HepMC Nature of problem: Monte-Carlo simulation of elastic nucleon-nucleon collisions Solution method: Implementation of some of the most prominent phenomenological/theoretical models providing cumulative distribution function that is used for random event generation. Running time: Strongly depends on the task, but typically below 1 h.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

PubMed

Parton, Daniel L; Grinaway, Patrick B; Hanson, Sonya M; Beauchamp, Kyle A; Chodera, John D

2016-06-01

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences-from a single sequence to an entire superfamily-and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics-such as Markov state models (MSMs)-which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates. Ensembler is free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded from https://github.com/choderalab/ensembler.

An open-source framework for stress-testing non-invasive foetal ECG extraction algorithms.

PubMed

Andreotti, Fernando; Behar, Joachim; Zaunseder, Sebastian; Oster, Julien; Clifford, Gari D

2016-05-01

Over the past decades, many studies have been published on the extraction of non-invasive foetal electrocardiogram (NI-FECG) from abdominal recordings. Most of these contributions claim to obtain excellent results in detecting foetal QRS (FQRS) complexes in terms of location. A small subset of authors have investigated the extraction of morphological features from the NI-FECG. However, due to the shortage of available public databases, the large variety of performance measures employed and the lack of open-source reference algorithms, most contributions cannot be meaningfully assessed. This article attempts to address these issues by presenting a standardised methodology for stress testing NI-FECG algorithms, including absolute data, as well as extraction and evaluation routines. To that end, a large database of realistic artificial signals was created, totaling 145.8 h of multichannel data and over one million FQRS complexes. An important characteristic of this dataset is the inclusion of several non-stationary events (e.g. foetal movements, uterine contractions and heart rate fluctuations) that are critical for evaluating extraction routines. To demonstrate our testing methodology, three classes of NI-FECG extraction algorithms were evaluated: blind source separation (BSS), template subtraction (TS) and adaptive methods (AM). Experiments were conducted to benchmark the performance of eight NI-FECG extraction algorithms on the artificial database focusing on: FQRS detection and morphological analysis (foetal QT and T/QRS ratio). The overall median FQRS detection accuracies (i.e. considering all non-stationary events) for the best performing methods in each group were 99.9% for BSS, 97.9% for AM and 96.0% for TS. Both FQRS detections and morphological parameters were shown to heavily depend on the extraction techniques and signal-to-noise ratio. Particularly, it is shown that their evaluation in the source domain, obtained after using a BSS technique, should be avoided. Data, extraction algorithms and evaluation routines were released as part of the fecgsyn toolbox on Physionet under an GNU GPL open-source license. This contribution provides a standard framework for benchmarking and regulatory testing of NI-FECG extraction algorithms.

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.

Automated generation of lattice QCD Feynman rules

NASA Astrophysics Data System (ADS)

Hart, A.; von Hippel, G. M.; Horgan, R. R.; Müller, E. H.

2009-12-01

The derivation of the Feynman rules for lattice perturbation theory from actions and operators is complicated, especially for highly improved actions such as HISQ. This task is, however, both important and particularly suitable for automation. We describe a suite of software to generate and evaluate Feynman rules for a wide range of lattice field theories with gluons and (relativistic and/or heavy) quarks. Our programs are capable of dealing with actions as complicated as (m)NRQCD and HISQ. Automated differentiation methods are used to calculate also the derivatives of Feynman diagrams. Program summaryProgram title: HiPPY, HPsrc Catalogue identifier: AEDX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv2 (see Additional comments below) No. of lines in distributed program, including test data, etc.: 513 426 No. of bytes in distributed program, including test data, etc.: 4 893 707 Distribution format: tar.gz Programming language: Python, Fortran95 Computer: HiPPy: Single-processor workstations. HPsrc: Single-processor workstations and MPI-enabled multi-processor systems Operating system: HiPPy: Any for which Python v2.5.x is available. HPsrc: Any for which a standards-compliant Fortran95 compiler is available Has the code been vectorised or parallelised?: Yes RAM: Problem specific, typically less than 1 GB for either code Classification: 4.4, 11.5 Nature of problem: Derivation and use of perturbative Feynman rules for complicated lattice QCD actions. Solution method: An automated expansion method implemented in Python (HiPPy) and code to use expansions to generate Feynman rules in Fortran95 (HPsrc). Restrictions: No general restrictions. Specific restrictions are discussed in the text. Additional comments: The HiPPy and HPsrc codes are released under the second version of the GNU General Public Licence (GPL v2). Therefore anyone is free to use or modify the code for their own calculations. As part of the licensing, we ask that any publications including results from the use of this code or of modifications of it cite Refs. [1,2] as well as this paper. Finally, we also ask that details of these publications, as well as of any bugs or required or useful improvements of this core code, would be communicated to us. Running time: Very problem specific, depending on the complexity of the Feynman rules and the number of integration points. Typically between a few minutes and several weeks. The installation tests provided with the program code take only a few seconds to run. References:A. Hart, G.M. von Hippel, R.R. Horgan, L.C. Storoni, Automatically generating Feynman rules for improved lattice eld theories, J. Comput. Phys. 209 (2005) 340-353, doi:10.1016/j.jcp.2005.03.010, arXiv:hep-lat/0411026. M. Lüscher, P. Weisz, Efficient Numerical Techniques for Perturbative Lattice Gauge Theory Computations, Nucl. Phys. B 266 (1986) 309, doi:10.1016/0550-3213(86)90094-5.

Antinociceptive activity of Inula britannica L. and patuletin: In vivo and possible mechanisms studies.

PubMed

Zarei, Mohammad; Mohammadi, Saeed; Komaki, Alireza

2018-06-12

Inula britannica L. is a predominant medicinal plant traditionally utilized in the treatments of arthritis and back pain in Iranian folk medicine. The purpose of this research was to evaluate the antinociceptive effects of Inula britannica L. flower essential oil (IBLEO) and one of its major constituents, Patuletin (Pn), in male mice. In this study, we used pain assessment tests including acetic acid-induced writhing, tail-flick (TF), formalin induced paw licking (FIPL) model, and glutamate-induced paw licking (GPL). For understanding the supposed antinociceptive mechanisms of IBLEO, opioid and L-arginine/NO/cGMP/ KATP pathways were examined. In the TF, writhing, GPL, and FIPL tests, a dosage of 100 mg/kg of IBLEO showed noteworthy antinociceptive effects in comparison with control (p < 0.05). In writhing test, administration of selective opioid antagonists (naltrindole, nor-binaltorphimine, and naloxonazine) attenuated the antinociceptive effect of IBLEO in comparison with control (p < 0.001). Both methylene blue and glibenclamide blocked the antinociceptive effect of IBLEO (p < 0.05), but the administration of L-arginine or sodium nitroprusside fundamentally potentiated the antinociception induced by IBLEO in phase II of the FIPL (p < 0.05). Additionally, patuletin showed significant antinociceptive effects in writhing, FIPL, and GPL tests (p < 0.01). The results of this examination showed that IBLEO and Pn have antinociceptive effects. The modulation of glutamatergic systems by opioid receptors could be involved, at least in part, in these effects. Our data also suggest the activation of the L-arginine/NO/cGMP/KATP pathway in IBLEO antinociceptive effects. Copyright © 2018 Elsevier B.V. All rights reserved.

Effects of obesity and gestational diabetes mellitus on placental phospholipids.

PubMed

Uhl, Olaf; Demmelmair, Hans; Segura, María Teresa; Florido, Jesús; Rueda, Ricardo; Campoy, Cristina; Koletzko, Berthold

2015-08-01

Gestational diabetes mellitus (GDM) is associated with adverse effects in the offspring. The composition of placental glycerophospholipids (GPL) is known to be altered in GDM and might reflect an aberrant fatty acid transfer across the placenta and thus affect the foetal body composition. The aim of this study was to investigate possible effects of obesity and GDM, respectively, on placental GPL species composition. We investigated molecular species of phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylserine (PS) in term placentas from controls (lean non-diabetic, body-mass-index [BMI] 18-24.9k g/m(2), n=31), obese non-diabetics (BMI ≥30 kg/m(2), n=17) and lean diabetics (n=15), using liquid chromatography - triple quadrupole mass spectrometry. PE(16:0/22:6) and PE(18:0/20:4) were increased in GDM and decreased species were PC(18:0/20:3), PC(18:1/20:3) and PS(18:0/18:2). A consistent difference between BMI related changes and changes caused by GDM was not observed. Arachidonic acid percentages of cord blood correlated with placental PC(16:0/20:4), whereas foetal docosahexaenoic acid correlated to placental PE species. Furthermore, a positive correlation of placental weight was found to levels of PE containing arachidonic acid. We demonstrated that obesity and GDM are associated with decreased dihomo-gamma-linolenic acid and increased arachidonic acid and docosahexaenoic acid contents of placental GPL, with unknown consequences for the foetus. PC(16:0/20:4) was identified as the major component for the supply of arachidonic acid to the foetal circulation, whereas PE containing arachidonic acid was found to be associated to the placental and infant growth. Copyright © 2015. Published by Elsevier Ireland Ltd.

Risk stratification of gallbladder polyps (1-2 cm) for surgical intervention with 18F-FDG PET/CT.

PubMed

Lee, Jaehoon; Yun, Mijin; Kim, Kyoung-Sik; Lee, Jong-Doo; Kim, Chun K

2012-03-01

We assessed the value of (18)F-FDG uptake in the gallbladder polyp (GP) in risk stratification for surgical intervention and the optimal cutoff level of the parameters derived from GP (18)F-FDG uptake for differentiating malignant from benign etiologies in a select, homogeneous group of patients with 1- to 2-cm GPs. Fifty patients with 1- to 2-cm GPs incidentally found on the CT portion of PET/CT were retrospectively analyzed. All patients had histologic diagnoses. GP (18)F-FDG activity was visually scored positive (≥liver) or negative (

Emplacement of Basaltic Lava Flows: the Legacy of GPL Walker

NASA Astrophysics Data System (ADS)

Cashman, K. V.

2005-12-01

Through his early field measurements of lava flow morphology, G.P.L. Walker established a framework for examination of the dynamics of lava flow emplacement that is still in place today. I will examine this legacy as established by three early papers: (1) his 1967 paper, where he defined a relationship between the thickness of recent Etna lava flows and the slope over which they flowed, a relationship that he ascribed to lava viscosity; (2) his 1971 paper, which defined a relationship between lava flux and the formation of simple and compound flow units that he used to infer high effusion rates for the emplacement of some flood basalt lavas; and (3) his often-cited 1973 paper, which related the length of lava flows to their average effusion rate. These three papers, all similar in their basic approach of using field measurements of lava flow morphology to extract fundamental relationships between eruption conditions (magma flux and rheology) and emplacement style (flow length and thickness), firmly established the relationship between flow morphology and emplacement dynamics that has since been widely applied not only to subaerial lava flows, but also to the interpretation of flows in submarine and planetary environments. Important extensions of these concepts have been provided by improved field observation methods, particularly for analysis of flowing lava, by laboratory measurements of lava rheology, by the application of analog experiments to lava flow dynamics, and by steady improvement of numerical techniques to model the flow of lava over complex terrain. The real legacy of G.P.L. Walker's field measurement approach, however, may lie in the future, as new topographic measurement techniques such as LIDAR hold exciting promise for truly quantitative analysis of lava flow morphologies and their relationship to flow dynamics.

GPL Report: Educational R&D in a Tough Budget Year.

ERIC Educational Resources Information Center

Florio, David H.

1979-01-01

This report examines funding and activities of the National Institute of Education (NIE) to demonstrate how educational inquiry is doing in obtaining federal financial support. An overview of specific areas NIE plans to investigate if adequate funds are allocated is presented. (EB)

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.

Roles for Cell Wall Glycopeptidolipid in Surface Adherence and Planktonic Dispersal of Mycobacterium avium

EPA Science Inventory

The opportunistic pathogen Mycobacterium avium is a significant inhabitant of biofilms in drinking water distribution systems. M. avium expresses on its cell surface serovar-specific glycopeptidolipids (ssGPLs). Studies have implicated the core GPL in biofilm formation by M. aviu...

Kmonodium, a Program for the Numerical Solution of the One-Dimensional Schrodinger Equation

ERIC Educational Resources Information Center

Angeli, Celestino; Borini, Stefano; Cimiraglia, Renzo

2005-01-01

A very simple strategy for the solution of the Schrodinger equation of a particle moving in one dimension subjected to a generic potential is presented. This strategy is implemented in a computer program called Kmonodium, which is free and distributed under the General Public License (GPL).

A Numerical Fit of Analytical to Simulated Density Profiles in Dark Matter Haloes

NASA Astrophysics Data System (ADS)

Caimmi, R.; Marmo, C.; Valentinuzzi, T.

2005-06-01

Analytical and geometrical properties of generalized power-law (GPL) density profiles are investigated in detail. In particular, a one-to-one correspondence is found between mathematical parameters (a scaling radius, r_0, a scaling density, rho_0, and three exponents, alpha, beta, gamma), and geometrical parameters (the coordinates of the intersection of the asymptotes, x_C, y_C, and three vertical intercepts, b, b_beta, b_gamma, related to the curve and the asymptotes, respectively): (r_0,rho_0,alpha,beta,gamma) <--> (x_C,y_C,b,b_beta,b_gamma). Then GPL density profiles are compared with simulated dark haloes (SDH) density profiles, and nonlinear least-absolute values and least-squares fits involving the above mentioned five parameters (RFSM5 method) are prescribed. More specifically, the sum of absolute values or squares of absolute logarithmic residuals, R_i= log rhoSDH(r_i)-log rhoGPL(r_i), is evaluated on 10^5 points making a 5- dimension hypergrid, through a few iterations. The size is progressively reduced around a fiducial minimum, and superpositions on nodes of earlier hypergrids are avoided. An application is made to a sample of 17 SDHs on the scale of cluster of galaxies, within a flat LambdaCDM cosmological model (Rasia et al. 2004). In dealing with the mean SDH density profile, a virial radius, rvir, averaged over the whole sample, is assigned, which allows the calculation of the remaining parameters. Using a RFSM5 method provides a better fit with respect to other methods. The geometrical parameters, averaged over the whole sample of best fitting GPL density profiles, yield (alpha,beta,gamma) approx(0.6,3.1,1.0), to be compared with (alpha,beta,gamma)=(1,3,1), i.e. the NFW density profile (Navarro et al. 1995, 1996, 1997), (alpha,beta,gamma)=(1.5,3,1.5) (Moore et al. 1998, 1999), (alpha,beta,gamma)=(1,2.5,1) (Rasia et al. 2004); and, in addition, gamma approx 1.5 (Hiotelis 2003), deduced from the application of a RFSM5 method, but using a different definition of scaled radius, or concentration; and gamma approx 1.2-1.3 deduced from more recent high-resolution simulations (Diemand et al. 2004, Reed et al. 2005). No evident correlation is found between SDH dynamical state (relaxed or merging) and asymptotic inner slope of the fitting logarithmic density profile or (for SDH comparable virial masses) scaled radius. Mean values and standard deviations of some parameters are calculated, and in particular the decimal logarithm of the scaled radius, xivir, reads < log xivir >=0.74 and sigma_s log xivir=0.15-0.17, consistent with previous results related to NFW density profiles. It provides additional support to the idea, that NFW density profiles may be considered as a convenient way to parametrize SDH density profiles, without implying that it necessarily produces the best possible fit (Bullock et al. 2001). A certain degree of degeneracy is found in fitting GPL to SDH density profiles. If it is intrinsic to the RFSM5 method or it could be reduced by the next generation of high-resolution simulations, still remains an open question.

allantools: Allan deviation calculation

NASA Astrophysics Data System (ADS)

Wallin, Anders E. E.; Price, Danny C.; Carson, Cantwell G.; Meynadier, Frédéric

2018-04-01

allantools calculates Allan deviation and related time & frequency statistics. The library is written in Python and has a GPL v3+ license. It takes input data that is either evenly spaced observations of either fractional frequency, or phase in seconds. Deviations are calculated for given tau values in seconds. Several noise generators for creating synthetic datasets are also included.

Axial postbuckling analysis of multilayer functionally graded composite nanoplates reinforced with GPLs based on nonlocal strain gradient theory

NASA Astrophysics Data System (ADS)

Sahmani, S.; Aghdam, M. M.

2017-11-01

In this paper, a new size-dependent inhomogeneous plate model is constructed to analyze the nonlinear buckling and postbuckling characteristics of multilayer functionally graded composite nanoplates reinforced with graphene platelet (GPL) nanofillers under axial compressive load. To this purpose, the nonlocal strain gradient theory of elasticity is implemented into a refined hyperbolic shear deformation plate theory. The mechanical properties of multilayer graphene platelet-reinforced composite (GPLRC) nanoplates are evaluated based upon the Halpin-Tsai micromechanical scheme. The weight fraction of randomly dispersed GPLs remain constant in each individual layer, which results in U-GPLRC nanoplate, or changes layerwise in accordance with three different functionally graded patterns, which make X-GPLRC, O-GPLRC and A-GPLRC nanoplates. Via a two-stepped perturbation technique, explicit analytical expressions for nonlocal strain gradient stability paths are established for layerwise functionally graded GPLRC nanoplates. It is demonstrated that both the nonlocal and strain gradient size dependencies are more significant for multilayer GPLRC nanoplates filling by GPL nanofillers with higher length-to-thickness and width-to-thickness ratios.

SEGY to ASCII: Conversion and Plotting Program

USGS Publications Warehouse

Goldman, Mark R.

1999-01-01

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

Coding coarse grained polymer model for LAMMPS and its application to polymer crystallization

NASA Astrophysics Data System (ADS)

Luo, Chuanfu; Sommer, Jens-Uwe

2009-08-01

We present a patch code for LAMMPS to implement a coarse grained (CG) model of poly(vinyl alcohol) (PVA). LAMMPS is a powerful molecular dynamics (MD) simulator developed at Sandia National Laboratories. Our patch code implements tabulated angular potential and Lennard-Jones-9-6 (LJ96) style interaction for PVA. Benefited from the excellent parallel efficiency of LAMMPS, our patch code is suitable for large-scale simulations. This CG-PVA code is used to study polymer crystallization, which is a long-standing unsolved problem in polymer physics. By using parallel computing, cooling and heating processes for long chains are simulated. The results show that chain-folded structures resembling the lamellae of polymer crystals are formed during the cooling process. The evolution of the static structure factor during the crystallization transition indicates that long-range density order appears before local crystalline packing. This is consistent with some experimental observations by small/wide angle X-ray scattering (SAXS/WAXS). During the heating process, it is found that the crystalline regions are still growing until they are fully melted, which can be confirmed by the evolution both of the static structure factor and average stem length formed by the chains. This two-stage behavior indicates that melting of polymer crystals is far from thermodynamic equilibrium. Our results concur with various experiments. It is the first time that such growth/reorganization behavior is clearly observed by MD simulations. Our code can be easily used to model other type of polymers by providing a file containing the tabulated angle potential data and a set of appropriate parameters. Program summaryProgram title: lammps-cgpva Catalogue identifier: AEDE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU's GPL No. of lines in distributed program, including test data, etc.: 940 798 No. of bytes in distributed program, including test data, etc.: 12 536 245 Distribution format: tar.gz Programming language: C++/MPI Computer: Tested on Intel-x86 and AMD64 architectures. Should run on any architecture providing a C++ compiler Operating system: Tested under Linux. Any other OS with C++ compiler and MPI library should suffice Has the code been vectorized or parallelized?: Yes RAM: Depends on system size and how many CPUs are used Classification: 7.7 External routines: LAMMPS ( http://lammps.sandia.gov/), FFTW ( http://www.fftw.org/) Nature of problem: Implementing special tabular angle potentials and Lennard-Jones-9-6 style interactions of a coarse grained polymer model for LAMMPS code. Solution method: Cubic spline interpolation of input tabulated angle potential data. Restrictions: The code is based on a former version of LAMMPS. Unusual features.: Any special angular potential can be used if it can be tabulated. Running time: Seconds to weeks, depending on system size, speed of CPU and how many CPUs are used. The test run provided with the package takes about 5 minutes on 4 AMD's opteron (2.6 GHz) CPUs. References:D. Reith, H. Meyer, F. Müller-Plathe, Macromolecules 34 (2001) 2335-2345. H. Meyer, F. Müller-Plathe, J. Chem. Phys. 115 (2001) 7807. H. Meyer, F. Müller-Plathe, Macromolecules 35 (2002) 1241-1252.

Transcription Factor Information System (TFIS): A Tool for Detection of Transcription Factor Binding Sites.

PubMed

Narad, Priyanka; Kumar, Abhishek; Chakraborty, Amlan; Patni, Pranav; Sengupta, Abhishek; Wadhwa, Gulshan; Upadhyaya, K C

2017-09-01

Transcription factors are trans-acting proteins that interact with specific nucleotide sequences known as transcription factor binding site (TFBS), and these interactions are implicated in regulation of the gene expression. Regulation of transcriptional activation of a gene often involves multiple interactions of transcription factors with various sequence elements. Identification of these sequence elements is the first step in understanding the underlying molecular mechanism(s) that regulate the gene expression. For in silico identification of these sequence elements, we have developed an online computational tool named transcription factor information system (TFIS) for detecting TFBS for the first time using a collection of JAVA programs and is mainly based on TFBS detection using position weight matrix (PWM). The database used for obtaining position frequency matrices (PFM) is JASPAR and HOCOMOCO, which is an open-access database of transcription factor binding profiles. Pseudo-counts are used while converting PFM to PWM, and TFBS detection is carried out on the basis of percent score taken as threshold value. TFIS is equipped with advanced features such as direct sequence retrieving from NCBI database using gene identification number and accession number, detecting binding site for common TF in a batch of gene sequences, and TFBS detection after generating PWM from known raw binding sequences in addition to general detection methods. TFIS can detect the presence of potential TFBSs in both the directions at the same time. This feature increases its efficiency. And the results for this dual detection are presented in different colors specific to the orientation of the binding site. Results obtained by the TFIS are more detailed and specific to the detected TFs as integration of more informative links from various related web servers are added in the result pages like Gene Ontology, PAZAR database and Transcription Factor Encyclopedia in addition to NCBI and UniProt. Common TFs like SP1, AP1 and NF-KB of the Amyloid beta precursor gene is easily detected using TFIS along with multiple binding sites. In another scenario of embryonic developmental process, TFs of the FOX family (FOXL1 and FOXC1) were also identified. TFIS is platform-independent which is publicly available along with its support and documentation at http://tfistool.appspot.com and http://www.bioinfoplus.com/tfis/ . TFIS is licensed under the GNU General Public License, version 3 (GPL-3.0).

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.

PubMed

Zych, Konrad; Li, Yang; van der Velde, Joeri K; Joosen, Ronny V L; Ligterink, Wilco; Jansen, Ritsert C; Arends, Danny

2015-02-19

Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under "GNU GPL v3". The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl .

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.

PubMed

Arnaiz, Olivier; Van Dijk, Erwin; Bétermier, Mireille; Lhuillier-Akakpo, Maoussi; de Vanssay, Augustin; Duharcourt, Sandra; Sallet, Erika; Gouzy, Jérôme; Sperling, Linda

2017-06-26

The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage. We generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource. We have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3' and 5' UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis regulatory motifs). The P. tetraurelia improved transcriptome resource, gene annotations for P. tetraurelia, P. biaurelia, P. sexaurelia and P. caudatum, and Paramecium-trained EuGene configuration are available through ParameciumDB ( http://paramecium.i2bc.paris-saclay.fr ). TrUC software is freely distributed under a GNU GPL v3 licence ( https://github.com/oarnaiz/TrUC ).

VO-Compatible Architecture for Managing and Processing Images of Moving Celestial Bodies : Application to the Gaia-GBOT Project

NASA Astrophysics Data System (ADS)

Barache, C.; Bouquillon, S.; Carlucci, T.; Taris, F.; Michel, L.; Altmann, M.

2013-10-01

The Ground Based Optical Tracking (GBOT) group is a part of the Data Processing and Analysis Consortium, the large consortium of over 400 scientists from many European countries, charged with the scientific conduction of the Gaia mission by ESA. The GBOT group is in charge of the optical part of tracking of the Gaia satellite. This optical tracking is necessary to allow the Gaia mission to fully reach its goal in terms of astrometry precision level. These observations will be done daily, during the 5 years of the mission, with the use of optical CCD frames taken by a small network of 1-2m class telescopes located all over the world. The requirements for the accuracy on the satellite position determination, with respect of the stars in the field of view, are 20 mas. These optical satellite positions will be sent weekly by GBOT to the SOC of ESAC and used with other kinds of observations (radio ranging and Doppler) by MOC of ESOC to improve the Gaia ephemeris. For this purpose, we developed a set of accurate astrometry reduction programs specially adapted for tracking moving objects. The inputs of these programs for each tracked target are an ephemeris and a set of FITS images. The outputs for each image are: a file containing all information about the detected objects, a catalogue file used for calibration, a TIFF file for visual explanation of the reduction result, and an improvement of the fits image header. The final result is an overview file containing only the data related to the target extracted from all the images. These programs are written in GNU Fortran 95 and provide results in VOTable format (supported by Virtual Observatory protocols). All these results are sent automatically into the GBOT Database which is built with the SAADA freeware. The user of this Database can archive and query the data but also, thanks to the delegate option provided by SAADA, select a set of images and directly run the GBOT reduction programs with a dedicated Web interface. For more information about SAADA (an Automatic System for Astronomy Data Archive under GPL license and VOcompatible), see the related paper Michel et al. (2013).

PALM-USM v1.0: A new urban surface model integrated into the PALM large-eddy simulation model

NASA Astrophysics Data System (ADS)

Resler, Jaroslav; Krč, Pavel; Belda, Michal; Juruš, Pavel; Benešová, Nina; Lopata, Jan; Vlček, Ondřej; Damašková, Daša; Eben, Kryštof; Derbek, Přemysl; Maronga, Björn; Kanani-Sühring, Farah

2017-10-01

Urban areas are an important part of the climate system and many aspects of urban climate have direct effects on human health and living conditions. This implies that reliable tools for local urban climate studies supporting sustainable urban planning are needed. However, a realistic implementation of urban canopy processes still poses a serious challenge for weather and climate modelling for the current generation of numerical models. To address this demand, a new urban surface model (USM), describing the surface energy processes for urban environments, was developed and integrated as a module into the PALM large-eddy simulation model. The development of the presented first version of the USM originated from modelling the urban heat island during summer heat wave episodes and thus implements primarily processes important in such conditions. The USM contains a multi-reflection radiation model for shortwave and longwave radiation with an integrated model of absorption of radiation by resolved plant canopy (i.e. trees, shrubs). Furthermore, it consists of an energy balance solver for horizontal and vertical impervious surfaces, and thermal diffusion in ground, wall, and roof materials, and it includes a simple model for the consideration of anthropogenic heat sources. The USM was parallelized using the standard Message Passing Interface and performance testing demonstrates that the computational costs of the USM are reasonable on typical clusters for the tested configurations. The module was fully integrated into PALM and is available via its online repository under the GNU General Public License (GPL). The USM was tested on a summer heat-wave episode for a selected Prague crossroads. The general representation of the urban boundary layer and patterns of surface temperatures of various surface types (walls, pavement) are in good agreement with in situ observations made in Prague. Additional simulations were performed in order to assess the sensitivity of the results to uncertainties in the material parameters, the domain size, and the general effect of the USM itself. The first version of the USM is limited to the processes most relevant to the study of summer heat waves and serves as a basis for ongoing development which will address additional processes of the urban environment and lead to improvements to extend the utilization of the USM to other environments and conditions.

Introducing an R-package for calculating channel width and other basic metrics for irregular river polygons

NASA Astrophysics Data System (ADS)

Golly, Antonius; Turowski, Jens

2017-04-01

The width of fluvial streams and channel beds is an important metric for a large number of hydraulic, geomorphic and ecologic applications. For example, for a given discharge the local channel width determines the water flow velocity and thus the sediment transport capacity of a reach. Since streams often have irregular shapes with uneven channel banks, the channel width strongly varies along the channel. Although, the geometry of streams or their beds can be measured easily in the field (e.g. with a Total Station or GPS) or from maps or aerial images in a GIS, the width of the stream cannot be identified objectively without further data processing, since the results are more or less irregular polygons with sometimes bended shapes. An objective quantification of the channel width and other metrics requires automated algorithms that are applicable over a range of channel shapes and spatial scales. Here, we present a lightweight software suite with a small number of functions that process 2D or 3D geometrical data of channels or channel beds. The software, written as an R-package, accepts various text data formats and can be configured through five parameters. It creates interactive overview plots (if desired) and produces three basic channel metrics: the centerline, the channel width along the centerline and the slope along the centerline. The centerline is an optimized line that minimizes the distances to both channel banks. This centerline gives also a measure for the real length and slope of the channel. From this centerline perpendicular transects are generated which allow for the calculation of the channel width where they intersect with the channel banks. Briefly, we present an example and demonstrate the importance of these metrics in a use case of a steep stream, the Erlenbach stream in Switzerland. We were motivated to develop and publish the algorithm in an open-source framework, since only proprietary solutions were available at that time. The software is developed in R and is published under GNU GPL meaning it is free to use, edit and copy. This makes the software available also to users who do not own a MATLAB or ARCMAP license for which similar products exist.

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

PubMed Central

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

2017-01-01

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

Investigating Advances in the Acquisition of Secure Systems Based on Open Architectures

DTIC Science & Technology

2012-08-30

markets (Guertin & Womble, 2012), efficient testing of component‐based OA...workalike of the closed‐source Second Life VW platform. Second Life (2012) is the current market leader in rapid virtual world development and...Strong Copyleft GPL, AGPL Many rights; obligations on “nearby” works Proprietary CTL , EULAs, TOSs Few rights Typical rights

BOINC: compute for science

Science.gov Websites

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

Two-Dimensional Nuclear Magnetic Resonance Structure Determination Module for Introductory Biochemistry: Synthesis and Structural Characterization of Lyso-Glycerophospholipids

ERIC Educational Resources Information Center

Garrett, Teresa A.; Rose, Rebecca L.; Bell, Sidney M.

2013-01-01

In this laboratory module, introductory biochemistry students are exposed to two-dimensional [superscript 1]H-nuclear magnetic resonance of glycerophospholipids (GPLs). Working in groups of three, students enzymatically synthesized and purified a variety of 2-acyl lyso GPLs. The structure of the 2-acyl lyso GPL was verified using [superscript…

Chemical Stockpile Disposal Program. Monitoring Concept Plan

DTIC Science & Technology

1987-09-10

Government Owned Contractor Operated GPL General Population Limit H Bis (2-chloroethyl) sulfide or Levinstein Mustard (75% purity) P HCI Hydrogen Chloride... government agencies, will provide technical expertise and equipment necessary to monitor affected areas and resources. 2-25 SECTIO 3 PROCESS CONTROL AND...conditions and to issue correct emergency response notifications, if required. The process sensors work in conjunction with the process control system and

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

Challenges in the Development and Evolution of Secure Open Architecture Command and Control Systems (Briefing Charts)

DTIC Science & Technology

2013-06-01

widgets for an OA system Design-time architecture: Browser, email, widget, DB, OS Go ogle Instance architecture: Chrome, Gmail, Google...provides functionally similar components or applications compatible with an OA system design Firefox Browser, WP, calendar Opera Instance...architecture: Firefox , AbiWord, Evolution, Fedora GPL Ab1Word Google Docs Instance ardlitecture: Fire fox, OR Google cal., Google Docs, Fedora

PAL: A Positional Astronomy Library

NASA Astrophysics Data System (ADS)

Jenness, T.; Berry, D. S.

2013-10-01

PAL is a new positional astronomy library written in C that attempts to retain the SLALIB API but is distributed with an open source GPL license. The library depends on the IAU SOFA library wherever a SOFA routine exists and uses the most recent nutation and precession models. Currently about 100 of the 200 SLALIB routines are available. Interfaces are also available from Perl and Python. PAL is freely available via github.

Regional changes in CNS and retinal glycerophospholipid profiles with age: a molecular blueprint[S

PubMed Central

Hopiavuori, Blake R.; Agbaga, Martin-Paul; Brush, Richard S.; Sullivan, Michael T.; Sonntag, William E.; Anderson, Robert E.

2017-01-01

We present here a quantitative molecular blueprint of the three major glycerophospholipid (GPL) classes, phosphatidylcholine (PC), phosphatidylserine (PS), and phosphatidylethanolamine (PE), in retina and six regions of the brain in C57Bl6 mice at 2, 10, and 26 months of age. We found an age-related increase in molecular species containing saturated and monoenoic FAs and an overall decrease in the longer-chain PUFA molecular species across brain regions, with loss of DHA-containing molecular species as the most consistent and dramatic finding. Although we found very-long-chain PUFAs (VLC-PUFAs) (⩾C28) in PC in the retina, no detectable levels were found in any brain region at any of the ages examined. All brain regions (except hippocampus and retina) showed a significant increase with age in PE plasmalogens. All three retina GPLs had di-PUFA molecular species (predominantly 44:12), which were most abundant in PS (∼30%). In contrast, low levels of di-PUFA GPL (1–2%) were found in all regions of the brain. This study provides a regional and age-related assessment of the brain’s lipidome with a level of detail, inclusion, and quantification that has not heretofore been published. PMID:28202633

HYPERDIRE-HYPERgeometric functions DIfferential REduction: Mathematica-based packages for the differential reduction of generalized hypergeometric functions: Lauricella function FC of three variables

NASA Astrophysics Data System (ADS)

Bytev, Vladimir V.; Kniehl, Bernd A.

2016-09-01

We present a further extension of the HYPERDIRE project, which is devoted to the creation of a set of Mathematica-based program packages for manipulations with Horn-type hypergeometric functions on the basis of differential equations. Specifically, we present the implementation of the differential reduction for the Lauricella function FC of three variables. Catalogue identifier: AEPP_v4_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPP_v4_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.: 243461 No. of bytes in distributed program, including test data, etc.: 61610782 Distribution format: tar.gz Programming language: Mathematica. Computer: All computers running Mathematica. Operating system: Operating systems running Mathematica. Classification: 4.4. Does the new version supersede the previous version?: No, it significantly extends the previous version. Nature of problem: Reduction of hypergeometric function FC of three variables to a set of basis functions. Solution method: Differential reduction. Reasons for new version: The extension package allows the user to handle the Lauricella function FC of three variables. Summary of revisions: The previous version goes unchanged. Running time: Depends on the complexity of the problem.

Streamlining the Process of Acquiring Secure Open Architecture Software Systems

DTIC Science & Technology

2013-10-08

Microsoft.NET, Enterprise Java Beans, GNU Lesser General Public License (LGPL) libraries, and data communication protocols like the Hypertext Transfer...NetBeans development environments),  customer relationship management (SugarCRM),  database management systems (PostgreSQL, MySQL ),  operating

FAST: FAST Analysis of Sequences Toolbox

PubMed Central

Lawrence, Travis J.; Kauffman, Kyle T.; Amrine, Katherine C. H.; Carper, Dana L.; Lee, Raymond S.; Becich, Peter J.; Canales, Claudia J.; Ardell, David H.

2015-01-01

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought. PMID:26042145

Biosynthesis of UDP-GlcNAc, UndPP-GlcNAc and UDP-GlcNAcA Involves Three Easily Distinguished 4-Epimerase Enzymes, Gne, Gnu and GnaB

PubMed Central

Cunneen, Monica M.; Liu, Bin; Wang, Lei; Reeves, Peter R.

2013-01-01

We have undertaken an extensive survey of a group of epimerases originally named Gne, that were thought to be responsible for inter-conversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylgalactosamine (UDP-GalNAc). The analysis builds on recent work clarifying the specificity of some of these epimerases. We find three well defined clades responsible for inter-conversion of the gluco- and galacto-configuration at C4 of different N-acetylhexosamines. Their major biological roles are the formation of UDP-GalNAc, UDP-N-acetylgalactosaminuronic acid (UDP-GalNAcA) and undecaprenyl pyrophosphate-N-acetylgalactosamine (UndPP-GalNAc) from the corresponding glucose forms. We propose that the clade of UDP-GlcNAcA epimerase genes be named gnaB and the clade of UndPP-GlcNAc epimerase genes be named gnu, while the UDP-GlcNAc epimerase genes retain the name gne. The Gne epimerases, as now defined after exclusion of those to be named GnaB or Gnu, are in the same clade as the GalE 4-epimerases for inter-conversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal). This work brings clarity to an area that had become quite confusing. The identification of distinct enzymes for epimerisation of UDP-GlcNAc, UDP-GlcNAcA and UndPP-GlcNAc will greatly facilitate allocation of gene function in polysaccharide gene clusters, including those found in bacterial genome sequences. A table of the accession numbers for the 295 proteins used in the analysis is provided to enable the major tree to be regenerated with the inclusion of additional proteins of interest. This and other suggestions for annotation of 4-epimerase genes will facilitate annotation. PMID:23799153

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.

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

Investigating Advances in the Acquisition of Systems Based on Open Architecture and Open Source Software

DTIC Science & Technology

2011-08-01

dominates the global mobile application market and mobile computing software ecosystems. But overall, OA systems are not necessarily excluded from...License 3.0 (OSL)  Corel Transactional License ( CTL ) The licenses were chosen to represent a variety of kinds of licenses, and include one...proprietary ( CTL ), three academic (Apache, BSD, MIT), and six reciprocal licenses (CPL, EPL, GPL, LGPL, MPL, OSL) that take varying approaches in

MinFinder: Locating all the local minima of a function

NASA Astrophysics Data System (ADS)

Tsoulos, Ioannis G.; Lagaris, Isaac E.

2006-01-01

A new stochastic clustering algorithm is introduced that aims to locate all the local minima of a multidimensional continuous and differentiable function inside a bounded domain. The accompanying software (MinFinder) is written in ANSI C++. However, the user may code his objective function either in C++, C or Fortran 77. We compare the performance of this new method to the performance of Multistart and Topographical Multilevel Single Linkage Clustering on a set of benchmark problems. Program summaryTitle of program:MinFinder Catalogue identifier:ADWU Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWU Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which is has been tested:The tool is designed to be portable in all systems running the GNU C++ compiler Installation:University of Ioannina, Greece Programming language used:GNU-C++, GNU-C, GNU Fortran 77 Memory required to execute with typical data:200 KB No. of bits in a word:32 No. of processors used:1 Has the code been vectorized or parallelized?:no No. of lines in distributed program, including test data, etc.:5797 No. of bytes in distributed program, including test data, etc.:588 121 Distribution format:gzipped tar file Nature of the physical 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, employing a "least squares" type of objective, one may encounter many local minima that do not correspond to solutions, i.e. they are far from zero. Method of solution:Using a uniform pdf, points are sampled from the rectangular search 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. The employed local procedure is a BFGS version due to Powell. Further searching is terminated when all the local minima inside the search domain are thought to be found. This is accomplished via the double-box rule. Typical running time:Depending on the objective function

CVXPY: A Python-Embedded Modeling Language for Convex Optimization.

PubMed

Diamond, Steven; Boyd, Stephen

2016-04-01

CVXPY is a domain-specific language for convex optimization embedded in Python. It allows the user to express convex optimization problems in a natural syntax that follows the math, rather than in the restrictive standard form required by solvers. CVXPY makes it easy to combine convex optimization with high-level features of Python such as parallelism and object-oriented design. CVXPY is available at http://www.cvxpy.org/ under the GPL license, along with documentation and examples.

Developing Novel Conjugate HIV-1 Subunit Therapeutic Vaccines.

DTIC Science & Technology

1996-06-01

significant CD4-binding was observed for gpl20-KLH conjugates prepared using 1 -ethyl- 3 -( 3 - dimethylaminopropyl )carbodiimide hydrochloride (EDC). EDC...Management and Budget, Paperwork Reduction Project (0704-0188), Washington, DC 20503. 1 . AGENCY USE ONLY (Leave blank) 2. REPORT DATE 3 . REPORT TYPE AND...FOREWORD 3 TABLE OF CONTENTS 4 INTRODUCTION 5 RESULTS 6 Specific Aim # 1 : Production and characterization of HIV-JlV and HIV-1jR_ gp120 6 Development and

Mycobacterium avium Genes Associated with the Ability To Form a Biofilm

PubMed Central

Yamazaki, Yoshitaka; Danelishvili, Lia; Wu, Martin; MacNab, Molly; Bermudez, Luiz E.

2006-01-01

Mycobacterium avium is widely distributed in the environment, and it is chiefly found in water and soil. M. avium, as well as Mycobacterium smegmatis, has been recognized to produce a biofilm or biofilm-like structure. We screened an M. avium green fluorescent protein (GFP) promoter library in M. smegmatis for genes involved in biofilm formation on polyvinyl chloride (PVC) plates. Clones associated with increased GFP expression ≥2.0-fold over the baseline were sequenced. Seventeen genes, most encoding proteins of the tricarboxylic acid (TCA) cycle and GDP-mannose and fatty acid biosynthesis, were identified. Their regulation in M. avium was confirmed by examining the expression of a set of genes by real-time PCR after incubation on PVC plates. In addition, screening of 2,000 clones of a transposon mutant bank constructed using M. avium strain A5, a mycobacterial strain with the ability to produce large amounts of biofilm, revealed four mutants with an impaired ability to form biofilm. Genes interrupted by transposons were homologues of M. tuberculosis 6-oxodehydrogenase (sucA), enzymes of the TCA cycle, protein synthetase (pstB), enzymes of glycopeptidolipid (GPL) synthesis, and Rv1565c (a hypothetical membrane protein). In conclusion, it appears that GPL biosynthesis, including the GDP-mannose biosynthesis pathway, is the most important pathway involved in the production of M. avium biofilm. PMID:16391123

Deletion of a dehydratase important for intracellular growth and cording renders rough Mycobacterium abscessus avirulent

PubMed Central

Halloum, Iman; Carrère-Kremer, Séverine; Blaise, Mickael; Viljoen, Albertus; Bernut, Audrey; Le Moigne, Vincent; Vilchèze, Catherine; Guérardel, Yann; Lutfalla, Georges; Herrmann, Jean-Louis; Jacobs, William R.; Kremer, Laurent

2016-01-01

Mycobacterium abscessus (Mabs) is a rapidly growing Mycobacterium and an emerging pathogen in humans. Transitioning from a smooth (S) high-glycopeptidolipid (GPL) producer to a rough (R) low-GPL producer is associated with increased virulence in zebrafish, which involves the formation of massive serpentine cords, abscesses, and rapid larval death. Generating a cord-deficient Mabs mutant would allow us to address the contribution of cording in the physiopathological signs of the R variant. Herein, a deletion mutant of MAB_4780, encoding a dehydratase, distinct from the β-hydroxyacyl-ACP dehydratase HadABC complex, was constructed in the R morphotype. This mutant exhibited an alteration of the mycolic acid composition and a pronounced defect in cording. This correlated with an extremely attenuated phenotype not only in wild-type but also in immunocompromised zebrafish embryos lacking either macrophages or neutrophils. The abolition of granuloma formation in embryos infected with the dehydratase mutant was associated with a failure to replicate in macrophages, presumably due to limited inhibition of the phagolysosomal fusion. Overall, these results indicate that MAB_4780 is required for Mabs to successfully establish acute and lethal infections. Therefore, targeting MAB_4780 may represent an attractive antivirulence strategy to control Mabs infections, refractory to most standard chemotherapeutic interventions. The combination of a dehydratase assay with a high-resolution crystal structure of MAB_4780 opens the way to identify such specific inhibitors. PMID:27385830

Interfaces for Distributed Systems of Information Servers.

ERIC Educational Resources Information Center

Kahle, Brewster M.; And Others

1993-01-01

Describes five interfaces to remote, full-text databases accessed through distributed systems of servers. These are WAIStation for the Macintosh, XWAIS for X-Windows, GWAIS for Gnu-Emacs; SWAIS for dumb terminals, and Rosebud for the Macintosh. Sixteen illustrations provide examples of display screens. Problems and needed improvements are…

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

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.

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.

CVXPY: A Python-Embedded Modeling Language for Convex Optimization

PubMed Central

Diamond, Steven; Boyd, Stephen

2016-01-01

CVXPY is a domain-specific language for convex optimization embedded in Python. It allows the user to express convex optimization problems in a natural syntax that follows the math, rather than in the restrictive standard form required by solvers. CVXPY makes it easy to combine convex optimization with high-level features of Python such as parallelism and object-oriented design. CVXPY is available at http://www.cvxpy.org/ under the GPL license, along with documentation and examples. PMID:27375369

Modeling and Simulation of Fleet Air Defense Systems Using EADSIM

DTIC Science & Technology

1993-06-01

LT DAVID VAN VELDHUIZEN PHILLIPS LABORATORY/WST 3550ABERDEEN AVE SE KIRTLAND AFB NM 87117-5776 85 PLESSEY POC: Paul Markwardt Addr: PLESSEY ELECTRONICS...LAIL, JR. Addr: PEO, GPALS ATTN SFAE-GPL-TMD-SI-B (LAIL) PO BOX 1500 HUNTSVILLE AL 35807-301 84 PHILLIPS LABORATORY POC: L. David Van Velclhuizen Addr...SHURE PO BOX 92957 EL SEGUNDO CA 90009-2957 107 TRW-HUNTSVILLE POC: Don Owens Addr: TRW 213 WYNN DRIVE ATTN DON OWENS HUNTSVILLE AL 35805 108 TRW

SCAMP: Automatic Astrometric and Photometric Calibration

NASA Astrophysics Data System (ADS)

Bertin, Emmanuel

2010-10-01

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

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…

Design, Development, and Testing of a Network Frequency Selection Service (NFSS)

DTIC Science & Technology

1994-02-14

mercial simulation software (Sim++), word processor ( FrameMaker ), editor (Gnu Emacs), software ver- sion control (Revision Control System (RCS)), system...of FrameMaker ".mif" files. When viewed using FrameMaker or a PostScript reader, each page of results appears as two columns by four rows of graphics

Modular Open-Source Software for Item Factor Analysis

ERIC Educational Resources Information Center

Pritikin, Joshua N.; Hunter, Micheal D.; Boker, Steven M.

2015-01-01

This article introduces an item factor analysis (IFA) module for "OpenMx," a free, open-source, and modular statistical modeling package that runs within the R programming environment on GNU/Linux, Mac OS X, and Microsoft Windows. The IFA module offers a novel model specification language that is well suited to programmatic generation…

Mighty Math[TM] Zoo Zillions[TM]. [CD-ROM].

ERIC Educational Resources Information Center

1996

Zoo Zillions contains five activities for grades K-2: Annie's Jungle Trail, 3D Gallery, Number Line Express, Gnu Ewe Boutique, and Fish Stories. These activities enable children to review and practice basic mathematics skills; identify three-dimensional shapes, watch them in motion, and create their own three-dimensional designs; locate numbers…

OpenMP-accelerated SWAT simulation using Intel C and FORTRAN compilers: Development and benchmark

NASA Astrophysics Data System (ADS)

Ki, Seo Jin; Sugimura, Tak; Kim, Albert S.

2015-02-01

We developed a practical method to accelerate execution of Soil and Water Assessment Tool (SWAT) using open (free) computational resources. The SWAT source code (rev 622) was recompiled using a non-commercial Intel FORTRAN compiler in Ubuntu 12.04 LTS Linux platform, and newly named iOMP-SWAT in this study. GNU utilities of make, gprof, and diff were used to develop the iOMP-SWAT package, profile memory usage, and check identicalness of parallel and serial simulations. Among 302 SWAT subroutines, the slowest routines were identified using GNU gprof, and later modified using Open Multiple Processing (OpenMP) library in an 8-core shared memory system. In addition, a C wrapping function was used to rapidly set large arrays to zero by cross compiling with the original SWAT FORTRAN package. A universal speedup ratio of 2.3 was achieved using input data sets of a large number of hydrological response units. As we specifically focus on acceleration of a single SWAT run, the use of iOMP-SWAT for parameter calibrations will significantly improve the performance of SWAT optimization.

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

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.

Carnivore fecal chemicals suppress feeding by Alpine goats (Capra hircus).

PubMed

Weldon, P J; Graham, D P; Mears, L P

1993-12-01

The efficacy of carnivore and ungulate fecal chemicals in suppressing the feeding behavior of Alpine goats (Capra hircus) was examined. In the first four experiments, goats were offered food covered with paper strips treated with fecal extracts of the Bengal tiger, Siberian tiger, African lion, and brown bear, respectively; food covered with solvent-treated and untreated (plain) papers served as controls in each experiment. Goats made fewer head entries into, and ate less food from, buckets containing fecal extracts. In the fifth experiment, goats were offered food covered with paper strips treated with fecal extracts of the puma, Dorcas gazelle, white-bearded gnu, and conspecifics; food covered with solvent-treated and plain papers again served as controls. The amounts of food consumed from buckets containing puma, gazelle, gnu, and solvent treatments were statistically indistinguishable, but less food was consumed from them than from buckets containing the goat-scented or plain papers. No significant differences among treatments were detected with respect to head entries. Field experiments are needed on the use of predator-derived chemicals to reduce damage by goats to vegetation.

Expanded breadth of the T-cell response to mosaic HIV-1 envelope DNA vaccination

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

Korber, Bette; Fischer, William; Wallstrom, Timothy

2009-01-01

An effective AIDS vaccine must control highly diverse circulating strains of HIV-1. Among HIV -I gene products, the envelope (Env) protein contains variable as well as conserved regions. In this report, an informatic approach to the design of T-cell vaccines directed to HIV -I Env M group global sequences was tested. Synthetic Env antigens were designed to express mosaics that maximize the inclusion of common potential Tcell epitope (PTE) 9-mers and minimize the inclusion of rare epitopes likely to elicit strain-specific responses. DNA vaccines were evaluated using intracellular cytokine staining (ICS) in inbred mice with a standardized panel of highlymore » conserved 15-mer PTE peptides. I, 2 and 3 mosaic sets were developed that increased theoretical epitope coverage. The breadth and magnitude ofT-cell immunity stimulated by these vaccines were compared to natural strain Env's; additional comparisons were performed on mutant Env's, including gpl60 or gpl45 with or without V regions and gp41 deletions. Among them, the 2 or 3 mosaic Env sets elicited the optimal CD4 and CD8 responses. These responses were most evident in CD8 T cells; the 3 mosaic set elicited responses to an average of 8 peptide pools compared to 2 pools for a set of3 natural Env's. Synthetic mosaic HIV -I antigens can therefore induce T-cell responses with expanded breadth and may facilitate the development of effective T -cell-based HIV -1 vaccines.« less

Tera-Op Reliable Intelligently Adaptive Processing System (TRIPS)

DTIC Science & Technology

2004-04-01

flop creates a loadable FIFO queue, fifo pload. A prototype of the HML simulator is implemented using a functional language OCaml . The language type...Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 7.1.2 Hardware Meta Language ...operates on the TRIPS Intermediate Language (TIL) produced by the Scale compiler. We also adapted the gnu binary utilities to implement an assembler and

autokonf - A Configuration Script Generator Implemented in Perl

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

Reus, J F

This paper discusses configuration scripts in general and the scripting language issues involved. A brief description of GNU autoconf is provided along with a contrasting overview of autokonf, a configuration script generator implemented in Perl, whose macros are implemented in Perl, generating a configuration script in Perl. It is very portable, easily extensible, and readily mastered.

Distributed Transmitter Localization by Power Difference of Arrival (PDOA) on a Network of GNU Radio Sensors

DTIC Science & Technology

2015-02-03

requiring the least hardware investment is to localize by received signal strength [1, 4, 5]. Because our intended scenario of low-complexity...MHz were taken with a spectrum analyzer program on the USRP and a range finder was used to measure the distance between the emitter and sensor

Cross-Border Collaboration in History among Nordic Students: A Case Study about Creating Innovative ICT Didactic Models

ERIC Educational Resources Information Center

Spante, Maria; Karlsen, Asgjerd Vea; Nortvig, Anne-Mette; Christiansen, Rene B.

2014-01-01

Gränsöverskridande Nordisk Undervisning/Utdanelse (GNU, meaning Cross-Border Nordic Education), the larger Nordic project, under which this case study was carried out, aims at developing innovative, cross-border teaching models in different subject domains in elementary school, including mathematics, language, science, social studies and history.…

Timescape: a simple space-time interpolation geostatistical Algorithm

NASA Astrophysics Data System (ADS)

Ciolfi, Marco; Chiocchini, Francesca; Gravichkova, Olga; Pisanelli, Andrea; Portarena, Silvia; Scartazza, Andrea; Brugnoli, Enrico; Lauteri, Marco

2016-04-01

Environmental sciences include both time and space variability in their datasets. Some established tools exist for both spatial interpolation and time series analysis alone, but mixing space and time variability calls for compromise: Researchers are often forced to choose which is the main source of variation, neglecting the other. We propose a simple algorithm, which can be used in many fields of Earth and environmental sciences when both time and space variability must be considered on equal grounds. The algorithm has already been implemented in Java language and the software is currently available at https://sourceforge.net/projects/timescapeglobal/ (it is published under GNU-GPL v3.0 Free Software License). The published version of the software, Timescape Global, is focused on continent- to Earth-wide spatial domains, using global longitude-latitude coordinates for samples localization. The companion Timescape Local software is currently under development ad will be published with an open license as well; it will use projected coordinates for a local to regional space scale. The basic idea of the Timescape Algorithm consists in converting time into a sort of third spatial dimension, with the addition of some causal constraints, which drive the interpolation including or excluding observations according to some user-defined rules. The algorithm is applicable, as a matter of principle, to anything that can be represented with a continuous variable (a scalar field, technically speaking). The input dataset should contain position, time and observed value of all samples. Ancillary data can be included in the interpolation as well. After the time-space conversion, Timescape follows basically the old-fashioned IDW (Inverse Distance Weighted) interpolation Algorithm, although users have a wide choice of customization options that, at least partially, overcome some of the known issues of IDW. The three-dimensional model produced by the Timescape Algorithm can be explored in many ways, including the extraction of time series at fixed locations and GIS layers at constant times, allowing for the inclusion of the model in the users' established workflow. The software requirements are relatively modest since it has been purposely designed for potential users in various research field with a limited computing power at their disposal. Any respectful modern PC or laptop can run it. Users however need a separate database for sample data and models storage because these can be quite bulky in terms of data output: a single model can be composed of several billions of voxels (three-dimensional discrete cells, a sort of 3D pixels). Running times range from a few minutes for sketch models to some days of evaluation for a full-size model, depending on the users' hardware and model size.

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

PubMed Central

Ebhardt, H Alexander; Wiese, Kay C; Unrau, Peter J

2006-01-01

Background DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2-5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. Results Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on Conclusion Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6-8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2,3,10,11]. PMID:16584563

A Global Fitting Approach For Doppler Broadening Thermometry

NASA Astrophysics Data System (ADS)

Amodio, Pasquale; Moretti, Luigi; De Vizia, Maria Domenica; Gianfrani, Livio

2014-06-01

Very recently, a spectroscopic determination of the Boltzmann constant, kB, has been performed at the Second University of Naples by means of a rather sophisticated implementation of Doppler Broadening Thermometry (DBT)1. Performed on a 18O-enriched water sample, at a wavelength of 1.39 µm, the experiment has provided a value for kB with a combined uncertainty of 24 parts over 106, which is the best result obtained so far, by using an optical method. In the spectral analysis procedure, the partially correlated speed-dependent hard-collision (pC-SDHC) model was adopted. The uncertainty budget has clearly revealed that the major contributions come from the statistical uncertainty (type A) and from the uncertainty associated to the line-shape model (type B)2. In the present work, we present the first results of a theoretical and numerical work aimed at reducing these uncertainty components. It is well known that molecular line shapes exhibit clear deviations from the time honoured Voigt profile. Even in the case of a well isolated spectral line, under the influence of binary collisions, in the Doppler regime, the shape can be quite complicated by the joint occurrence of velocity-change collisions and speed-dependent effects. The partially correlated speed-dependent Keilson-Storer profile (pC-SDKS) has been recently proposed as a very realistic model, capable of reproducing very accurately the absorption spectra for self-colliding water molecules, in the near infrared3. Unfortunately, the model is so complex that it cannot be implemented into a fitting routine for the analysis of experimental spectra. Therefore, we have developed a MATLAB code to simulate a variety of H218O spectra in thermodynamic conditions identical to the one of our DBT experiment, using the pC-SDKS model. The numerical calculations to determine such a profile have a very large computational cost, resulting from a very sophisticated iterative procedure. Hence, the numerically simulated spectra (with the addition of random noise) have been used to test the validity of simplified line shape models, such as the speed-dependent Galatry (SDG) profile and pC-SDHC model. In particular, we have used the global fitting procedure that is described in Amodio et al4. Such a procedure is very effective in reducing the uncertainty resulting from statistical correlation among free parameters. Therefore, the analysis of large amounts of simulated spectra has allowed us to study the influence of the choice of the model and quantify the achievable precision and accuracy levels, at the present value of the signal-to-noise ratio. freely redistributable under the GPL http://www.gnu.org.

Technical Note: FreeCT_ICD: An Open Source Implementation of a Model-Based Iterative Reconstruction Method using Coordinate Descent Optimization for CT Imaging Investigations.

PubMed

Hoffman, John M; Noo, Frédéric; Young, Stefano; Hsieh, Scott S; McNitt-Gray, Michael

2018-06-01

To facilitate investigations into the impacts of acquisition and reconstruction parameters on quantitative imaging, radiomics and CAD using CT imaging, we previously released an open source implementation of a conventional weighted filtered backprojection reconstruction called FreeCT_wFBP. Our purpose was to extend that work by providing an open-source implementation of a model-based iterative reconstruction method using coordinate descent optimization, called FreeCT_ICD. Model-based iterative reconstruction offers the potential for substantial radiation dose reduction, but can impose substantial computational processing and storage requirements. FreeCT_ICD is an open source implementation of a model-based iterative reconstruction method that provides a reasonable tradeoff between these requirements. This was accomplished by adapting a previously proposed method that allows the system matrix to be stored with a reasonable memory requirement. The method amounts to describing the attenuation coefficient using rotating slices that follow the helical geometry. In the initially-proposed version, the rotating slices are themselves described using blobs. We have replaced this description by a unique model that relies on tri-linear interpolation together with the principles of Joseph's method. This model offers an improvement in memory requirement while still allowing highly accurate reconstruction for conventional CT geometries. The system matrix is stored column-wise and combined with an iterative coordinate descent (ICD) optimization. The result is FreeCT_ICD, which is a reconstruction program developed on the Linux platform using C++ libraries and the open source GNU GPL v2.0 license. The software is capable of reconstructing raw projection data of helical CT scans. In this work, the software has been described and evaluated by reconstructing datasets exported from a clinical scanner which consisted of an ACR accreditation phantom dataset and a clinical pediatric thoracic scan. For the ACR phantom, image quality was comparable to clinical reconstructions as well as reconstructions using open-source FreeCT_wFBP software. The pediatric thoracic scan also yielded acceptable results. In addition, we did not observe any deleterious impact in image quality associated with the utilization of rotating slices. These evaluations also demonstrated reasonable tradeoffs in storage requirements and computational demands. FreeCT_ICD is an open-source implementation of a model-based iterative reconstruction method that extends the capabilities of previously released open source reconstruction software and provides the ability to perform vendor-independent reconstructions of clinically acquired raw projection data. This implementation represents a reasonable tradeoff between storage and computational requirements and has demonstrated acceptable image quality in both simulated and clinical image datasets. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Benchmarking GNU Radio Kernels and Multi-Processor Scheduling

DTIC Science & Technology

2013-01-14

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

Automatic Astrometric and Photometric Calibration with SCAMP

NASA Astrophysics Data System (ADS)

Bertin, E.

2006-07-01

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

67 FR 24495 - United States v. Microsoft Corporation; Public Comments; Notice (MTC-00003461 - MTC-00007629)

Federal Register 2010, 2011, 2012, 2013, 2014

2002-05-03

... (web-serving software), Linux, Perl, and those who are building a compatible & free version of MS`s..., Argument from Design Argument from Design-Web & Multimedia [email protected] http://www.ardes.com MTC-00003464... organization could be a good target for this effort. Their web address is http:// www.gnu.org/. This effort...

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

PubMed

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

2011-04-15

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

Development of a Multi-frequency Interferometer Telescope for Radio Astronomy (MITRA)

NASA Astrophysics Data System (ADS)

Ingala, Dominique Guelord Kumamputu

2015-03-01

This dissertation describes the development and construction of the Multi-frequency Interferometer Telescope for Radio Astronomy (MITRA) at the Durban University of Technology. The MITRA station consists of 2 antenna arrays separated by a baseline distance of 8 m. Each array consists of 8 Log-Periodic Dipole Antennas (LPDAs) operating from 200 MHz to 800 MHz. The design and construction of the LPDA antenna and receiver system is described. The receiver topology provides an equivalent noise temperature of 113.1 K and 55.1 dB of gain. The Intermediate Frequency (IF) stage was designed to produce a fixed IF frequency of 800 MHz. The digital Back-End and correlator were implemented using a low cost Software Defined Radio (SDR) platform and Gnu-Radio software. Gnu-Octave was used for data analysis to generate the relevant received signal parameters including total power, real, and imaginary, magnitude and phase components. Measured results show that interference fringes were successfully detected within the bandwidth of the receiver using a Radio Frequency (RF) generator as a simulated source. This research was presented at the IEEE Africon 2013 / URSI Session Mauritius, and published in the proceedings.

cit: hypothesis testing software for mediation analysis in genomic applications.

PubMed

Millstein, Joshua; Chen, Gary K; Breton, Carrie V

2016-08-01

The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data/models accommodated by the software and (iii) low power of common multiple testing approaches. The causal inference test (CIT) is based on hypothesis testing rather than estimation, allowing the testable assumptions to be evaluated in the determination of statistical significance. A user-friendly software package provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators. It can handle single and multiple binary and continuous instrumental variables, binary or continuous outcome variables and adjustment covariates. Also, the permutation-based FDR option provides a non-parametric implementation. Simulation studies demonstrate the validity of the cit package and show a substantial advantage of permutation-based FDR over other common multiple testing strategies. The cit open-source R package is freely available from the CRAN website (https://cran.r-project.org/web/packages/cit/index.html) with embedded C ++ code that utilizes the GNU Scientific Library, also freely available (http://www.gnu.org/software/gsl/). joshua.millstein@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

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.

Substrate Efflux Propensity Is the Key Determinant of Ca2+-independent Phospholipase A-β (iPLAβ)-mediated Glycerophospholipid Hydrolysis*

PubMed Central

Batchu, Krishna Chaithanya; Hokynar, Kati; Jeltsch, Michael; Mattonet, Kenny; Somerharju, Pentti

2015-01-01

The A-type phospholipases (PLAs) are key players in glycerophospholipid (GPL) homeostasis and in mammalian cells; Ca2+-independent PLA-β (iPLAβ) in particular has been implicated in this essential process. However, the regulation of this enzyme, which is necessary to avoid futile competition between synthesis and degradation, is not understood. Recently, we provided evidence that the efflux of the substrate molecules from the bilayer is the rate-limiting step in the hydrolysis of GPLs by some secretory (nonhomeostatic) PLAs. To study whether this is the case with iPLAβ as well, a mass spectrometric assay was employed to determine the rate of hydrolysis of multiple saturated and unsaturated GPL species in parallel using micelles or vesicle bilayers as the macrosubstrate. With micelles, the hydrolysis decreased with increasing acyl chain length independent of unsaturation, and modest discrimination between acyl positional isomers was observed, presumably due to the differences in the structure of the sn-1 and sn-2 acyl-binding sites of the protein. In striking contrast, no significant discrimination between positional isomers was observed with bilayers, and the rate of hydrolysis decreased with the acyl chain length logarithmically and far more than with micelles. These data provide compelling evidence that efflux of the substrate molecule from the bilayer, which also decreases monotonously with acyl chain length, is the rate-determining step in iPLAβ-mediated hydrolysis of GPLs in membranes. This finding is intriguing as it may help to understand how homeostatic PLAs are regulated and how degradation and biosynthesis are coordinated. PMID:25713085

Rocket Propellant Ducts (Cryogenic Fuel Lines): First Cut Approximations and Design Guidance

NASA Technical Reports Server (NTRS)

Brewer, William V.

1998-01-01

The design team has to set parameters before analysis can take place. Analysis is customarily a thorough and time consuming process which can take weeks or even months. Only when analysis is complete can the designer obtain feedback. If margins are negative, the process must be repeated to a greater or lesser degree until satisfactory results are achieved. Reduction of the number of iterations thru this loop would beneficially conserve time and resources. The task was to develop relatively simple, easy to use, guidelines and analytic tools that allow the designer to evaluate what effect various alternatives may have on performance as the design progresses. "Easy to use" is taken to mean closed form approximations and the use of graphic methods. "Simple" implies that 2-d and quasi 3-d approximations be exploited to whatever degree is useful before more resource intensive methods are applied. The objective is to avoid the grosser violation of performance margins at the outset. Initial efforts are focused on thermal expansion/contraction and rigid body kinematics as they relate to propellant duct displacements in the gimbal plane loop (GPL). The purpose of the loop is to place two flexible joints on the same two orthogonal intersecting axes as those of the rocket motor gimbals. This supposes the ducting will flex predictably with independent rotations corresponding to those of the motor gimbal actions. It can be shown that if GPL joint axes do not coincide with motor gimbal axes, displacement incompatibilities result in less predictable movement of the ducts.

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/.

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).