Using the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, P. J.; Berriman, G. B.; DuPrie, K.; Hanisch, R. J.; Mink, J. D.; Nemiroff, R. J.; Shamir, L.; Wallin, J. F.

2013-01-01

The Astrophysics Source Code Library (ASCL) is a free on-line registry of source codes that are of interest to astrophysicists; with over 500 codes, it is the largest collection of scientist-written astrophysics programs in existence. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are available either via a download site or from an identified source. An advisory committee formed in 2011 provides input and guides the development and expansion of the ASCL, and since January 2012, all accepted ASCL entries are indexed by ADS. Though software is increasingly important for the advancement of science in astrophysics, these methods are still often hidden from view or difficult to find. The ASCL (ascl.net/) seeks to improve the transparency and reproducibility of research by making these vital methods discoverable, and to provide recognition and incentive to those who write and release programs useful for astrophysics research. This poster provides a description of the ASCL, an update on recent additions, and the changes in the astrophysics community we are starting to see because of the ASCL.

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele

2001-01-01

This viewgraph presentation provides information on support sources available for the automatic parallelization of computer program. CAPTools, a support tool developed at the University of Greenwich, transforms, with user guidance, existing sequential Fortran code into parallel message passing code. Comparison routines are then run for debugging purposes, in essence, ensuring that the code transformation was accurate.

A Conference on Spacecraft Charging Technology - 1978, held at U.S. Air Force Academy, Colorado Springs, Colorado, October 31 - November 2, 1978.

DTIC Science & Technology

1978-01-01

complex, applications of the code . NASCAP CODE DESCRIPTION The NASCAP code is a finite-element spacecraft-charging simulation that is written in FORTRAN ...transport code POEM (ref. 1), is applicable to arbitrary dielectrics, source spectra, and current time histories. The code calculations are illustrated by...iaxk ’. Vlbouced _DstributionL- 9TNA Availability Codes %ELECTEf Nationa Aeronautics and Dist. Spec al TAvalland/or. MAY 2 21980 Space Administration

A Regularization Approach to Blind Deblurring and Denoising of QR Barcodes.

PubMed

van Gennip, Yves; Athavale, Prashant; Gilles, Jérôme; Choksi, Rustum

2015-09-01

QR bar codes are prototypical images for which part of the image is a priori known (required patterns). Open source bar code readers, such as ZBar, are readily available. We exploit both these facts to provide and assess purely regularization-based methods for blind deblurring of QR bar codes in the presence of noise.

AN OPEN-SOURCE NEUTRINO RADIATION HYDRODYNAMICS CODE FOR CORE-COLLAPSE SUPERNOVAE

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

O’Connor, Evan, E-mail: evanoconnor@ncsu.edu; CITA, Canadian Institute for Theoretical Astrophysics, Toronto, M5S 3H8

2015-08-15

We present an open-source update to the spherically symmetric, general-relativistic hydrodynamics, core-collapse supernova (CCSN) code GR1D. The source code is available at http://www.GR1Dcode.org. We extend its capabilities to include a general-relativistic treatment of neutrino transport based on the moment formalisms of Shibata et al. and Cardall et al. We pay special attention to implementing and testing numerical methods and approximations that lessen the computational demand of the transport scheme by removing the need to invert large matrices. This is especially important for the implementation and development of moment-like transport methods in two and three dimensions. A critical component of neutrinomore » transport calculations is the neutrino–matter interaction coefficients that describe the production, absorption, scattering, and annihilation of neutrinos. In this article we also describe our open-source neutrino interaction library NuLib (available at http://www.nulib.org). We believe that an open-source approach to describing these interactions is one of the major steps needed to progress toward robust models of CCSNe and robust predictions of the neutrino signal. We show, via comparisons to full Boltzmann neutrino-transport simulations of CCSNe, that our neutrino transport code performs remarkably well. Furthermore, we show that the methods and approximations we employ to increase efficiency do not decrease the fidelity of our results. We also test the ability of our general-relativistic transport code to model failed CCSNe by evolving a 40-solar-mass progenitor to the onset of collapse to a black hole.« less

BenMAP Downloads

EPA Pesticide Factsheets

Download the current and legacy versions of the BenMAP program. Download configuration and aggregation/pooling/valuation files to estimate benefits. BenMAP-CE is free and open source software, and the source code is available upon request.

Top ten reasons to register your code with the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; DuPrie, Kimberly; Berriman, G. Bruce; Mink, Jessica D.; Nemiroff, Robert J.; Robitaille, Thomas; Schmidt, Judy; Shamir, Lior; Shortridge, Keith; Teuben, Peter J.; Wallin, John F.; Warmels, Rein

2017-01-01

With 1,400 codes, the Astrophysics Source Code Library (ASCL, ascl.net) is the largest indexed resource for codes used in astronomy research in existence. This free online registry was established in 1999, is indexed by Web of Science and ADS, and is citable, with citations to its entries tracked by ADS. Registering your code with the ASCL is easy with our online submissions system. Making your software available for examination shows confidence in your research and makes your research more transparent, reproducible, and falsifiable. ASCL registration allows your software to be cited on its own merits and provides a citation that is trackable and accepted by all astronomy journals and journals such as Science and Nature. Registration also allows others to find your code more easily. This presentation covers the benefits of registering astronomy research software with the ASCL.

Open source clustering software.

PubMed

de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

2004-06-12

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

Student-reported school drinking fountain availability by youth characteristics and state plumbing codes.

PubMed

Onufrak, Stephen J; Park, Sohyun; Wilking, Cara

2014-04-17

Caloric intake among children could be reduced if sugar-sweetened beverages were replaced by plain water. School drinking water infrastructure is dictated in part by state plumbing codes, which generally require a minimum ratio of drinking fountains to students. Actual availability of drinking fountains in schools and how availability differs according to plumbing codes is unknown. We abstracted state plumbing code data and used the 2010 YouthStyles survey data from 1,196 youth aged 9 through 18 years from 47 states. We assessed youth-reported school drinking fountain or dispenser availability and differences in availability according to state plumbing codes, sociodemographic characteristics, and area-level characteristics. Overall, 57.3% of youth reported that drinking fountains or dispensers in their schools were widely available, 40.1% reported there were only a few, and 2.6% reported that there were no working fountains. Reported fountain availability differed significantly (P < .01) by race/ethnicity, census region, the fountain to student ratio specified in plumbing codes, and whether plumbing codes allowed substitution of nonplumbed water sources for plumbed fountains. "Widely available" fountain access ranged from 45.7% in the West to 65.4% in the Midwest and was less common where state plumbing codes required 1 fountain per more than 100 students (45.4%) compared with 1 fountain per 100 students (60.1%) or 1 fountain per fewer than 100 students (57.6%). Interventions designed to increase consumption of water may want to consider the role of plumbing codes in availability of school drinking fountains.

The moving mesh code SHADOWFAX

NASA Astrophysics Data System (ADS)

Vandenbroucke, B.; De Rijcke, S.

2016-07-01

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

Combining structured and unstructured data to identify a cohort of ICU patients who received dialysis

PubMed Central

Abhyankar, Swapna; Demner-Fushman, Dina; Callaghan, Fiona M; McDonald, Clement J

2014-01-01

Objective To develop a generalizable method for identifying patient cohorts from electronic health record (EHR) data—in this case, patients having dialysis—that uses simple information retrieval (IR) tools. Methods We used the coded data and clinical notes from the 24 506 adult patients in the Multiparameter Intelligent Monitoring in Intensive Care database to identify patients who had dialysis. We used SQL queries to search the procedure, diagnosis, and coded nursing observations tables based on ICD-9 and local codes. We used a domain-specific search engine to find clinical notes containing terms related to dialysis. We manually validated the available records for a 10% random sample of patients who potentially had dialysis and a random sample of 200 patients who were not identified as having dialysis based on any of the sources. Results We identified 1844 patients that potentially had dialysis: 1481 from the three coded sources and 1624 from the clinical notes. Precision for identifying dialysis patients based on available data was estimated to be 78.4% (95% CI 71.9% to 84.2%) and recall was 100% (95% CI 86% to 100%). Conclusions Combining structured EHR data with information from clinical notes using simple queries increases the utility of both types of data for cohort identification. Patients identified by more than one source are more likely to meet the inclusion criteria; however, including patients found in any of the sources increases recall. This method is attractive because it is available to researchers with access to EHR data and off-the-shelf IR tools. PMID:24384230

Student-Reported School Drinking Fountain Availability by Youth Characteristics and State Plumbing Codes

PubMed Central

Park, Sohyun; Wilking, Cara

2014-01-01

Introduction Caloric intake among children could be reduced if sugar-sweetened beverages were replaced by plain water. School drinking water infrastructure is dictated in part by state plumbing codes, which generally require a minimum ratio of drinking fountains to students. Actual availability of drinking fountains in schools and how availability differs according to plumbing codes is unknown. Methods We abstracted state plumbing code data and used the 2010 YouthStyles survey data from 1,196 youth aged 9 through 18 years from 47 states. We assessed youth-reported school drinking fountain or dispenser availability and differences in availability according to state plumbing codes, sociodemographic characteristics, and area-level characteristics. Results Overall, 57.3% of youth reported that drinking fountains or dispensers in their schools were widely available, 40.1% reported there were only a few, and 2.6% reported that there were no working fountains. Reported fountain availability differed significantly (P < .01) by race/ethnicity, census region, the fountain to student ratio specified in plumbing codes, and whether plumbing codes allowed substitution of nonplumbed water sources for plumbed fountains. “Widely available” fountain access ranged from 45.7% in the West to 65.4% in the Midwest and was less common where state plumbing codes required 1 fountain per more than 100 students (45.4%) compared with 1 fountain per 100 students (60.1%) or 1 fountain per fewer than 100 students (57.6%). Conclusion Interventions designed to increase consumption of water may want to consider the role of plumbing codes in availability of school drinking fountains. PMID:24742393

FRAGS: estimation of coding sequence substitution rates from fragmentary data

PubMed Central

Swart, Estienne C; Hide, Winston A; Seoighe, Cathal

2004-01-01

Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the coding sequence divergence of orthologous genes. Although complete genome sequence data are not available for all organisms, fragmentary sequence data can provide accurate estimates of substitution rates provided that an appropriate and consistent methodology is used and that differences in the estimates obtainable from different data sources are taken into account. Results We have developed FRAGS, an application framework that uses existing, freely available software components to construct in-frame alignments and estimate coding substitution rates from fragmentary sequence data. Coding sequence substitution estimates for human and chimpanzee sequences, generated by FRAGS, reveal that methodological differences can give rise to significantly different estimates of important substitution parameters. The estimated substitution rates were also used to infer upper-bounds on the amount of sequencing error in the datasets that we have analysed. Conclusion We have developed a system that performs robust estimation of substitution rates for orthologous sequences from a pair of organisms. Our system can be used when fragmentary genomic or transcript data is available from one of the organisms and the other is a completely sequenced genome within the Ensembl database. As well as estimating substitution statistics our system enables the user to manage and query alignment and substitution data. PMID:15005802

Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

2013-12-01

Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third-party library to provide hydrologic flow, energy transport, and biogeochemical capability to the community land model, CLM, part of the open-source community earth system model (CESM) for climate. In this presentation, the advantages and disadvantages of open source software development in support of geoscience research at government laboratories, universities, and the private sector are discussed. Since the code is open-source (i.e. it's transparent and readily available to competitors), the PFLOTRAN team's development strategy within a competitive research environment is presented. Finally, the developers discuss their approach to object-oriented programming and the leveraging of modern Fortran in support of collaborative geoscience research as the Fortran standard evolves among compiler vendors.

Data Collection Handbook to Support Modeling Impacts of Radioactive Material in Soil and Building Structures

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

Yu, Charley; Kamboj, Sunita; Wang, Cheng

2015-09-01

This handbook is an update of the 1993 version of the Data Collection Handbook and the Radionuclide Transfer Factors Report to support modeling the impact of radioactive material in soil. Many new parameters have been added to the RESRAD Family of Codes, and new measurement methodologies are available. A detailed review of available parameter databases was conducted in preparation of this new handbook. This handbook is a companion document to the user manuals when using the RESRAD (onsite) and RESRAD-OFFSITE code. It can also be used for RESRAD-BUILD code because some of the building-related parameters are included in this handbook.more » The RESRAD (onsite) has been developed for implementing U.S. Department of Energy Residual Radioactive Material Guidelines. Hydrogeological, meteorological, geochemical, geometrical (size, area, depth), crops and livestock, human intake, source characteristic, and building characteristic parameters are used in the RESRAD (onsite) code. The RESRAD-OFFSITE code is an extension of the RESRAD (onsite) code and can also model the transport of radionuclides to locations outside the footprint of the primary contamination. This handbook discusses parameter definitions, typical ranges, variations, and measurement methodologies. It also provides references for sources of additional information. Although this handbook was developed primarily to support the application of RESRAD Family of Codes, the discussions and values are valid for use of other pathway analysis models and codes.« less

Injecting Artificial Memory Errors Into a Running Computer Program

NASA Technical Reports Server (NTRS)

Bornstein, Benjamin J.; Granat, Robert A.; Wagstaff, Kiri L.

2008-01-01

Single-event upsets (SEUs) or bitflips are computer memory errors caused by radiation. BITFLIPS (Basic Instrumentation Tool for Fault Localized Injection of Probabilistic SEUs) is a computer program that deliberately injects SEUs into another computer program, while the latter is running, for the purpose of evaluating the fault tolerance of that program. BITFLIPS was written as a plug-in extension of the open-source Valgrind debugging and profiling software. BITFLIPS can inject SEUs into any program that can be run on the Linux operating system, without needing to modify the program s source code. Further, if access to the original program source code is available, BITFLIPS offers fine-grained control over exactly when and which areas of memory (as specified via program variables) will be subjected to SEUs. The rate of injection of SEUs is controlled by specifying either a fault probability or a fault rate based on memory size and radiation exposure time, in units of SEUs per byte per second. BITFLIPS can also log each SEU that it injects and, if program source code is available, report the magnitude of effect of the SEU on a floating-point value or other program variable.

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

PubMed

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

2006-03-01

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

The DDN (Defense Data Network) Course,

DTIC Science & Technology

1986-04-01

devices will share the same node-to-node channels. * Simultaneous availability of source and destination is not required. * Speed and code conversion can...address multiple addresses simultaneously 3) Disadvantages of Message Switching Systems Not suited to real time or interactive use * Long and highly...transmission b) Unlike message switching, packet switching requires the -. simultaneous availability of source and destination. 64 -4 ) ..xa...e s

A Comprehensive review on the open source hackable text editor-ATOM

NASA Astrophysics Data System (ADS)

Sumangali, K.; Borra, Lokesh; Suraj Mishra, Amol

2017-11-01

This document represents a comprehensive study of “Atom”, one of the best open-source code editors available with many features built-in to support multitude of programming environments and to provide a more productive toolset for developers.

IgSimulator: a versatile immunosequencing simulator.

PubMed

Safonova, Yana; Lapidus, Alla; Lill, Jennie

2015-10-01

The recent introduction of next-generation sequencing technologies to antibody studies have resulted in a growing number of immunoinformatics tools for antibody repertoire analysis. However, benchmarking these newly emerging tools remains problematic since the gold standard datasets that are needed to validate these tools are typically not available. Since simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools, we developed the IgSimulator tool that addresses various complications in generating realistic antibody repertoires. IgSimulator's code has modular structure and can be easily adapted to new requirements to simulation. IgSimulator is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from yana-safonova.github.io/ig_simulator. safonova.yana@gmail.com 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.

BioCIDER: a Contextualisation InDEx for biological Resources discovery

PubMed Central

Horro, Carlos; Cook, Martin; Attwood, Teresa K.; Brazas, Michelle D.; Hancock, John M.; Palagi, Patricia; Corpas, Manuel; Jimenez, Rafael

2017-01-01

Abstract Summary The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded. Availability and Implementation BioCIDER (www.biocider.org) is an open-source platform. Documentation is available online (https://goo.gl/Klc51G), and source code is freely available via GitHub (https://github.com/BioCIDER). The BioJS widget that enables websites to embed contextualization is available from the BioJS registry (http://biojs.io/). All code is released under an MIT licence. Contact carlos.horro@earlham.ac.uk or rafael.jimenez@elixir-europe.org or manuel@repositive.io PMID:28407033

An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code, with Application to WASP-12b

NASA Astrophysics Data System (ADS)

Harrington, Joseph; Blecic, Jasmina; Cubillos, Patricio; Rojo, Patricio; Loredo, Thomas J.; Bowman, M. Oliver; Foster, Andrew S. D.; Stemm, Madison M.; Lust, Nate B.

2015-01-01

Atmospheric retrievals for solar-system planets typically fit, either with a minimizer or by eye, a synthetic spectrum to high-resolution (Δλ/λ ~ 1000-100,000) data with S/N > 100 per point. In contrast, exoplanet data often have S/N ~ 10 per point, and may have just a few points representing bandpasses larger than 1 um. To derive atmospheric constraints and robust parameter uncertainty estimates from such data requires a Bayesian approach. To date there are few investigators with the relevant codes, none of which are publicly available. We are therefore pleased to announce the open-source Bayesian Atmospheric Radiative Transfer (BART) code. BART uses a Bayesian phase-space explorer to drive a radiative-transfer model through the parameter phase space, producing the most robust estimates available for the thermal profile and chemical abundances in the atmosphere. We present an overview of the code and an initial application to Spitzer eclipse data for WASP-12b. We invite the community to use and improve BART via the open-source development site GitHub.com. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code, and Application to WASP-12b

NASA Astrophysics Data System (ADS)

Harrington, Joseph; Blecic, Jasmina; Cubillos, Patricio; Rojo, Patricio M.; Loredo, Thomas J.; Bowman, Matthew O.; Foster, Andrew S.; Stemm, Madison M.; Lust, Nate B.

2014-11-01

Atmospheric retrievals for solar-system planets typically fit, either with a minimizer or by eye, a synthetic spectrum to high-resolution (Δλ/λ ~ 1000-100,000) data with S/N > 100 per point. In contrast, exoplanet data often have S/N ~ 10 per point, and may have just a few points representing bandpasses larger than 1 um. To derive atmospheric constraints and robust parameter uncertainty estimates from such data requires a Bayesian approach. To date there are few investigators with the relevant codes, none of which are publicly available. We are therefore pleased to announce the open-source Bayesian Atmospheric Radiative Transfer (BART) code. BART uses a Bayesian phase-space explorer to drive a radiative-transfer model through the parameter phase space, producing the most robust estimates available for the thermal profile and chemical abundances in the atmosphere. We present an overview of the code and an initial application to Spitzer eclipse data for WASP-12b. We invite the community to use and improve BART via the open-source development site GitHub.com. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

CTF Theory Manual

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

Avramova, Maria N.; Salko, Robert K.

Coolant-Boiling in Rod Arrays|Two Fluids (COBRA-TF) is a thermal/ hydraulic (T/H) simulation code designed for light water reactor (LWR) vessel analysis. It uses a two-fluid, three-field (i.e. fluid film, fluid drops, and vapor) modeling approach. Both sub-channel and 3D Cartesian forms of 9 conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and had been used and modified by several institutions over the last few decades. COBRA-TF also found use at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Management Group (RDFMG) and has been improved, updated, andmore » subsequently re-branded as CTF. As part of the improvement process, it was necessary to generate sufficient documentation for the open-source code which had lacked such material upon being adopted by RDFMG. This document serves mainly as a theory manual for CTF, detailing the many two-phase heat transfer, drag, and important accident scenario models contained in the code as well as the numerical solution process utilized. Coding of the models is also discussed, all with consideration for updates that have been made when transitioning from COBRA-TF to CTF. Further documentation outside of this manual is also available at RDFMG which focus on code input deck generation and source code global variable and module listings.« less

Scalable video transmission over Rayleigh fading channels using LDPC codes

NASA Astrophysics Data System (ADS)

Bansal, Manu; Kondi, Lisimachos P.

2005-03-01

In this paper, we investigate an important problem of efficiently utilizing the available resources for video transmission over wireless channels while maintaining a good decoded video quality and resilience to channel impairments. Our system consists of the video codec based on 3-D set partitioning in hierarchical trees (3-D SPIHT) algorithm and employs two different schemes using low-density parity check (LDPC) codes for channel error protection. The first method uses the serial concatenation of the constant-rate LDPC code and rate-compatible punctured convolutional (RCPC) codes. Cyclic redundancy check (CRC) is used to detect transmission errors. In the other scheme, we use the product code structure consisting of a constant rate LDPC/CRC code across the rows of the `blocks' of source data and an erasure-correction systematic Reed-Solomon (RS) code as the column code. In both the schemes introduced here, we use fixed-length source packets protected with unequal forward error correction coding ensuring a strictly decreasing protection across the bitstream. A Rayleigh flat-fading channel with additive white Gaussian noise (AWGN) is modeled for the transmission. The rate-distortion optimization algorithm is developed and carried out for the selection of source coding and channel coding rates using Lagrangian optimization. The experimental results demonstrate the effectiveness of this system under different wireless channel conditions and both the proposed methods (LDPC+RCPC/CRC and RS+LDPC/CRC) outperform the more conventional schemes such as those employing RCPC/CRC.

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

PubMed

Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

2015-01-01

Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

Bring out your codes! Bring out your codes! (Increasing Software Visibility and Re-use)

NASA Astrophysics Data System (ADS)

Allen, A.; Berriman, B.; Brunner, R.; Burger, D.; DuPrie, K.; Hanisch, R. J.; Mann, R.; Mink, J.; Sandin, C.; Shortridge, K.; Teuben, P.

2013-10-01

Progress is being made in code discoverability and preservation, but as discussed at ADASS XXI, many codes still remain hidden from public view. With the Astrophysics Source Code Library (ASCL) now indexed by the SAO/NASA Astrophysics Data System (ADS), the introduction of a new journal, Astronomy & Computing, focused on astrophysics software, and the increasing success of education efforts such as Software Carpentry and SciCoder, the community has the opportunity to set a higher standard for its science by encouraging the release of software for examination and possible reuse. We assembled representatives of the community to present issues inhibiting code release and sought suggestions for tackling these factors. The session began with brief statements by panelists; the floor was then opened for discussion and ideas. Comments covered a diverse range of related topics and points of view, with apparent support for the propositions that algorithms should be readily available, code used to produce published scientific results should be made available, and there should be discovery mechanisms to allow these to be found easily. With increased use of resources such as GitHub (for code availability), ASCL (for code discovery), and a stated strong preference from the new journal Astronomy & Computing for code release, we expect to see additional progress over the next few years.

GANDALF - Graphical Astrophysics code for N-body Dynamics And Lagrangian Fluids

NASA Astrophysics Data System (ADS)

Hubber, D. A.; Rosotti, G. P.; Booth, R. A.

2018-01-01

GANDALF is a new hydrodynamics and N-body dynamics code designed for investigating planet formation, star formation and star cluster problems. GANDALF is written in C++, parallelized with both OPENMP and MPI and contains a PYTHON library for analysis and visualization. The code has been written with a fully object-oriented approach to easily allow user-defined implementations of physics modules or other algorithms. The code currently contains implementations of smoothed particle hydrodynamics, meshless finite-volume and collisional N-body schemes, but can easily be adapted to include additional particle schemes. We present in this paper the details of its implementation, results from the test suite, serial and parallel performance results and discuss the planned future development. The code is freely available as an open source project on the code-hosting website github at https://github.com/gandalfcode/gandalf and is available under the GPLv2 license.

Phase 1 Validation Testing and Simulation for the WEC-Sim Open Source Code

NASA Astrophysics Data System (ADS)

Ruehl, K.; Michelen, C.; Gunawan, B.; Bosma, B.; Simmons, A.; Lomonaco, P.

2015-12-01

WEC-Sim is an open source code to model wave energy converters performance in operational waves, developed by Sandia and NREL and funded by the US DOE. The code is a time-domain modeling tool developed in MATLAB/SIMULINK using the multibody dynamics solver SimMechanics, and solves the WEC's governing equations of motion using the Cummins time-domain impulse response formulation in 6 degrees of freedom. The WEC-Sim code has undergone verification through code-to-code comparisons; however validation of the code has been limited to publicly available experimental data sets. While these data sets provide preliminary code validation, the experimental tests were not explicitly designed for code validation, and as a result are limited in their ability to validate the full functionality of the WEC-Sim code. Therefore, dedicated physical model tests for WEC-Sim validation have been performed. This presentation provides an overview of the WEC-Sim validation experimental wave tank tests performed at the Oregon State University's Directional Wave Basin at Hinsdale Wave Research Laboratory. Phase 1 of experimental testing was focused on device characterization and completed in Fall 2015. Phase 2 is focused on WEC performance and scheduled for Winter 2015/2016. These experimental tests were designed explicitly to validate the performance of WEC-Sim code, and its new feature additions. Upon completion, the WEC-Sim validation data set will be made publicly available to the wave energy community. For the physical model test, a controllable model of a floating wave energy converter has been designed and constructed. The instrumentation includes state-of-the-art devices to measure pressure fields, motions in 6 DOF, multi-axial load cells, torque transducers, position transducers, and encoders. The model also incorporates a fully programmable Power-Take-Off system which can be used to generate or absorb wave energy. Numerical simulations of the experiments using WEC-Sim will be presented. These simulations highlight the code features included in the latest release of WEC-Sim (v1.2), including: wave directionality, nonlinear hydrostatics and hydrodynamics, user-defined wave elevation time-series, state space radiation, and WEC-Sim compatibility with BEMIO (open source AQWA/WAMI/NEMOH coefficient parser).

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Bayesian Atmospheric Radiative Transfer (BART)Thermochemical Equilibrium Abundance (TEA) Code and Application to WASP-43b

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, Matthew O.; Cubillos, Patricio E.; Stemm, Madison; Foster, Andrew

2014-11-01

We present a new, open-source, Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. TEA uses the Gibbs-free-energy minimization method with an iterative Lagrangian optimization scheme. It initializes the radiative-transfer calculation in our Bayesian Atmospheric Radiative Transfer (BART) code. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. The code is tested against the original method developed by White at al. (1958), the analytic method developed by Burrows and Sharp (1999), and the Newton-Raphson method implemented in the open-source Chemical Equilibrium with Applications (CEA) code. TEA is written in Python and is available to the community via the open-source development site GitHub.com. We also present BART applied to eclipse depths of WASP-43b exoplanet, constraining atmospheric thermal and chemical parameters. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

Augmenting Traditional Static Analysis With Commonly Available Metadata

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

Cook, Devin

Developers and security analysts have been using static analysis for a long time to analyze programs for defects and vulnerabilities with some success. Generally a static analysis tool is run on the source code for a given program, flagging areas of code that need to be further inspected by a human analyst. These areas may be obvious bugs like potential bu er over flows, information leakage flaws, or the use of uninitialized variables. These tools tend to work fairly well - every year they find many important bugs. These tools are more impressive considering the fact that they only examinemore » the source code, which may be very complex. Now consider the amount of data available that these tools do not analyze. There are many pieces of information that would prove invaluable for finding bugs in code, things such as a history of bug reports, a history of all changes to the code, information about committers, etc. By leveraging all this additional data, it is possible to nd more bugs with less user interaction, as well as track useful metrics such as number and type of defects injected by committer. This dissertation provides a method for leveraging development metadata to find bugs that would otherwise be difficult to find using standard static analysis tools. We showcase two case studies that demonstrate the ability to find 0day vulnerabilities in large and small software projects by finding new vulnerabilities in the cpython and Roundup open source projects.« less

Electron transport model of dielectric charging

NASA Technical Reports Server (NTRS)

Beers, B. L.; Hwang, H. C.; Lin, D. L.; Pine, V. W.

1979-01-01

A computer code (SCCPOEM) was assembled to describe the charging of dielectrics due to irradiation by electrons. The primary purpose for developing the code was to make available a convenient tool for studying the internal fields and charge densities in electron-irradiated dielectrics. The code, which is based on the primary electron transport code POEM, is applicable to arbitrary dielectrics, source spectra, and current time histories. The code calculations are illustrated by a series of semianalytical solutions. Calculations to date suggest that the front face electric field is insufficient to cause breakdown, but that bulk breakdown fields can easily be exceeded.

Monitoring the use and outcomes of new devices and procedures: how does coding affect what Hospital Episode Statistics contribute? Lessons from 12 emerging procedures 2006-10.

PubMed

Patrick, Hannah; Sims, Andrew; Burn, Julie; Bousfield, Derek; Colechin, Elaine; Reay, Christopher; Alderson, Neil; Goode, Stephen; Cunningham, David; Campbell, Bruce

2013-03-01

New devices and procedures are often introduced into health services when the evidence base for their efficacy and safety is limited. The authors sought to assess the availability and accuracy of routinely collected Hospital Episodes Statistics (HES) data in the UK and their potential contribution to the monitoring of new procedures. Four years of HES data (April 2006-March 2010) were analysed to identify episodes of hospital care involving a sample of 12 new interventional procedures. HES data were cross checked against other relevant sources including national or local registers and manufacturers' information. HES records were available for all 12 procedures during the entire study period. Comparative data sources were available from national (5), local (2) and manufacturer (2) registers. Factors found to affect comparisons were miscoding, alternative coding and inconsistent use of subsidiary codes. The analysis of provider coverage showed that HES is sensitive at detecting centres which carry out procedures, but specificity is poor in some cases. Routinely collected HES data have the potential to support quality improvements and evidence-based commissioning of devices and procedures in health services but achievement of this potential depends upon the accurate coding of procedures.

TEA: A Code Calculating Thermochemical Equilibrium Abundances

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver

2016-07-01

We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. We tested the code against the method of Burrows & Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows & Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but with higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.

TEA: A CODE CALCULATING THERMOCHEMICAL EQUILIBRIUM ABUNDANCES

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

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver, E-mail: jasmina@physics.ucf.edu

2016-07-01

We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature–pressure pairs. We tested the code against the method of Burrows and Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows and Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but withmore » higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.« less

ALPHACAL: A new user-friendly tool for the calibration of alpha-particle sources.

PubMed

Timón, A Fernández; Vargas, M Jurado; Gallardo, P Álvarez; Sánchez-Oro, J; Peralta, L

2018-05-01

In this work, we present and describe the program ALPHACAL, specifically developed for the calibration of alpha-particle sources. It is therefore more user-friendly and less time-consuming than multipurpose codes developed for a wide range of applications. The program is based on the recently developed code AlfaMC, which simulates specifically the transport of alpha particles. Both cylindrical and point sources mounted on the surface of polished backings can be simulated, as is the convention in experimental measurements of alpha-particle sources. In addition to the efficiency calculation and determination of the backscattering coefficient, some additional tools are available to the user, like the visualization of energy spectrum, use of energy cut-off or low-energy tail corrections. ALPHACAL has been implemented in C++ language using QT library, so it is available for Windows, MacOs and Linux platforms. It is free and can be provided under request to the authors. Copyright © 2018 Elsevier Ltd. All rights reserved.

Smart photonic networks and computer security for image data

NASA Astrophysics Data System (ADS)

Campello, Jorge; Gill, John T.; Morf, Martin; Flynn, Michael J.

1998-02-01

Work reported here is part of a larger project on 'Smart Photonic Networks and Computer Security for Image Data', studying the interactions of coding and security, switching architecture simulations, and basic technologies. Coding and security: coding methods that are appropriate for data security in data fusion networks were investigated. These networks have several characteristics that distinguish them form other currently employed networks, such as Ethernet LANs or the Internet. The most significant characteristics are very high maximum data rates; predominance of image data; narrowcasting - transmission of data form one source to a designated set of receivers; data fusion - combining related data from several sources; simple sensor nodes with limited buffering. These characteristics affect both the lower level network design and the higher level coding methods.Data security encompasses privacy, integrity, reliability, and availability. Privacy, integrity, and reliability can be provided through encryption and coding for error detection and correction. Availability is primarily a network issue; network nodes must be protected against failure or routed around in the case of failure. One of the more promising techniques is the use of 'secret sharing'. We consider this method as a special case of our new space-time code diversity based algorithms for secure communication. These algorithms enable us to exploit parallelism and scalable multiplexing schemes to build photonic network architectures. A number of very high-speed switching and routing architectures and their relationships with very high performance processor architectures were studied. Indications are that routers for very high speed photonic networks can be designed using the very robust and distributed TCP/IP protocol, if suitable processor architecture support is available.

TANDEM: matching proteins with tandem mass spectra.

PubMed

Craig, Robertson; Beavis, Ronald C

2004-06-12

Tandem mass spectra obtained from fragmenting peptide ions contain some peptide sequence specific information, but often there is not enough information to sequence the original peptide completely. Several proprietary software applications have been developed to attempt to match the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching. The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors.

ONR Far East Scientific Bulletin, Volume 7, Number 2, April-June 1982,

DTIC Science & Technology

1982-01-01

contained source code . - PAL (Program Automation Language) PAL is a system design language that automatically generates an executable program from a...NTIS c3&1 DTIC TliB Unn ’l.- A ElJustitt for _ By - Distrib~tion Availability Codes Avail and/or Di st Speojal iii 0- CONTENTS~ P age r’A Gflmpse at...tools exist at ECL in prototype forms. Like most major computer manufacturers, they have also extended high level languages such as FORTRAN , COBOL

The Impact of Causality on Information-Theoretic Source and Channel Coding Problems

ERIC Educational Resources Information Center

Palaiyanur, Harikrishna R.

2011-01-01

This thesis studies several problems in information theory where the notion of causality comes into play. Causality in information theory refers to the timing of when information is available to parties in a coding system. The first part of the thesis studies the error exponent (or reliability function) for several communication problems over…

A plug-in to Eclipse for VHDL source codes: functionalities

NASA Astrophysics Data System (ADS)

Niton, B.; Poźniak, K. T.; Romaniuk, R. S.

The paper presents an original application, written by authors, which supports writing and edition of source codes in VHDL language. It is a step towards fully automatic, augmented code writing for photonic and electronic systems, also systems based on FPGA and/or DSP processors. An implementation is described, based on VEditor. VEditor is a free license program. Thus, the work presented in this paper supplements and extends this free license. The introduction characterizes shortly available tools on the market which serve for aiding the design processes of electronic systems in VHDL. Particular attention was put on plug-ins to the Eclipse environment and Emacs program. There are presented detailed properties of the written plug-in such as: programming extension conception, and the results of the activities of formatter, re-factorizer, code hider, and other new additions to the VEditor program.

Flow Instability Tests for a Particle Bed Reactor Nuclear Thermal Rocket Fuel Element

DTIC Science & Technology

1993-05-01

2.0 with GWBASIC or higher (DOS 5.0 was installed on the machine). Since the source code was written in BASIC, it was easy to make modifications...8217 AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE Approved for Public Release IAW 190-1 Distribution Unlimited MICHAEL M. BRICKER, SMSgt, USAF Chief...Administration 13. ABSTRACT (Maximum 200 words) i.14. SUBJECT TERMS 15. NUMBER OF PAGES 339 16. PRICE CODE 󈧕. SECURITY CLASSIFICATION 18. SECURITY

Syndrome-source-coding and its universal generalization. [error correcting codes for data compression

NASA Technical Reports Server (NTRS)

Ancheta, T. C., Jr.

1976-01-01

A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A 'universal' generalization of syndrome-source-coding is formulated which provides robustly effective distortionless coding of source ensembles. Two examples are given, comparing the performance of noiseless universal syndrome-source-coding to (1) run-length coding and (2) Lynch-Davisson-Schalkwijk-Cover universal coding for an ensemble of binary memoryless sources.

An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities

PubMed Central

Fenwick, Matthew; Sesanker, Colbert; Schiller, Martin R.; Ellis, Heidi JC; Hinman, M. Lee; Vyas, Jay; Gryk, Michael R.

2012-01-01

Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org). PMID:25328913

An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities.

PubMed

Fenwick, Matthew; Sesanker, Colbert; Schiller, Martin R; Ellis, Heidi Jc; Hinman, M Lee; Vyas, Jay; Gryk, Michael R

2012-01-01

Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org).

Open Source Software Development Experiences on the Students' Resumes: Do They Count?--Insights from the Employers' Perspectives

ERIC Educational Resources Information Center

Long, Ju

2009-01-01

Open Source Software (OSS) is a major force in today's Information Technology (IT) landscape. Companies are increasingly using OSS in mission-critical applications. The transparency of the OSS technology itself with openly available source codes makes it ideal for students to participate in the OSS project development. OSS can provide unique…

Advanced turboprop noise prediction: Development of a code at NASA Langley based on recent theoretical results

NASA Technical Reports Server (NTRS)

Farassat, F.; Dunn, M. H.; Padula, S. L.

1986-01-01

The development of a high speed propeller noise prediction code at Langley Research Center is described. The code utilizes two recent acoustic formulations in the time domain for subsonic and supersonic sources. The structure and capabilities of the code are discussed. Grid size study for accuracy and speed of execution on a computer is also presented. The code is tested against an earlier Langley code. Considerable increase in accuracy and speed of execution are observed. Some examples of noise prediction of a high speed propeller for which acoustic test data are available are given. A brisk derivation of formulations used is given in an appendix.

Advanced turboprop noise prediction based on recent theoretical results

NASA Technical Reports Server (NTRS)

Farassat, F.; Padula, S. L.; Dunn, M. H.

1987-01-01

The development of a high speed propeller noise prediction code at Langley Research Center is described. The code utilizes two recent acoustic formulations in the time domain for subsonic and supersonic sources. The structure and capabilities of the code are discussed. Grid size study for accuracy and speed of execution on a computer is also presented. The code is tested against an earlier Langley code. Considerable increase in accuracy and speed of execution are observed. Some examples of noise prediction of a high speed propeller for which acoustic test data are available are given. A brisk derivation of formulations used is given in an appendix.

SNPConvert: SNP Array Standardization and Integration in Livestock Species.

PubMed

Nicolazzi, Ezequiel Luis; Marras, Gabriele; Stella, Alessandra

2016-06-09

One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git.

Cross-Layer Design for Video Transmission over Wireless Rician Slow-Fading Channels Using an Adaptive Multiresolution Modulation and Coding Scheme

NASA Astrophysics Data System (ADS)

Pei, Yong; Modestino, James W.

2007-12-01

We describe a multilayered video transport scheme for wireless channels capable of adapting to channel conditions in order to maximize end-to-end quality of service (QoS). This scheme combines a scalable H.263+ video source coder with unequal error protection (UEP) across layers. The UEP is achieved by employing different channel codes together with a multiresolution modulation approach to transport the different priority layers. Adaptivity to channel conditions is provided through a joint source-channel coding (JSCC) approach which attempts to jointly optimize the source and channel coding rates together with the modulation parameters to obtain the maximum achievable end-to-end QoS for the prevailing channel conditions. In this work, we model the wireless links as slow-fading Rician channel where the channel conditions can be described in terms of the channel signal-to-noise ratio (SNR) and the ratio of specular-to-diffuse energy[InlineEquation not available: see fulltext.]. The multiresolution modulation/coding scheme consists of binary rate-compatible punctured convolutional (RCPC) codes used together with nonuniform phase-shift keyed (PSK) signaling constellations. Results indicate that this adaptive JSCC scheme employing scalable video encoding together with a multiresolution modulation/coding approach leads to significant improvements in delivered video quality for specified channel conditions. In particular, the approach results in considerably improved graceful degradation properties for decreasing channel SNR.

Home energy management (HEM) database: A list with coded attributes of 308 devices commercially available in the US.

PubMed

Pritoni, Marco; Ford, Rebecca; Karlin, Beth; Sanguinetti, Angela

2018-02-01

Policymakers worldwide are currently discussing whether to include home energy management (HEM) products in their portfolio of technologies to reduce carbon emissions and improve grid reliability. However, very little data is available about these products. Here we present the results of an extensive review including 308 HEM products available on the US market in 2015-2016. We gathered these data from publicly available sources such as vendor websites, online marketplaces and other vendor documents. A coding guide was developed iteratively during the data collection and utilized to classify the devices. Each product was coded based on 96 distinct attributes, grouped into 11 categories: Identifying information, Product components, Hardware, Communication, Software, Information - feedback, Information - feedforward, Control, Utility interaction, Additional benefits and Usability. The codes describe product features and functionalities, user interaction and interoperability with other devices. A mix of binary attributes and more descriptive codes allow to sort and group data without losing important qualitative information. The information is stored in a large spreadsheet included with this article, along with an explanatory coding guide. This dataset is analyzed and described in a research article entitled "Categories and functionality of smart home technology for energy management" (Ford et al., 2017) [1].

A new software for deformation source optimization, the Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, H.; Dutta, R.; Jonsson, S.; Mai, P. M.

2017-12-01

Modern studies of crustal deformation and the related source estimation, including magmatic and tectonic sources, increasingly use non-linear optimization strategies to estimate geometric and/or kinematic source parameters and often consider both jointly, geodetic and seismic data. Bayesian inference is increasingly being used for estimating posterior distributions of deformation source model parameters, given measured/estimated/assumed data and model uncertainties. For instance, some studies consider uncertainties of a layered medium and propagate these into source parameter uncertainties, while others use informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed to efficiently explore the high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational burden of these methods is high and estimation codes are rarely made available along with the published results. Even if the codes are accessible, it is usually challenging to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in deformation source estimations, we undertook the effort of developing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package builds on the pyrocko seismological toolbox (www.pyrocko.org), and uses the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat), and we encourage and solicit contributions to the project. Here, we present our strategy for developing BEAT and show application examples; especially the effect of including the model prediction uncertainty of the velocity model in following source optimizations: full moment tensor, Mogi source, moderate strike-slip earth-quake.

CMCpy: Genetic Code-Message Coevolution Models in Python

PubMed Central

Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

2013-01-01

Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367

Design of an Orbital Inspection Satellite

DTIC Science & Technology

1986-12-01

ADDRESS (City, State, and ZIP Code ) 10. SOURCE OF FUNDING NUMBERS PROGRAM PROJECT TASK WORK UNITELEMENT NO. NO. NO. CCESSION NO. 11. TITLE (include...Captain, USAF Dh t ibutioni Availabiity Codes Avail adlor Dist [Special December 1986 Approved for public release; distribution...lends itself to the technique of multi -objective analysis. The final step is planning for action. This communicates the entire systems engineering

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

PubMed

Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian; Hippler, Michael

2011-04-15

We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily. Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at http://www.proteomatic.org. michael.specht@uni-muenster.de Supplementary data are available at Bioinformatics online.

MCNP capabilities for nuclear well logging calculations

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

Forster, R.A.; Little, R.C.; Briesmeister, J.F.

The Los Alamos Radiation Transport Code System (LARTCS) consists of state-of-the-art Monte Carlo and discrete ordinates transport codes and data libraries. This paper discusses how the general-purpose continuous-energy Monte Carlo code MCNP ({und M}onte {und C}arlo {und n}eutron {und p}hoton), part of the LARTCS, provides a computational predictive capability for many applications of interest to the nuclear well logging community. The generalized three-dimensional geometry of MCNP is well suited for borehole-tool models. SABRINA, another component of the LARTCS, is a graphics code that can be used to interactively create a complex MCNP geometry. Users can define many source and tallymore » characteristics with standard MCNP features. The time-dependent capability of the code is essential when modeling pulsed sources. Problems with neutrons, photons, and electrons as either single particle or coupled particles can be calculated with MCNP. The physics of neutron and photon transport and interactions is modeled in detail using the latest available cross-section data.« less

Fast in-memory elastic full-waveform inversion using consumer-grade GPUs

NASA Astrophysics Data System (ADS)

Sivertsen Bergslid, Tore; Birger Raknes, Espen; Arntsen, Børge

2017-04-01

Full-waveform inversion (FWI) is a technique to estimate subsurface properties by using the recorded waveform produced by a seismic source and applying inverse theory. This is done through an iterative optimization procedure, where each iteration requires solving the wave equation many times, then trying to minimize the difference between the modeled and the measured seismic data. Having to model many of these seismic sources per iteration means that this is a highly computationally demanding procedure, which usually involves writing a lot of data to disk. We have written code that does forward modeling and inversion entirely in memory. A typical HPC cluster has many more CPUs than GPUs. Since FWI involves modeling many seismic sources per iteration, the obvious approach is to parallelize the code on a source-by-source basis, where each core of the CPU performs one modeling, and do all modelings simultaneously. With this approach, the GPU is already at a major disadvantage in pure numbers. Fortunately, GPUs can more than make up for this hardware disadvantage by performing each modeling much faster than a CPU. Another benefit of parallelizing each individual modeling is that it lets each modeling use a lot more RAM. If one node has 128 GB of RAM and 20 CPU cores, each modeling can use only 6.4 GB RAM if one is running the node at full capacity with source-by-source parallelization on the CPU. A parallelized per-source code using GPUs can use 64 GB RAM per modeling. Whenever a modeling uses more RAM than is available and has to start using regular disk space the runtime increases dramatically, due to slow file I/O. The extremely high computational speed of the GPUs combined with the large amount of RAM available for each modeling lets us do high frequency FWI for fairly large models very quickly. For a single modeling, our GPU code outperforms the single-threaded CPU-code by a factor of about 75. Successful inversions have been run on data with frequencies up to 40 Hz for a model of 2001 by 600 grid points with 5 m grid spacing and 5000 time steps, in less than 2.5 minutes per source. In practice, using 15 nodes (30 GPUs) to model 101 sources, each iteration took approximately 9 minutes. For reference, the same inversion run with our CPU code uses two hours per iteration. This was done using only a very simple wavefield interpolation technique, saving every second timestep. Using a more sophisticated checkpointing or wavefield reconstruction method would allow us to increase this model size significantly. Our results show that ordinary gaming GPUs are a viable alternative to the expensive professional GPUs often used today, when performing large scale modeling and inversion in geophysics.

DLRS: gene tree evolution in light of a species tree.

PubMed

Sjöstrand, Joel; Sennblad, Bengt; Arvestad, Lars; Lagergren, Jens

2012-11-15

PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts

PubMed Central

Ravagli, Carlo; Pognan, Francois

2017-01-01

Summary: The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting. Availability and implementation: The source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com. This software is designed to run on a Java EE application server and store data in a relational database. Contact: philippe.marc@novartis.com PMID:27605099

ClinicalCodes: an online clinical codes repository to improve the validity and reproducibility of research using electronic medical records.

PubMed

Springate, David A; Kontopantelis, Evangelos; Ashcroft, Darren M; Olier, Ivan; Parisi, Rosa; Chamapiwa, Edmore; Reeves, David

2014-01-01

Lists of clinical codes are the foundation for research undertaken using electronic medical records (EMRs). If clinical code lists are not available, reviewers are unable to determine the validity of research, full study replication is impossible, researchers are unable to make effective comparisons between studies, and the construction of new code lists is subject to much duplication of effort. Despite this, the publication of clinical codes is rarely if ever a requirement for obtaining grants, validating protocols, or publishing research. In a representative sample of 450 EMR primary research articles indexed on PubMed, we found that only 19 (5.1%) were accompanied by a full set of published clinical codes and 32 (8.6%) stated that code lists were available on request. To help address these problems, we have built an online repository where researchers using EMRs can upload and download lists of clinical codes. The repository will enable clinical researchers to better validate EMR studies, build on previous code lists and compare disease definitions across studies. It will also assist health informaticians in replicating database studies, tracking changes in disease definitions or clinical coding practice through time and sharing clinical code information across platforms and data sources as research objects.

ClinicalCodes: An Online Clinical Codes Repository to Improve the Validity and Reproducibility of Research Using Electronic Medical Records

PubMed Central

Springate, David A.; Kontopantelis, Evangelos; Ashcroft, Darren M.; Olier, Ivan; Parisi, Rosa; Chamapiwa, Edmore; Reeves, David

2014-01-01

Lists of clinical codes are the foundation for research undertaken using electronic medical records (EMRs). If clinical code lists are not available, reviewers are unable to determine the validity of research, full study replication is impossible, researchers are unable to make effective comparisons between studies, and the construction of new code lists is subject to much duplication of effort. Despite this, the publication of clinical codes is rarely if ever a requirement for obtaining grants, validating protocols, or publishing research. In a representative sample of 450 EMR primary research articles indexed on PubMed, we found that only 19 (5.1%) were accompanied by a full set of published clinical codes and 32 (8.6%) stated that code lists were available on request. To help address these problems, we have built an online repository where researchers using EMRs can upload and download lists of clinical codes. The repository will enable clinical researchers to better validate EMR studies, build on previous code lists and compare disease definitions across studies. It will also assist health informaticians in replicating database studies, tracking changes in disease definitions or clinical coding practice through time and sharing clinical code information across platforms and data sources as research objects. PMID:24941260

Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering

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

Campbell, Michael T.; Safdari, Masoud; Kress, Jessica E.

The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enablemore » coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site. There are over 100 unit tests provided that run through the Illinois Rocstar Application Development (IRAD) lightweight testing infrastructure that is also supplied along with IMPACT. The package as a whole provides an excellent base for developing high-quality multiphysics applications using modern software development practices. To facilitate understanding how to utilize IMPACT effectively, two multiphysics systems have been developed and are available open-source through gitHUB. The simpler of the two systems, named ElmerFoamFSI in the repository, is a multiphysics, fluid-structure-interaction (FSI) coupling of the solid mechanics package Elmer with a fluid dynamics module from OpenFOAM. This coupling illustrates how to combine software packages that are unrelated by either author or architecture and combine them into a robust, parallel multiphysics system. A more complex multiphysics tool is the Illinois Rocstar Rocstar Multiphysics code that was rebuilt during the project around IMPACT. Rocstar Multiphysics was already an HPC multiphysics tool, but now that it has been rearchitected around IMPACT, it can be readily expanded to capture new and different physics in the future. In fact, during this project, the Elmer and OpenFOAM tools were also coupled into Rocstar Multiphysics and demonstrated. The full Rocstar Multiphysics codebase is also available on gitHUB, and licensed for any organization to use as they wish. Finally, the new IMPACT product is already being used in several multiphysics code coupling projects for the Air Force, NASA and the Missile Defense Agency, and initial work on expansion of the IMPACT-enabled Rocstar Multiphysics has begun in support of a commercial company. These initiatives promise to expand the interest and reach of IMPACT and Rocstar Multiphysics, ultimately leading to the envisioned standardization and consortium of users that was one of the goals of this project.« less

Synchrotron Radiation Workshop (SRW)

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

Chubar, O.; Elleaume, P.

2013-03-01

"Synchrotron Radiation Workshop" (SRW) is a physical optics computer code for calculation of detailed characteristics of Synchrotron Radiation (SR) generated by relativistic electrons in magnetic fields of arbitrary configuration and for simulation of the radiation wavefront propagation through optical systems of beamlines. Frequency-domain near-field methods are used for the SR calculation, and the Fourier-optics based approach is generally used for the wavefront propagation simulation. The code enables both fully- and partially-coherent radiation propagation simulations in steady-state and in frequency-/time-dependent regimes. With these features, the code has already proven its utility for a large number of applications in infrared, UV, softmore » and hard X-ray spectral range, in such important areas as analysis of spectral performances of new synchrotron radiation sources, optimization of user beamlines, development of new optical elements, source and beamline diagnostics, and even complete simulation of SR based experiments. Besides the SR applications, the code can be efficiently used for various simulations involving conventional lasers and other sources. SRW versions interfaced to Python and to IGOR Pro (WaveMetrics), as well as cross-platform library with C API, are available.« less

OpenSQUID: A Flexible Open-Source Software Framework for the Control of SQUID Electronics

DOE PAGES

Jaeckel, Felix T.; Lafler, Randy J.; Boyd, S. T. P.

2013-02-06

We report commercially available computer-controlled SQUID electronics are usually delivered with software providing a basic user interface for adjustment of SQUID tuning parameters, such as bias current, flux offset, and feedback loop settings. However, in a research context it would often be useful to be able to modify this code and/or to have full control over all these parameters from researcher-written software. In the case of the STAR Cryoelectronics PCI/PFL family of SQUID control electronics, the supplied software contains modules for automatic tuning and noise characterization, but does not provide an interface for user code. On the other hand, themore » Magnicon SQUIDViewer software package includes a public application programming interface (API), but lacks auto-tuning and noise characterization features. To overcome these and other limitations, we are developing an "open-source" framework for controlling SQUID electronics which should provide maximal interoperability with user software, a unified user interface for electronics from different manufacturers, and a flexible platform for the rapid development of customized SQUID auto-tuning and other advanced features. Finally, we have completed a first implementation for the STAR Cryoelectronics hardware and have made the source code for this ongoing project available to the research community on SourceForge (http://opensquid.sourceforge.net) under the GNU public license.« less

The HYPE Open Source Community

NASA Astrophysics Data System (ADS)

Strömbäck, L.; Pers, C.; Isberg, K.; Nyström, K.; Arheimer, B.

2013-12-01

The Hydrological Predictions for the Environment (HYPE) model is a dynamic, semi-distributed, process-based, integrated catchment model. It uses well-known hydrological and nutrient transport concepts and can be applied for both small and large scale assessments of water resources and status. In the model, the landscape is divided into classes according to soil type, vegetation and altitude. The soil representation is stratified and can be divided in up to three layers. Water and substances are routed through the same flow paths and storages (snow, soil, groundwater, streams, rivers, lakes) considering turn-over and transformation on the way towards the sea. HYPE has been successfully used in many hydrological applications at SMHI. For Europe, we currently have three different models; The S-HYPE model for Sweden; The BALT-HYPE model for the Baltic Sea; and the E-HYPE model for the whole Europe. These models simulate hydrological conditions and nutrients for their respective areas and are used for characterization, forecasts, and scenario analyses. Model data can be downloaded from hypeweb.smhi.se. In addition, we provide models for the Arctic region, the Arab (Middle East and Northern Africa) region, India, the Niger River basin, the La Plata Basin. This demonstrates the applicability of the HYPE model for large scale modeling in different regions of the world. An important goal with our work is to make our data and tools available as open data and services. For this aim we created the HYPE Open Source Community (OSC) that makes the source code of HYPE available for anyone interested in further development of HYPE. The HYPE OSC (hype.sourceforge.net) is an open source initiative under the Lesser GNU Public License taken by SMHI to strengthen international collaboration in hydrological modeling and hydrological data production. The hypothesis is that more brains and more testing will result in better models and better code. The code is transparent and can be changed and learnt from. New versions of the main code are delivered frequently. HYPE OSC is open to everyone interested in hydrology, hydrological modeling and code development - e.g. scientists, authorities, and consultancies. By joining the HYPE OSC you get access a state-of-the-art operational hydrological model. The HYPE source code is designed to efficiently handle large scale modeling for forecast, hindcast and climate applications. The code is under constant development to improve the hydrological processes, efficiency and readability. In the beginning of 2013 we released a version with new and better modularization based on hydrological processes. This will make the code easier to understand and further develop for a new user. An important challenge in this process is to produce code that is easy for anyone to understand and work with, but still maintain the properties that make the code efficient enough for large scale applications. Input from the HYPE Open Source Community is an important source for future improvements of the HYPE model. Therefore, by joining the community you become an active part of the development, get access to the latest features and can influence future versions of the model.

MIST: An Open Source Environmental Modelling Programming Language Incorporating Easy to Use Data Parallelism.

NASA Astrophysics Data System (ADS)

Bellerby, Tim

2014-05-01

Model Integration System (MIST) is open-source environmental modelling programming language that directly incorporates data parallelism. The language is designed to enable straightforward programming structures, such as nested loops and conditional statements to be directly translated into sequences of whole-array (or more generally whole data-structure) operations. MIST thus enables the programmer to use well-understood constructs, directly relating to the mathematical structure of the model, without having to explicitly vectorize code or worry about details of parallelization. A range of common modelling operations are supported by dedicated language structures operating on cell neighbourhoods rather than individual cells (e.g.: the 3x3 local neighbourhood needed to implement an averaging image filter can be simply accessed from within a simple loop traversing all image pixels). This facility hides details of inter-process communication behind more mathematically relevant descriptions of model dynamics. The MIST automatic vectorization/parallelization process serves both to distribute work among available nodes and separately to control storage requirements for intermediate expressions - enabling operations on very large domains for which memory availability may be an issue. MIST is designed to facilitate efficient interpreter based implementations. A prototype open source interpreter is available, coded in standard FORTRAN 95, with tools to rapidly integrate existing FORTRAN 77 or 95 code libraries. The language is formally specified and thus not limited to FORTRAN implementation or to an interpreter-based approach. A MIST to FORTRAN compiler is under development and volunteers are sought to create an ANSI-C implementation. Parallel processing is currently implemented using OpenMP. However, parallelization code is fully modularised and could be replaced with implementations using other libraries. GPU implementation is potentially possible.

QGene 4.0, an extensible Java QTL-analysis platform.

PubMed

Joehanes, Roby; Nelson, James C

2008-12-01

Of many statistical methods developed to date for quantitative trait locus (QTL) analysis, only a limited subset are available in public software allowing their exploration, comparison and practical application by researchers. We have developed QGene 4.0, a plug-in platform that allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Software and documentation are available at http://coding.plantpath.ksu.edu/qgene. Source code is available on request.

22 CFR 228.54 - Suppliers of services-foreign government-owned organizations.

Code of Federal Regulations, 2011 CFR

2011-04-01

... organizations. 228.54 Section 228.54 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT RULES ON SOURCE... contract will be open to firms from countries or areas included in the authorized geographic code and... interested in competing for the contract. (c) Services are not available from any other source. (d) Foreign...

EUPDF: An Eulerian-Based Monte Carlo Probability Density Function (PDF) Solver. User's Manual

NASA Technical Reports Server (NTRS)

Raju, M. S.

1998-01-01

EUPDF is an Eulerian-based Monte Carlo PDF solver developed for application with sprays, combustion, parallel computing and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and spray solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type. The manual provides the user with the coding required to couple the PDF code to any given flow code and a basic understanding of the EUPDF code structure as well as the models involved in the PDF formulation. The source code of EUPDF will be available with the release of the National Combustion Code (NCC) as a complete package.

Syndrome source coding and its universal generalization

NASA Technical Reports Server (NTRS)

Ancheta, T. C., Jr.

1975-01-01

A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A universal generalization of syndrome-source-coding is formulated which provides robustly-effective, distortionless, coding of source ensembles.

Mod3DMT and EMTF: Free Software for MT Data Processing and Inversion

NASA Astrophysics Data System (ADS)

Egbert, G. D.; Kelbert, A.; Meqbel, N. M.

2017-12-01

"ModEM" was developed at Oregon State University as a modular system for inversion of electromagnetic (EM) geophysical data (Egbert and Kelbert, 2012; Kelbert et al., 2014). Although designed for more general (frequency domain) EM applications, and originally intended as a testbed for exploring inversion search and regularization strategies, our own initial uses of ModEM were for 3-D imaging of the deep crust and upper mantle at large scales. Since 2013 we have offered a version of the source code suitable for 3D magnetotelluric (MT) inversion on an "as is, user beware" basis for free for non-commercial applications. This version, which we refer to as Mod3DMT, has since been widely used by the international MT community. Over 250 users have registered to download the source code, and at least 50 MT studies in the refereed literature, covering locations around the globe at a range of spatial scales, cite use of ModEM for 3D inversion. For over 30 years I have also made MT processing software available for free use. In this presentation, I will discuss my experience with these freely available (but perhaps not truly open-source) computer codes. Although users are allowed to make modifications to the codes (on conditions that they provide a copy of the modified version) only a handful of users have tried to make any modification, and only rarely are modifications even reported, much less provided back to the developers.

Open source software to control Bioflo bioreactors.

PubMed

Burdge, David A; Libourel, Igor G L

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW.

Open Source Software to Control Bioflo Bioreactors

PubMed Central

Burdge, David A.; Libourel, Igor G. L.

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW. PMID:24667828

An Assessment of Some Design Constraints on Heat Production of a 3D Conceptual EGS Model Using an Open-Source Geothermal Reservoir Simulation Code

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

Yidong Xia; Mitch Plummer; Robert Podgorney

2016-02-01

Performance of heat production process over a 30-year period is assessed in a conceptual EGS model with a geothermal gradient of 65K per km depth in the reservoir. Water is circulated through a pair of parallel wells connected by a set of single large wing fractures. The results indicate that the desirable output electric power rate and lifespan could be obtained under suitable material properties and system parameters. A sensitivity analysis on some design constraints and operation parameters indicates that 1) the fracture horizontal spacing has profound effect on the long-term performance of heat production, 2) the downward deviation anglemore » for the parallel doublet wells may help overcome the difficulty of vertical drilling to reach a favorable production temperature, and 3) the thermal energy production rate and lifespan has close dependence on water mass flow rate. The results also indicate that the heat production can be improved when the horizontal fracture spacing, well deviation angle, and production flow rate are under reasonable conditions. To conduct the reservoir modeling and simulations, an open-source, finite element based, fully implicit, fully coupled hydrothermal code, namely FALCON, has been developed and used in this work. Compared with most other existing codes that are either closed-source or commercially available in this area, this new open-source code has demonstrated a code development strategy that aims to provide an unparalleled easiness for user-customization and multi-physics coupling. Test results have shown that the FALCON code is able to complete the long-term tests efficiently and accurately, thanks to the state-of-the-art nonlinear and linear solver algorithms implemented in the code.« less

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

PubMed Central

2013-01-01

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com. PMID:24295440

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

PubMed

Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

2014-02-07

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

SU-E-T-103: Development and Implementation of Web Based Quality Control Software

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

Studinski, R; Taylor, R; Angers, C

Purpose: Historically many radiation medicine programs have maintained their Quality Control (QC) test results in paper records or Microsoft Excel worksheets. Both these approaches represent significant logistical challenges, and are not predisposed to data review and approval. It has been our group's aim to develop and implement web based software designed not just to record and store QC data in a centralized database, but to provide scheduling and data review tools to help manage a radiation therapy clinics Equipment Quality control program. Methods: The software was written in the Python programming language using the Django web framework. In order tomore » promote collaboration and validation from other centres the code was made open source and is freely available to the public via an online source code repository. The code was written to provide a common user interface for data entry, formalize the review and approval process, and offer automated data trending and process control analysis of test results. Results: As of February 2014, our installation of QAtrack+ has 180 tests defined in its database and has collected ∼22 000 test results, all of which have been reviewed and approved by a physicist via QATrack+'s review tools. These results include records for quality control of Elekta accelerators, CT simulators, our brachytherapy programme, TomoTherapy and Cyberknife units. Currently at least 5 other centres are known to be running QAtrack+ clinically, forming the start of an international user community. Conclusion: QAtrack+ has proven to be an effective tool for collecting radiation therapy QC data, allowing for rapid review and trending of data for a wide variety of treatment units. As free and open source software, all source code, documentation and a bug tracker are available to the public at https://bitbucket.org/tohccmedphys/qatrackplus/.« less

NPTFit: A Code Package for Non-Poissonian Template Fitting

NASA Astrophysics Data System (ADS)

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R.

2017-06-01

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ˜GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allow for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.

TIME-DEPENDENT MULTI-GROUP MULTI-DIMENSIONAL RELATIVISTIC RADIATIVE TRANSFER CODE BASED ON SPHERICAL HARMONIC DISCRETE ORDINATE METHOD

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

Tominaga, Nozomu; Shibata, Sanshiro; Blinnikov, Sergei I., E-mail: tominaga@konan-u.ac.jp, E-mail: sshibata@post.kek.jp, E-mail: Sergei.Blinnikov@itep.ru

We develop a time-dependent, multi-group, multi-dimensional relativistic radiative transfer code, which is required to numerically investigate radiation from relativistic fluids that are involved in, e.g., gamma-ray bursts and active galactic nuclei. The code is based on the spherical harmonic discrete ordinate method (SHDOM) which evaluates a source function including anisotropic scattering in spherical harmonics and implicitly solves the static radiative transfer equation with ray tracing in discrete ordinates. We implement treatments of time dependence, multi-frequency bins, Lorentz transformation, and elastic Thomson and inelastic Compton scattering to the publicly available SHDOM code. Our code adopts a mixed-frame approach; the source functionmore » is evaluated in the comoving frame, whereas the radiative transfer equation is solved in the laboratory frame. This implementation is validated using various test problems and comparisons with the results from a relativistic Monte Carlo code. These validations confirm that the code correctly calculates the intensity and its evolution in the computational domain. The code enables us to obtain an Eddington tensor that relates the first and third moments of intensity (energy density and radiation pressure) and is frequently used as a closure relation in radiation hydrodynamics calculations.« less

Finite-SNR analysis for partial relaying cooperation with channel coding and opportunistic relay selection

NASA Astrophysics Data System (ADS)

Vu, Thang X.; Duhamel, Pierre; Chatzinotas, Symeon; Ottersten, Bjorn

2017-12-01

This work studies the performance of a cooperative network which consists of two channel-coded sources, multiple relays, and one destination. To achieve high spectral efficiency, we assume that a single time slot is dedicated to relaying. Conventional network-coded-based cooperation (NCC) selects the best relay which uses network coding to serve the two sources simultaneously. The bit error rate (BER) performance of NCC with channel coding, however, is still unknown. In this paper, we firstly study the BER of NCC via a closed-form expression and analytically show that NCC only achieves diversity of order two regardless of the number of available relays and the channel code. Secondly, we propose a novel partial relaying-based cooperation (PARC) scheme to improve the system diversity in the finite signal-to-noise ratio (SNR) regime. In particular, closed-form expressions for the system BER and diversity order of PARC are derived as a function of the operating SNR value and the minimum distance of the channel code. We analytically show that the proposed PARC achieves full (instantaneous) diversity order in the finite SNR regime, given that an appropriate channel code is used. Finally, numerical results verify our analysis and demonstrate a large SNR gain of PARC over NCC in the SNR region of interest.

PV_LIB Toolbox v. 1.3

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

2015-12-09

PV_LIB comprises a library of Matlab? code for modeling photovoltaic (PV) systems. Included are functions to compute solar position and to estimate irradiance in the PV system's plane of array, cell temperature, PV module electrical output, and conversion from DC to AC power. Also included are functions that aid in determining parameters for module performance models from module characterization testing. PV_LIB is open source code primarily intended for research and academic purposes. All algorithms are documented in openly available literature with the appropriate references included in comments within the code.

Modification of codes NUALGAM and BREMRAD, Volume 1

NASA Technical Reports Server (NTRS)

Steyn, J. J.; Huang, R.; Firstenberg, H.

1971-01-01

The NUGAM2 code predicts forward and backward angular energy differential and integrated distributions for gamma photons and fluorescent radiation emerging from finite laminar transport media. It determines buildup and albedo data for scientific research and engineering purposes; it also predicts the emission characteristics of finite radioisotope sources. The results are shown to be in very good agreement with available published data. The code predicts data for many situations in which no published data is available in the energy range up to 5 MeV. The NUGAM3 code predicts the pulse height response of inorganic (NaI and CsI) scintillation detectors to gamma photons. Because it allows the scintillator to be clad and mounted on a photomultiplier as in the experimental or industrial application, it is a more practical and thus useful code than others previously reported. Results are in excellent agreement with published Monte Carlo and experimental data in the energy range up to 4.5 MeV.

GSE, data management system programmers/User' manual

NASA Technical Reports Server (NTRS)

Schlagheck, R. A.; Dolerhie, B. D., Jr.; Ghiglieri, F. J.

1974-01-01

The GSE data management system is a computerized program which provides for a central storage source for key data associated with the mechanical ground support equipment (MGSE). Eight major sort modes can be requested by the user. Attributes that are printed automatically with each sort include the GSE end item number, description, class code, functional code, fluid media, use location, design responsibility, weight, cost, quantity, dimensions, and applicable documents. Multiple subsorts are available for the class code, functional code, fluid media, use location, design responsibility, and applicable document categories. These sorts and how to use them are described. The program and GSE data bank may be easily updated and expanded.

Fac-Back-OPAC: An Open Source Interface to Your Library System

ERIC Educational Resources Information Center

Beccaria, Mike; Scott, Dan

2007-01-01

The new Fac-Back-OPAC (a faceted backup OPAC) is built on code that was originally developed by Casey Durfee in February 2007. It represents the convergence of two prominent trends in library tools: the decoupling of discovery tools from the traditional integrated library system (ILS) and the use of readily available open source components to…

Studying the laws of software evolution in a long-lived FLOSS project.

PubMed

Gonzalez-Barahona, Jesus M; Robles, Gregorio; Herraiz, Israel; Ortega, Felipe

2014-07-01

Some free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long-lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case. © 2013 The Authors. Journal of Software: Evolution and Process published by John Wiley & Sons Ltd.

RMG An Open Source Electronic Structure Code for Multi-Petaflops Calculations

NASA Astrophysics Data System (ADS)

Briggs, Emil; Lu, Wenchang; Hodak, Miroslav; Bernholc, Jerzy

RMG (Real-space Multigrid) is an open source, density functional theory code for quantum simulations of materials. It solves the Kohn-Sham equations on real-space grids, which allows for natural parallelization via domain decomposition. Either subspace or Davidson diagonalization, coupled with multigrid methods, are used to accelerate convergence. RMG is a cross platform open source package which has been used in the study of a wide range of systems, including semiconductors, biomolecules, and nanoscale electronic devices. It can optionally use GPU accelerators to improve performance on systems where they are available. The recently released versions (>2.0) support multiple GPU's per compute node, have improved performance and scalability, enhanced accuracy and support for additional hardware platforms. New versions of the code are regularly released at http://www.rmgdft.org. The releases include binaries for Linux, Windows and MacIntosh systems, automated builds for clusters using cmake, as well as versions adapted to the major supercomputing installations and platforms. Several recent, large-scale applications of RMG will be discussed.

Studying the laws of software evolution in a long-lived FLOSS project

PubMed Central

Gonzalez-Barahona, Jesus M; Robles, Gregorio; Herraiz, Israel; Ortega, Felipe

2014-01-01

Some free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long-lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case. © 2013 The Authors. Journal of Software: Evolution and Process published by John Wiley & Sons Ltd. PMID:25893093

Software on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

. Development Tools View list of tools for build automation, version control, and high-level or specialized scripting. Toolchains Learn about the available toolchains to build applications from source code

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

PubMed

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

2014-03-01

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

A Spherical Active Coded Aperture for 4π Gamma-ray Imaging

DOE PAGES

Hellfeld, Daniel; Barton, Paul; Gunter, Donald; ...

2017-09-22

Gamma-ray imaging facilitates the efficient detection, characterization, and localization of compact radioactive sources in cluttered environments. Fieldable detector systems employing active planar coded apertures have demonstrated broad energy sensitivity via both coded aperture and Compton imaging modalities. But, planar configurations suffer from a limited field-of-view, especially in the coded aperture mode. In order to improve upon this limitation, we introduce a novel design by rearranging the detectors into an active coded spherical configuration, resulting in a 4pi isotropic field-of-view for both coded aperture and Compton imaging. This work focuses on the low- energy coded aperture modality and the optimization techniquesmore » used to determine the optimal number and configuration of 1 cm 3 CdZnTe coplanar grid detectors on a 14 cm diameter sphere with 192 available detector locations.« less

ACON: a multipurpose production controller for plasma physics codes

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

Snell, C.

1983-01-01

ACON is a BCON controller designed to run large production codes on the CTSS Cray-1 or the LTSS 7600 computers. ACON can also be operated interactively, with input from the user's terminal. The controller can run one code or a sequence of up to ten codes during the same job. Options are available to get and save Mass storage files, to perform Historian file updating operations, to compile and load source files, and to send out print and film files. Special features include ability to retry after Mass failures, backup options for saving files, startup messages for the various codes,more » and ability to reserve specified amounts of computer time after successive code runs. ACON's flexibility and power make it useful for running a number of different production codes.« less

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

Hellfeld, Daniel; Barton, Paul; Gunter, Donald

Gamma-ray imaging facilitates the efficient detection, characterization, and localization of compact radioactive sources in cluttered environments. Fieldable detector systems employing active planar coded apertures have demonstrated broad energy sensitivity via both coded aperture and Compton imaging modalities. But, planar configurations suffer from a limited field-of-view, especially in the coded aperture mode. In order to improve upon this limitation, we introduce a novel design by rearranging the detectors into an active coded spherical configuration, resulting in a 4pi isotropic field-of-view for both coded aperture and Compton imaging. This work focuses on the low- energy coded aperture modality and the optimization techniquesmore » used to determine the optimal number and configuration of 1 cm 3 CdZnTe coplanar grid detectors on a 14 cm diameter sphere with 192 available detector locations.« less

Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models.

PubMed

Jardine, Bartholomew; Raymond, Gary M; Bassingthwaighte, James B

2015-01-01

The Modular Program Constructor (MPC) is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML) ( http://www.physiome.org/jsim/) that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models. A major obstacle in writing complex models for physiological processes is the large amount of time it takes to model the myriad processes taking place simultaneously in cells, tissues, and organs. MPC replaces this task with code-generating algorithms that take model code from several different existing models and produce model code for a new JSim model. This is particularly useful during multi-scale model development where many variants are to be configured and tested against data. MPC encodes and preserves information about how a model is built from its simpler model modules, allowing the researcher to quickly substitute or update modules for hypothesis testing. MPC is implemented in Java and requires JSim to use its output. MPC source code and documentation are available at http://www.physiome.org/software/MPC/.

Open Source Subtitle Editor Software Study for Section 508 Close Caption Applications

NASA Technical Reports Server (NTRS)

Murphy, F. Brandon

2013-01-01

This paper will focus on a specific item within the NASA Electronic Information Accessibility Policy - Multimedia Presentation shall have synchronized caption; thus making information accessible to a person with hearing impairment. This synchronized caption will assist a person with hearing or cognitive disability to access the same information as everyone else. This paper focuses on the research and implementation for CC (subtitle option) support to video multimedia. The goal of this research is identify the best available open-source (free) software to achieve synchronized captions requirement and achieve savings, while meeting the security requirement for Government information integrity and assurance. CC and subtitling are processes that display text within a video to provide additional or interpretive information for those whom may need it or those whom chose it. Closed captions typically show the transcription of the audio portion of a program (video) as it occurs (either verbatim or in its edited form), sometimes including non-speech elements (such as sound effects). The transcript can be provided by a third party source or can be extracted word for word from the video. This feature can be made available for videos in two forms: either Soft-Coded or Hard-Coded. Soft-Coded is the more optional version of CC, where you can chose to turn them on if you want, or you can turn them off. Most of the time, when using the Soft-Coded option, the transcript is also provided to the view along-side the video. This option is subject to compromise, whereas the transcript is merely a text file that can be changed by anyone who has access to it. With this option the integrity of the CC is at the mercy of the user. Hard-Coded CC is a more permanent form of CC. A Hard-Coded CC transcript is embedded within a video, without the option of removal.

Open Rotor Noise Prediction Methods at NASA Langley- A Technology Review

NASA Technical Reports Server (NTRS)

Farassat, F.; Dunn, Mark H.; Tinetti, Ana F.; Nark, Douglas M.

2009-01-01

Open rotors are once again under consideration for propulsion of the future airliners because of their high efficiency. The noise generated by these propulsion systems must meet the stringent noise standards of today to reduce community impact. In this paper we review the open rotor noise prediction methods available at NASA Langley. We discuss three codes called ASSPIN (Advanced Subsonic-Supersonic Propeller Induced Noise), FW - Hpds (Ffowcs Williams-Hawkings with penetrable data surface) and the FSC (Fast Scattering Code). The first two codes are in the time domain and the third code is a frequency domain code. The capabilities of these codes and the input data requirements as well as the output data are presented. Plans for further improvements of these codes are discussed. In particular, a method based on equivalent sources is outlined to get rid of spurious signals in the FW - Hpds code.

Monte Carlo dosimetric characterization of the Flexisource Co-60 high-dose-rate brachytherapy source using PENELOPE.

PubMed

Almansa, Julio F; Guerrero, Rafael; Torres, Javier; Lallena, Antonio M

60 Co sources have been commercialized as an alternative to 192 Ir sources for high-dose-rate (HDR) brachytherapy. One of them is the Flexisource Co-60 HDR source manufactured by Elekta. The only available dosimetric characterization of this source is that of Vijande et al. [J Contemp Brachytherapy 2012; 4:34-44], whose results were not included in the AAPM/ESTRO consensus document. In that work, the dosimetric quantities were calculated as averages of the results obtained with the Geant4 and PENELOPE Monte Carlo (MC) codes, though for other sources, significant differences have been quoted between the values obtained with these two codes. The aim of this work is to perform the dosimetric characterization of the Flexisource Co-60 HDR source using PENELOPE. The MC simulation code PENELOPE (v. 2014) has been used. Following the recommendations of the AAPM/ESTRO report, the radial dose function, the anisotropy function, the air-kerma strength, the dose rate constant, and the absorbed dose rate in water have been calculated. The results we have obtained exceed those of Vijande et al. In particular, the absorbed dose rate constant is ∼0.85% larger. A similar difference is also found in the other dosimetric quantities. The effect of the electrons emitted in the decay of 60 Co, usually neglected in this kind of simulations, is significant up to the distances of 0.25 cm from the source. The systematic and significant differences we have found between PENELOPE results and the average values found by Vijande et al. point out that the dosimetric characterizations carried out with the various MC codes should be provided independently. Copyright © 2017 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

AirShow 1.0 CFD Software Users' Guide

NASA Technical Reports Server (NTRS)

Mohler, Stanley R., Jr.

2005-01-01

AirShow is visualization post-processing software for Computational Fluid Dynamics (CFD). Upon reading binary PLOT3D grid and solution files into AirShow, the engineer can quickly see how hundreds of complex 3-D structured blocks are arranged and numbered. Additionally, chosen grid planes can be displayed and colored according to various aerodynamic flow quantities such as Mach number and pressure. The user may interactively rotate and translate the graphical objects using the mouse. The software source code was written in cross-platform Java, C++, and OpenGL, and runs on Unix, Linux, and Windows. The graphical user interface (GUI) was written using Java Swing. Java also provides multiple synchronized threads. The Java Native Interface (JNI) provides a bridge between the Java code and the C++ code where the PLOT3D files are read, the OpenGL graphics are rendered, and numerical calculations are performed. AirShow is easy to learn and simple to use. The source code is available for free from the NASA Technology Transfer and Partnership Office.

Exo-Transmit: An Open-Source Code for Calculating Transmission Spectra for Exoplanet Atmospheres of Varied Composition

NASA Astrophysics Data System (ADS)

Kempton, Eliza M.-R.; Lupu, Roxana; Owusu-Asare, Albert; Slough, Patrick; Cale, Bryson

2017-04-01

We present Exo-Transmit, a software package to calculate exoplanet transmission spectra for planets of varied composition. The code is designed to generate spectra of planets with a wide range of atmospheric composition, temperature, surface gravity, and size, and is therefore applicable to exoplanets ranging in mass and size from hot Jupiters down to rocky super-Earths. Spectra can be generated with or without clouds or hazes with options to (1) include an optically thick cloud deck at a user-specified atmospheric pressure or (2) to augment the nominal Rayleigh scattering by a user-specified factor. The Exo-Transmit code is written in C and is extremely easy to use. Typically the user will only need to edit parameters in a single user input file in order to run the code for a planet of their choosing. Exo-Transmit is available publicly on Github with open-source licensing at https://github.com/elizakempton/Exo_Transmit.

Time synchronized video systems

NASA Technical Reports Server (NTRS)

Burnett, Ron

1994-01-01

The idea of synchronizing multiple video recordings to some type of 'range' time has been tried to varying degrees of success in the past. Combining this requirement with existing time code standards (SMPTE) and the new innovations in desktop multimedia however, have afforded an opportunity to increase the flexibility and usefulness of such efforts without adding costs over the traditional data recording and reduction systems. The concept described can use IRIG, GPS or a battery backed internal clock as the master time source. By converting that time source to Vertical Interval Time Code or Longitudinal Time Code, both in accordance with the SMPTE standards, the user will obtain a tape that contains machine/computer readable time code suitable for use with editing equipment that is available off-the-shelf. Accuracy on playback is then determined by the playback system chosen by the user. Accuracies of +/- 2 frames are common among inexpensive systems and complete frame accuracy is more a matter of the users' budget than the capability of the recording system.

Using National Drug Codes and drug knowledge bases to organize prescription records from multiple sources.

PubMed

Simonaitis, Linas; McDonald, Clement J

2009-10-01

The utility of National Drug Codes (NDCs) and drug knowledge bases (DKBs) in the organization of prescription records from multiple sources was studied. The master files of most pharmacy systems include NDCs and local codes to identify the products they dispense. We obtained a large sample of prescription records from seven different sources. These records carried a national product code or a local code that could be translated into a national product code via their formulary master. We obtained mapping tables from five DKBs. We measured the degree to which the DKB mapping tables covered the national product codes carried in or associated with the sample of prescription records. Considering the total prescription volume, DKBs covered 93.0-99.8% of the product codes from three outpatient sources and 77.4-97.0% of the product codes from four inpatient sources. Among the in-patient sources, invented codes explained 36-94% of the noncoverage. Outpatient pharmacy sources rarely invented codes, which comprised only 0.11-0.21% of their total prescription volume, compared with inpatient pharmacy sources for which invented codes comprised 1.7-7.4% of their prescription volume. The distribution of prescribed products was highly skewed, with 1.4-4.4% of codes accounting for 50% of the message volume and 10.7-34.5% accounting for 90% of the message volume. DKBs cover the product codes used by outpatient sources sufficiently well to permit automatic mapping. Changes in policies and standards could increase coverage of product codes used by inpatient sources.

Physics of cosmological cascades and observable properties

NASA Astrophysics Data System (ADS)

Fitoussi, T.; Belmont, R.; Malzac, J.; Marcowith, A.; Cohen-Tanugi, J.; Jean, P.

2017-04-01

TeV photons from extragalactic sources are absorbed in the intergalactic medium and initiate electromagnetic cascades. These cascades offer a unique tool to probe the properties of the universe at cosmological scales. We present a new Monte Carlo code dedicated to the physics of such cascades. This code has been tested against both published results and analytical approximations, and is made publicly available. Using this numerical tool, we investigate the main cascade properties (spectrum, halo extension and time delays), and study in detail their dependence on the physical parameters (extragalactic magnetic field, extragalactic background light, source redshift, source spectrum and beaming emission). The limitations of analytical solutions are emphasized. In particular, analytical approximations account only for the first generation of photons and higher branches of the cascade tree are neglected.

Software Engineering Laboratory (SEL) data and information policy

NASA Technical Reports Server (NTRS)

Mcgarry, Frank

1991-01-01

The policies and overall procedures that are used in distributing and in making available products of the Software Engineering Laboratory (SEL) are discussed. The products include project data and measures, project source code, reports, and software tools.

SeisCode: A seismological software repository for discovery and collaboration

NASA Astrophysics Data System (ADS)

Trabant, C.; Reyes, C. G.; Clark, A.; Karstens, R.

2012-12-01

SeisCode is a community repository for software used in seismological and related fields. The repository is intended to increase discoverability of such software and to provide a long-term home for software projects. Other places exist where seismological software may be found, but none meet the requirements necessary for an always current, easy to search, well documented, and citable resource for projects. Organizations such as IRIS, ORFEUS, and the USGS have websites with lists of available or contributed seismological software. Since the authors themselves do often not maintain these lists, the documentation often consists of a sentence or paragraph, and the available software may be outdated. Repositories such as GoogleCode and SourceForge, which are directly maintained by the authors, provide version control and issue tracking but do not provide a unified way of locating geophysical software scattered in and among countless unrelated projects. Additionally, projects are hosted at language-specific sites such as Mathworks and PyPI, in FTP directories, and in websites strewn across the Web. Search engines are only partially effective discovery tools, as the desired software is often hidden deep within the results. SeisCode provides software authors a place to present their software, codes, scripts, tutorials, and examples to the seismological community. Authors can choose their own level of involvement. At one end of the spectrum, the author might simply create a web page that points to an existing site. At the other extreme, an author may choose to leverage the many tools provided by SeisCode, such as a source code management tool with integrated issue tracking, forums, news feeds, downloads, wikis, and more. For software development projects with multiple authors, SeisCode can also be used as a central site for collaboration. SeisCode provides the community with an easy way to discover software, while providing authors a way to build a community around their software packages. IRIS invites the seismological community to browse and to submit projects to https://seiscode.iris.washington.edu/

ImgLib2--generic image processing in Java.

PubMed

Pietzsch, Tobias; Preibisch, Stephan; Tomancák, Pavel; Saalfeld, Stephan

2012-11-15

ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins. ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib. Supplementary data are available at Bioinformatics Online. saalfeld@mpi-cbg.de

Nature Research journals reproducibility policies and initiatives in the Earth sciences

NASA Astrophysics Data System (ADS)

VanDecar, J. C.

2016-12-01

The Nature Research journals strongly support the long-term endeavour by funders, institutions, researchers and publishers toward increasing the reliability and reproducibility of published research. In the Earth, space and environmental sciences this mainly takes the form of ensuring that underlying data and methods in each manuscript are made as transparent and accessible as possible. Supporting data must be made available to editors and peer reviewers at the time of submission for the purposes of evaluating each manuscript. But the preferred way to share data sets is via public repositories. When appropriate community repositories are available, we strongly encourage authors to deposit their data prior to publication. We also now require that a statement be included in each manuscript, under the heading "Data availability", indicating whether and how the data can be accessed, including any restrictions to access. To allow authors to describe their experimental design and methods in as much detail as necessary, the Nature Research journals have effectively abolished space restrictions on online methods sections. To further increase transparency, we also encourage authors to provide tables of the data behind graphs and figures as Source Data. This builds on our established data-deposition policy for specific experiments and large data sets. The Source Data is made available directly from the figure legend, for easy access. We also require that details of geological samples and palaeontological specimens include clear provenance information to ensure full transparency of the research methods. Palaeontological and type specimens must be deposited in a recognised museum or collection to permit free access by other researchers in perpetuity. Finally, authors must make available upon request, to editors and reviewers, any previously unreported custom computer code used to generate results that are reported in the paper and central to its main claims. For all studies using custom code that is deemed central to the conclusions, a statement must be included, under the heading "Code availability", indicating whether and how the code can be accessed, including any restrictions to access.

Disclosure of terminal illness to patients and families: diversity of governing codes in 14 Islamic countries.

PubMed

Abdulhameed, Hunida E; Hammami, Muhammad M; Mohamed, Elbushra A Hameed

2011-08-01

The consistency of codes governing disclosure of terminal illness to patients and families in Islamic countries has not been studied until now. To review available codes on disclosure of terminal illness in Islamic countries. DATA SOURCE AND EXTRACTION: Data were extracted through searches on Google and PubMed. Codes related to disclosure of terminal illness to patients or families were abstracted, and then classified independently by the three authors. Codes for 14 Islamic countries were located. Five codes were silent regarding informing the patient, seven allowed concealment, one mandated disclosure and one prohibited disclosure. Five codes were silent regarding informing the family, four allowed disclosure and five mandated/recommended disclosure. The Islamic Organization for Medical Sciences code was silent on both issues. Codes regarding disclosure of terminal illness to patients and families differed markedly among Islamic countries. They were silent in one-third of the codes, and tended to favour a paternalistic/utilitarian, family-centred approach over an autonomous, patient-centred approach.

Gap Analysis of Material Properties Data for Ferritic/Martensitic HT-9 Steel

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

Brown, Neil R.; Serrano De Caro, Magdalena; Rodriguez, Edward A.

2012-08-28

The US Department of Energy (DOE), Office of Nuclear Energy (NE), is supporting the development of an ASME Code Case for adoption of 12Cr-1Mo-VW ferritic/martensitic (F/M) steel, commonly known as HT-9, primarily for use in elevated temperature design of liquid-metal fast reactors (LMFR) and components. In 2011, Los Alamos National Laboratory (LANL) nuclear engineering staff began assisting in the development of a small modular reactor (SMR) design concept, previously known as the Hyperion Module, now called the Gen4 Module. LANL staff immediately proposed HT-9 for the reactor vessel and components, as well as fuel clad and ducting, due to itsmore » superior thermal qualities. Although the ASME material Code Case, for adoption of HT-9 as an approved elevated temperature material for LMFR service, is the ultimate goal of this project, there are several key deliverables that must first be successfully accomplished. The most important key deliverable is the research, accumulation, and documentation of specific material parameters; physical, mechanical, and environmental, which becomes the basis for an ASME Code Case. Time-independent tensile and ductility data and time-dependent creep and creep-rupture behavior are some of the material properties required for a successful ASME Code case. Although this report provides a cursory review of the available data, a much more comprehensive study of open-source data would be necessary. This report serves three purposes: (a) provides a list of already existing material data information that could ultimately be made available to the ASME Code, (b) determines the HT-9 material properties data missing from available sources that would be required and (c) estimates the necessary material testing required to close the gap. Ultimately, the gap analysis demonstrates that certain material properties testing will be required to fulfill the necessary information package for an ASME Code Case.« less

Metabolic Free Energy and Biological Codes: A 'Data Rate Theorem' Aging Model.

PubMed

Wallace, Rodrick

2015-06-01

A famous argument by Maturana and Varela (Autopoiesis and cognition. Reidel, Dordrecht, 1980) holds that the living state is cognitive at every scale and level of organization. Since it is possible to associate many cognitive processes with 'dual' information sources, pathologies can sometimes be addressed using statistical models based on the Shannon Coding, the Shannon-McMillan Source Coding, the Rate Distortion, and the Data Rate Theorems, which impose necessary conditions on information transmission and system control. Deterministic-but-for-error biological codes do not directly invoke cognition, but may be essential subcomponents within larger cognitive processes. A formal argument, however, places such codes within a similar framework, with metabolic free energy serving as a 'control signal' stabilizing biochemical code-and-translator dynamics in the presence of noise. Demand beyond available energy supply triggers punctuated destabilization of the coding channel, affecting essential biological functions. Aging, normal or prematurely driven by psychosocial or environmental stressors, must interfere with the routine operation of such mechanisms, initiating the chronic diseases associated with senescence. Amyloid fibril formation, intrinsically disordered protein logic gates, and cell surface glycan/lectin 'kelp bed' logic gates are reviewed from this perspective. The results generalize beyond coding machineries having easily recognizable symmetry modes, and strip a layer of mathematical complication from the study of phase transitions in nonequilibrium biological systems.

Joint Source-Channel Coding by Means of an Oversampled Filter Bank Code

NASA Astrophysics Data System (ADS)

Marinkovic, Slavica; Guillemot, Christine

2006-12-01

Quantized frame expansions based on block transforms and oversampled filter banks (OFBs) have been considered recently as joint source-channel codes (JSCCs) for erasure and error-resilient signal transmission over noisy channels. In this paper, we consider a coding chain involving an OFB-based signal decomposition followed by scalar quantization and a variable-length code (VLC) or a fixed-length code (FLC). This paper first examines the problem of channel error localization and correction in quantized OFB signal expansions. The error localization problem is treated as an[InlineEquation not available: see fulltext.]-ary hypothesis testing problem. The likelihood values are derived from the joint pdf of the syndrome vectors under various hypotheses of impulse noise positions, and in a number of consecutive windows of the received samples. The error amplitudes are then estimated by solving the syndrome equations in the least-square sense. The message signal is reconstructed from the corrected received signal by a pseudoinverse receiver. We then improve the error localization procedure by introducing a per-symbol reliability information in the hypothesis testing procedure of the OFB syndrome decoder. The per-symbol reliability information is produced by the soft-input soft-output (SISO) VLC/FLC decoders. This leads to the design of an iterative algorithm for joint decoding of an FLC and an OFB code. The performance of the algorithms developed is evaluated in a wavelet-based image coding system.

A CFD/CSD Interaction Methodology for Aircraft Wings

NASA Technical Reports Server (NTRS)

Bhardwaj, Manoj K.

1997-01-01

With advanced subsonic transports and military aircraft operating in the transonic regime, it is becoming important to determine the effects of the coupling between aerodynamic loads and elastic forces. Since aeroelastic effects can contribute significantly to the design of these aircraft, there is a strong need in the aerospace industry to predict these aero-structure interactions computationally. To perform static aeroelastic analysis in the transonic regime, high fidelity computational fluid dynamics (CFD) analysis tools must be used in conjunction with high fidelity computational structural fluid dynamics (CSD) analysis tools due to the nonlinear behavior of the aerodynamics in the transonic regime. There is also a need to be able to use a wide variety of CFD and CSD tools to predict these aeroelastic effects in the transonic regime. Because source codes are not always available, it is necessary to couple the CFD and CSD codes without alteration of the source codes. In this study, an aeroelastic coupling procedure is developed which will perform static aeroelastic analysis using any CFD and CSD code with little code integration. The aeroelastic coupling procedure is demonstrated on an F/A-18 Stabilator using NASTD (an in-house McDonnell Douglas CFD code) and NASTRAN. In addition, the Aeroelastic Research Wing (ARW-2) is used for demonstration of the aeroelastic coupling procedure by using ENSAERO (NASA Ames Research Center CFD code) and a finite element wing-box code (developed as part of this research).

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

NASA Astrophysics Data System (ADS)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

C++ software quality in the ATLAS experiment: tools and experience

NASA Astrophysics Data System (ADS)

Martin-Haugh, S.; Kluth, S.; Seuster, R.; Snyder, S.; Obreshkov, E.; Roe, S.; Sherwood, P.; Stewart, G. A.

2017-10-01

In this paper we explain how the C++ code quality is managed in ATLAS using a range of tools from compile-time through to run time testing and reflect on the substantial progress made in the last two years largely through the use of static analysis tools such as Coverity®, an industry-standard tool which enables quality comparison with general open source C++ code. Other available code analysis tools are also discussed, as is the role of unit testing with an example of how the GoogleTest framework can be applied to our codebase.

Vector radiative transfer code SORD: Performance analysis and quick start guide

NASA Astrophysics Data System (ADS)

Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Alexander; Holben, Brent; Kokhanovsky, Alexander

2017-10-01

We present a new open source polarized radiative transfer code SORD written in Fortran 90/95. SORD numerically simulates propagation of monochromatic solar radiation in a plane-parallel atmosphere over a reflecting surface using the method of successive orders of scattering (hence the name). Thermal emission is ignored. We did not improve the method in any way, but report the accuracy and runtime in 52 benchmark scenarios. This paper also serves as a quick start user's guide for the code available from ftp://maiac.gsfc.nasa.gov/pub/skorkin, from the JQSRT website, or from the corresponding (first) author.

Alpaca (Lama pacos) as a convenient source of recombinant camelid heavy chain antibodies (VHHs)

PubMed Central

Maass, David R.; Sepulveda, Jorge; Pernthaner, Anton; Shoemaker, Charles B.

2007-01-01

Recombinant single domain antibody fragments (VHHs) that derive from the unusual camelid heavy chain only IgG class (HCAbs) have many favourable properties compared with single-chain antibodies prepared from conventional IgG. As a result, VHHs have become widely used as binding reagents and are beginning to show potential as therapeutic agents. To date, the source of VHH genetic material has been camels and llamas despite their large size and limited availability. Here we demonstrate that the smaller, more tractable and widely available alpaca is an excellent source of VHH coding DNA. Alpaca sera IgG consists of about 50% HCAbs, mostly of the short-hinge variety. Sequencing of DNA encoding more than 50 random VHH and hinge domains permitted the design of PCR primers that will amplify virtually all alpaca VHH coding DNAs for phage display library construction. Alpacas were immunized with ovine tumour necrosis factor α (TNFα) and a VHH phage display library was prepared from a lymph node that drains the sites of immunizations and successfully employed in the isolation of VHHs that bind and neutralize ovine TNFα. PMID:17568607

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

PubMed

Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T; Chapman, Brad A; Cox, Cymon J; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J L

2009-06-01

The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.

NPTFit: A Code Package for Non-Poissonian Template Fitting

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

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R., E-mail: smsharma@princeton.edu, E-mail: nrodd@mit.edu, E-mail: bsafdi@mit.edu

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ∼GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allowmore » for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.« less

LSDCat: Detection and cataloguing of emission-line sources in integral-field spectroscopy datacubes

NASA Astrophysics Data System (ADS)

Herenz, Edmund Christian; Wisotzki, Lutz

2017-06-01

We present a robust, efficient, and user-friendly algorithm for detecting faint emission-line sources in large integral-field spectroscopic datacubes together with the public release of the software package Line Source Detection and Cataloguing (LSDCat). LSDCat uses a three-dimensional matched filter approach, combined with thresholding in signal-to-noise, to build a catalogue of individual line detections. In a second pass, the detected lines are grouped into distinct objects, and positions, spatial extents, and fluxes of the detected lines are determined. LSDCat requires only a small number of input parameters, and we provide guidelines for choosing appropriate values. The software is coded in Python and capable of processing very large datacubes in a short time. We verify the implementation with a source insertion and recovery experiment utilising a real datacube taken with the MUSE instrument at the ESO Very Large Telescope. The LSDCat software is available for download at http://muse-vlt.eu/science/tools and via the Astrophysics Source Code Library at http://ascl.net/1612.002

Simulation of Jet Noise with OVERFLOW CFD Code and Kirchhoff Surface Integral

NASA Technical Reports Server (NTRS)

Kandula, M.; Caimi, R.; Voska, N. (Technical Monitor)

2002-01-01

An acoustic prediction capability for supersonic axisymmetric jets was developed on the basis of OVERFLOW Navier-Stokes CFD (Computational Fluid Dynamics) code of NASA Langley Research Center. Reynolds-averaged turbulent stresses in the flow field are modeled with the aid of Spalart-Allmaras one-equation turbulence model. Appropriate acoustic and outflow boundary conditions were implemented to compute time-dependent acoustic pressure in the nonlinear source-field. Based on the specification of acoustic pressure, its temporal and normal derivatives on the Kirchhoff surface, the near-field and the far-field sound pressure levels are computed via Kirchhoff surface integral, with the Kirchhoff surface chosen to enclose the nonlinear sound source region described by the CFD code. The methods are validated by a comparison of the predictions of sound pressure levels with the available data for an axisymmetric turbulent supersonic (Mach 2) perfectly expanded jet.

Simulation of Supersonic Jet Noise with the Adaptation of Overflow CFD Code and Kirchhoff Surface Integral

NASA Technical Reports Server (NTRS)

Kandula, Max; Caimi, Raoul; Steinrock, T. (Technical Monitor)

2001-01-01

An acoustic prediction capability for supersonic axisymmetric jets was developed on the basis of OVERFLOW Navier-Stokes CFD (Computational Fluid Dynamics) code of NASA Langley Research Center. Reynolds-averaged turbulent stresses in the flow field are modeled with the aid of Spalart-Allmaras one-equation turbulence model. Appropriate acoustic and outflow boundary conditions were implemented to compute time-dependent acoustic pressure in the nonlinear source-field. Based on the specification of acoustic pressure, its temporal and normal derivatives on the Kirchhoff surface, the near-field and the far-field sound pressure levels are computed via Kirchhoff surface integral, with the Kirchhoff surface chosen to enclose the nonlinear sound source region described by the CFD code. The methods are validated by a comparison of the predictions of sound pressure levels with the available data for an axisymmetric turbulent supersonic (Mach 2) perfectly expanded jet.

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

PubMed Central

Ma, Jian; Casey, Cameron P.; Zheng, Xueyun; Ibrahim, Yehia M.; Wilkins, Christopher S.; Renslow, Ryan S.; Thomas, Dennis G.; Payne, Samuel H.; Monroe, Matthew E.; Smith, Richard D.; Teeguarden, Justin G.; Baker, Erin S.; Metz, Thomas O.

2017-01-01

Abstract Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results: We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation: PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Contact: erin.baker@pnnl.gov or thomas.metz@pnnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28505286

CUTEX: CUrvature Thresholding EXtractor

NASA Astrophysics Data System (ADS)

Molinari, S.; Schisano, E.; Faustini, F.; Pestalozzi, M.; di Giorgio, A. M.; Liu, S.

2017-08-01

CuTEx analyzes images in the infrared bands and extracts sources from complex backgrounds, particularly star-forming regions that offer the challenges of crowding, having a highly spatially variable background, and having no-psf profiles such as protostars in their accreting phase. The code is composed of two main algorithms, the first an algorithm for source detection, and the second for flux extraction. The code is originally written in IDL language and it was exported in the license free GDL language. CuTEx could be used in other bands or in scientific cases different from the native case. This software is also available as an on-line tool from the Multi-Mission Interactive Archive web pages dedicated to the Herschel Observatory.

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

PubMed Central

Washietl, Stefan; Findeiß, Sven; Müller, Stephan A.; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L.; Stadler, Peter F.; Goldman, Nick

2011-01-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied “out of the box,” without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as “noncoding.” RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode. PMID:21357752

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

PubMed

Washietl, Stefan; Findeiss, Sven; Müller, Stephan A; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L; Stadler, Peter F; Goldman, Nick

2011-04-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied "out of the box," without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as "noncoding." RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode.

A Multiphysics and Multiscale Software Environment for Modeling Astrophysical Systems

NASA Astrophysics Data System (ADS)

Portegies Zwart, Simon; McMillan, Steve; O'Nualláin, Breanndán; Heggie, Douglas; Lombardi, James; Hut, Piet; Banerjee, Sambaran; Belkus, Houria; Fragos, Tassos; Fregeau, John; Fuji, Michiko; Gaburov, Evghenii; Glebbeek, Evert; Groen, Derek; Harfst, Stefan; Izzard, Rob; Jurić, Mario; Justham, Stephen; Teuben, Peter; van Bever, Joris; Yaron, Ofer; Zemp, Marcel

We present MUSE, a software framework for tying together existing computational tools for different astrophysical domains into a single multiphysics, multiscale workload. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly-coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for a generalized stellar systems workload. MUSE has now reached a "Noah's Ark" milestone, with two available numerical solvers for each domain. MUSE can treat small stellar associations, galaxies and everything in between, including planetary systems, dense stellar clusters and galactic nuclei. Here we demonstrate an examples calculated with MUSE: the merger of two galaxies. In addition we demonstrate the working of MUSE on a distributed computer. The current MUSE code base is publicly available as open source at http://muse.li.

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts.

PubMed

Ravagli, Carlo; Pognan, Francois; Marc, Philippe

2017-01-01

The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting. The source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com This software is designed to run on a Java EE application server and store data in a relational database. philippe.marc@novartis.com. © The Author 2016. Published by Oxford University Press.

Subsurface Transport Over Multiple Phases Demonstration Software

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

2016-01-05

The STOMP simulator is a suite of numerical simulators developed by Pacific Northwest National Laboratory for addressing problems involving coupled multifluid hydrologic, thermal, geochemical, and geomechanical processes in the subsurface. The simulator has been applied to problems concerning environmental remediation, environmental stewardship, carbon sequestration, conventional petroleum production, and the production of unconventional hydrocarbon fuels. The simulator is copyrighted by Battelle Memorial Institute, and is available outside of PNNL via use agreements. To promote the open exchange of scientific ideas the simulator is provided as source code. A demonstration version of the simulator has been developed, which will provide potential newmore » users with an executable (not source code) implementation of the software royalty free. Demonstration versions will be offered via the STOMP website for all currently available operational modes of the simulator. The demonstration versions of the simulator will be configured with the direct banded linear system solver and have a limit of 1,000 active grid cells. This will provide potential new users with an opportunity to apply the code to simple problems, including many of the STOMP short course problems, without having to pay a license fee. Users will be required to register on the STOMP website prior to receiving an executable.« less

JavaGenes Molecular Evolution

NASA Technical Reports Server (NTRS)

Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

2007-01-01

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

Initial Integration of Noise Prediction Tools for Acoustic Scattering Effects

NASA Technical Reports Server (NTRS)

Nark, Douglas M.; Burley, Casey L.; Tinetti, Ana; Rawls, John W.

2008-01-01

This effort provides an initial glimpse at NASA capabilities available in predicting the scattering of fan noise from a non-conventional aircraft configuration. The Aircraft NOise Prediction Program, Fast Scattering Code, and the Rotorcraft Noise Model were coupled to provide increased fidelity models of scattering effects on engine fan noise sources. The integration of these codes led to the identification of several keys issues entailed in applying such multi-fidelity approaches. In particular, for prediction at noise certification points, the inclusion of distributed sources leads to complications with the source semi-sphere approach. Computational resource requirements limit the use of the higher fidelity scattering code to predict radiated sound pressure levels for full scale configurations at relevant frequencies. And, the ability to more accurately represent complex shielding surfaces in current lower fidelity models is necessary for general application to scattering predictions. This initial step in determining the potential benefits/costs of these new methods over the existing capabilities illustrates a number of the issues that must be addressed in the development of next generation aircraft system noise prediction tools.

Authorship Attribution of Source Code

ERIC Educational Resources Information Center

Tennyson, Matthew F.

2013-01-01

Authorship attribution of source code is the task of deciding who wrote a program, given its source code. Applications include software forensics, plagiarism detection, and determining software ownership. A number of methods for the authorship attribution of source code have been presented in the past. A review of those existing methods is…

Human Rights Texts: Converting Human Rights Primary Source Documents into Data.

PubMed

Fariss, Christopher J; Linder, Fridolin J; Jones, Zachary M; Crabtree, Charles D; Biek, Megan A; Ross, Ana-Sophia M; Kaur, Taranamol; Tsai, Michael

2015-01-01

We introduce and make publicly available a large corpus of digitized primary source human rights documents which are published annually by monitoring agencies that include Amnesty International, Human Rights Watch, the Lawyers Committee for Human Rights, and the United States Department of State. In addition to the digitized text, we also make available and describe document-term matrices, which are datasets that systematically organize the word counts from each unique document by each unique term within the corpus of human rights documents. To contextualize the importance of this corpus, we describe the development of coding procedures in the human rights community and several existing categorical indicators that have been created by human coding of the human rights documents contained in the corpus. We then discuss how the new human rights corpus and the existing human rights datasets can be used with a variety of statistical analyses and machine learning algorithms to help scholars understand how human rights practices and reporting have evolved over time. We close with a discussion of our plans for dataset maintenance, updating, and availability.

Human Rights Texts: Converting Human Rights Primary Source Documents into Data

PubMed Central

Fariss, Christopher J.; Linder, Fridolin J.; Jones, Zachary M.; Crabtree, Charles D.; Biek, Megan A.; Ross, Ana-Sophia M.; Kaur, Taranamol; Tsai, Michael

2015-01-01

We introduce and make publicly available a large corpus of digitized primary source human rights documents which are published annually by monitoring agencies that include Amnesty International, Human Rights Watch, the Lawyers Committee for Human Rights, and the United States Department of State. In addition to the digitized text, we also make available and describe document-term matrices, which are datasets that systematically organize the word counts from each unique document by each unique term within the corpus of human rights documents. To contextualize the importance of this corpus, we describe the development of coding procedures in the human rights community and several existing categorical indicators that have been created by human coding of the human rights documents contained in the corpus. We then discuss how the new human rights corpus and the existing human rights datasets can be used with a variety of statistical analyses and machine learning algorithms to help scholars understand how human rights practices and reporting have evolved over time. We close with a discussion of our plans for dataset maintenance, updating, and availability. PMID:26418817

Continuous integration and quality control for scientific software

NASA Astrophysics Data System (ADS)

Neidhardt, A.; Ettl, M.; Brisken, W.; Dassing, R.

2013-08-01

Modern software has to be stable, portable, fast and reliable. This is going to be also more and more important for scientific software. But this requires a sophisticated way to inspect, check and evaluate the quality of source code with a suitable, automated infrastructure. A centralized server with a software repository and a version control system is one essential part, to manage the code basis and to control the different development versions. While each project can be compiled separately, the whole code basis can also be compiled with one central “Makefile”. This is used to create automated, nightly builds. Additionally all sources are inspected automatically with static code analysis and inspection tools, which check well-none error situations, memory and resource leaks, performance issues, or style issues. In combination with an automatic documentation generator it is possible to create the developer documentation directly from the code and the inline comments. All reports and generated information are presented as HTML page on a Web server. Because this environment increased the stability and quality of the software of the Geodetic Observatory Wettzell tremendously, it is now also available for scientific communities. One regular customer is already the developer group of the DiFX software correlator project.

JADAMILU: a software code for computing selected eigenvalues of large sparse symmetric matrices

NASA Astrophysics Data System (ADS)

Bollhöfer, Matthias; Notay, Yvan

2007-12-01

A new software code for computing selected eigenvalues and associated eigenvectors of a real symmetric matrix is described. The eigenvalues are either the smallest or those closest to some specified target, which may be in the interior of the spectrum. The underlying algorithm combines the Jacobi-Davidson method with efficient multilevel incomplete LU (ILU) preconditioning. Key features are modest memory requirements and robust convergence to accurate solutions. Parameters needed for incomplete LU preconditioning are automatically computed and may be updated at run time depending on the convergence pattern. The software is easy to use by non-experts and its top level routines are written in FORTRAN 77. Its potentialities are demonstrated on a few applications taken from computational physics. Program summaryProgram title: JADAMILU Catalogue identifier: ADZT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZT_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.: 101 359 No. of bytes in distributed program, including test data, etc.: 7 493 144 Distribution format: tar.gz Programming language: Fortran 77 Computer: Intel or AMD with g77 and pgf; Intel EM64T or Itanium with ifort; AMD Opteron with g77, pgf and ifort; Power (IBM) with xlf90. Operating system: Linux, AIX RAM: problem dependent Word size: real:8; integer: 4 or 8, according to user's choice Classification: 4.8 Nature of problem: Any physical problem requiring the computation of a few eigenvalues of a symmetric matrix. Solution method: Jacobi-Davidson combined with multilevel ILU preconditioning. Additional comments: We supply binaries rather than source code because JADAMILU uses the following external packages: MC64. This software is copyrighted software and not freely available. COPYRIGHT (c) 1999 Council for the Central Laboratory of the Research Councils. AMD. Copyright (c) 2004-2006 by Timothy A. Davis, Patrick R. Amestoy, and Iain S. Duff. Source code is distributed by the authors under the GNU LGPL licence. BLAS. The reference BLAS is a freely-available software package. It is available from netlib via anonymous ftp and the World Wide Web. LAPACK. The complete LAPACK package or individual routines from LAPACK are freely available on netlib and can be obtained via the World Wide Web or anonymous ftp. For maximal benefit to the community, we added the sources we are proprietary of to the tar.gz file submitted for inclusion in the CPC library. However, as explained in the README file, users willing to compile the code instead of using binaries should first obtain the sources for the external packages mentioned above (email and/or web addresses are provided). Running time: Problem dependent; the test examples provided with the code only take a few seconds to run; timing results for large scale problems are given in Section 5.

Design pattern mining using distributed learning automata and DNA sequence alignment.

PubMed

Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

2014-01-01

Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns.

ProteoCloud: a full-featured open source proteomics cloud computing pipeline.

PubMed

Muth, Thilo; Peters, Julian; Blackburn, Jonathan; Rapp, Erdmann; Martens, Lennart

2013-08-02

We here present the ProteoCloud pipeline, a freely available, full-featured cloud-based platform to perform computationally intensive, exhaustive searches in a cloud environment using five different peptide identification algorithms. ProteoCloud is entirely open source, and is built around an easy to use and cross-platform software client with a rich graphical user interface. This client allows full control of the number of cloud instances to initiate and of the spectra to assign for identification. It also enables the user to track progress, and to visualize and interpret the results in detail. Source code, binaries and documentation are all available at http://proteocloud.googlecode.com. Copyright © 2012 Elsevier B.V. All rights reserved.

Software for Computing, Archiving, and Querying Semisimple Braided Monoidal Category Data

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

This software package collects various open source and freely available codes and algorithms to compute and archive the categorical data for certain semisimple braided monoidal categories. In particular, it computes the data for of group theoretical categories for academic research.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

PubMed Central

Hart, Reece K.; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A.

2015-01-01

Summary: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. Availability and implementation: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Contact: reecehart@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25273102

Software for universal noiseless coding

NASA Technical Reports Server (NTRS)

Rice, R. F.; Schlutsmeyer, A. P.

1981-01-01

An overview is provided of the universal noiseless coding algorithms as well as their relationship to the now available FORTRAN implementations. It is suggested that readers considering investigating the utility of these algorithms for actual applications should consult both NASA's Computer Software Management and Information Center (COSMIC) and descriptions of coding techniques provided by Rice (1979). Examples of applying these techniques have also been given by Rice (1975, 1979, 1980). Attention is given to reversible preprocessing, general implementation instructions, naming conventions, and calling arguments. A general applicability of the considered algorithms to solving practical problems is obtained because most real data sources can be simply transformed into the required form by appropriate preprocessing.

EPA Remote Sensing Information Gateway

NASA Astrophysics Data System (ADS)

Paulsen, H. K.; Szykman, J. J.; Plessel, T.; Freeman, M.; Dimmick, F.

2009-12-01

The Remote Sensing Information Gateway was developed by the U.S. Environmental Protection Agency (EPA) to assist researchers in easily obtaining and combining a variety of environmental datasets related to air quality research. Current datasets available include, but are not limited to surface PM2.5 and O3 data, satellite derived aerosol optical depth , and 3-dimensional output from U.S. EPA's Models 3/Community Multi-scale Air Quality (CMAQ) modeling system. The presentation will include a demonstration that illustrates several scenarios of how researchers use the tool to help them visualize and obtain data for their work; with a particular focus on episode analysis related to biomass burning impacts on air quality. The presentation will provide an overview on how RSIG works and how the code has been—and can be—adapted for other projects. One example is the Virtual Estuary, which focuses on automating the retrieval and pre-processing of a variety of data needed for estuarine research. RSIG’s source codes are freely available to researchers with permission from the EPA principal investigator, Dr. Jim Szykman. RSIG is available to the community and can be accessed online at http://www.epa.gov/rsig. Once the JAVA policy file is configured on your computer you can run the RSIG applet on your computer and connect to the RSIG server to visualize and retrieve available data sets. The applet allows the user to specify the temporal/spatial areas of interest, and the types of data to retrieve. The applet then communicates with RSIG subsetter codes located on the data owners’ remote servers; the subsetter codes assemble and transfer via ordinary Internet protocols only the specified data to the researcher’s computer. This is much faster than the usual method of transferring large files via FTP and greatly reduces network traffic. The RSIG applet then visualizes the transferred data on a latitude-longitude map, automatically locating the data in the correct geographic position. Images, animations, and aggregated data can be saved or exported in a variety of data formats: Binary External Data Representation (XDR) format (simple, efficient), NetCDF-COARDS format, NetCDF-IOAPI format (regridding the data to a CMAQ grid), HDF (unsubsetted satellite files), ASCII tab-delimited spreadsheet, MCMC (used for input into HB model), PNG images, MPG movies, KMZ movies (for display in Google Earth and similar applications), GeoTIFF RGB format and 32-bit float format. RSIG’s source codes are freely available to researchers with permission from the EPA. Contacts for obtaining RSIG code are available at the RSIG website.

The Numerical Electromagnetics Code (NEC) - A Brief History

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

Burke, G J; Miller, E K; Poggio, A J

The Numerical Electromagnetics Code, NEC as it is commonly known, continues to be one of the more widely used antenna modeling codes in existence. With several versions in use that reflect different levels of capability and availability, there are now 450 copies of NEC4 and 250 copies of NEC3 that have been distributed by Lawrence Livermore National Laboratory to a limited class of qualified recipients, and several hundred copies of NEC2 that had a recorded distribution by LLNL. These numbers do not account for numerous copies (perhaps 1000s) that were acquired through other means capitalizing on the open source code,more » the absence of distribution controls prior to NEC3 and the availability of versions on the Internet. In this paper we briefly review the history of the code that is concisely displayed in Figure 1. We will show how it capitalized on the research of prominent contributors in the early days of computational electromagnetics, how a combination of events led to the tri-service-supported code development program that ultimately led to NEC and how it evolved to the present day product. The authors apologize that space limitations do not allow us to provide a list of references or to acknowledge the numerous contributors to the code both of which can be found in the code documents.« less

Open-Source as a strategy for operational software - the case of Enki

NASA Astrophysics Data System (ADS)

Kolberg, Sjur; Bruland, Oddbjørn

2014-05-01

Since 2002, SINTEF Energy has been developing what is now known as the Enki modelling system. This development has been financed by Norway's largest hydropower producer Statkraft, motivated by a desire for distributed hydrological models in operational use. As the owner of the source code, Statkraft has recently decided on Open Source as a strategy for further development, and for migration from an R&D context to operational use. A current cooperation project is currently carried out between SINTEF Energy, 7 large Norwegian hydropower producers including Statkraft, three universities and one software company. Of course, the most immediate task is that of software maturing. A more important challenge, however, is one of gaining experience within the operational hydropower industry. A transition from lumped to distributed models is likely to also require revision of measurement program, calibration strategy, use of GIS and modern data sources like weather radar and satellite imagery. On the other hand, map based visualisations enable a richer information exchange between hydrologic forecasters and power market traders. The operating context of a distributed hydrology model within hydropower planning is far from settled. Being both a modelling framework and a library of plugin-routines to build models from, Enki supports the flexibility needed in this situation. Recent development has separated the core from the user interface, paving the way for a scripting API, cross-platform compilation, and front-end programs serving different degrees of flexibility, robustness and security. The open source strategy invites anyone to use Enki and to develop and contribute new modules. Once tested, the same modules are available for the operational versions of the program. A core challenge is to offer rigid testing procedures and mechanisms to reject routines in an operational setting, without limiting the experimentation with new modules. The Open Source strategy also has implications for building and maintaining competence around the source code and the advanced hydrological and statistical routines in Enki. Originally developed by hydrologists, the Enki code is now approaching a state where maintenance requires a background in professional software development. Without the advantage of proprietary source code, both hydrologic improvements and software maintenance depend on donations or development support on a case-to-case basis, a situation well known within the open source community. It remains to see whether these mechanisms suffice to keep Enki at the maintenance level required by the hydropower sector. ENKI is available from www.opensource-enki.org.

Neptune: An astrophysical smooth particle hydrodynamics code for massively parallel computer architectures

NASA Astrophysics Data System (ADS)

Sandalski, Stou

Smooth particle hydrodynamics is an efficient method for modeling the dynamics of fluids. It is commonly used to simulate astrophysical processes such as binary mergers. We present a newly developed GPU accelerated smooth particle hydrodynamics code for astrophysical simulations. The code is named neptune after the Roman god of water. It is written in OpenMP parallelized C++ and OpenCL and includes octree based hydrodynamic and gravitational acceleration. The design relies on object-oriented methodologies in order to provide a flexible and modular framework that can be easily extended and modified by the user. Several pre-built scenarios for simulating collisions of polytropes and black-hole accretion are provided. The code is released under the MIT Open Source license and publicly available at http://code.google.com/p/neptune-sph/.

HippDB: a database of readily targeted helical protein-protein interactions.

PubMed

Bergey, Christina M; Watkins, Andrew M; Arora, Paramjit S

2013-11-01

HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. arora@nyu.edu.

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.

Measuring Diagnoses: ICD Code Accuracy

PubMed Central

O'Malley, Kimberly J; Cook, Karon F; Price, Matt D; Wildes, Kimberly Raiford; Hurdle, John F; Ashton, Carol M

2005-01-01

Objective To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. Data Sources/Study Setting The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. Study Design/Methods We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. Principle Findings Main error sources along the “patient trajectory” include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the “paper trail” include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. Conclusions By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways. PMID:16178999

U.S. Seismic Design Maps Web Application

NASA Astrophysics Data System (ADS)

Martinez, E.; Fee, J.

2015-12-01

The application computes earthquake ground motion design parameters compatible with the International Building Code and other seismic design provisions. It is the primary method for design engineers to obtain ground motion parameters for multiple building codes across the country. When designing new buildings and other structures, engineers around the country use the application. Users specify the design code of interest, location, and other parameters to obtain necessary ground motion information consisting of a high-level executive summary as well as detailed information including maps, data, and graphs. Results are formatted such that they can be directly included in a final engineering report. In addition to single-site analysis, the application supports a batch mode for simultaneous consideration of multiple locations. Finally, an application programming interface (API) is available which allows other application developers to integrate this application's results into larger applications for additional processing. Development on the application has proceeded in an iterative manner working with engineers through email, meetings, and workshops. Each iteration provided new features, improved performance, and usability enhancements. This development approach positioned the application to be integral to the structural design process and is now used to produce over 1800 reports daily. Recent efforts have enhanced the application to be a data-driven, mobile-first, responsive web application. Development is ongoing, and source code has recently been published into the open-source community on GitHub. Open-sourcing the code facilitates improved incorporation of user feedback to add new features ensuring the application's continued success.

PyPanda: a Python package for gene regulatory network reconstruction

PubMed Central

van IJzendoorn, David G.P.; Glass, Kimberly; Quackenbush, John; Kuijjer, Marieke L.

2016-01-01

Summary: PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of ‘omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis. Availability and implementation: The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda. Contact: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl PMID:27402905

Biopython: freely available Python tools for computational molecular biology and bioinformatics

PubMed Central

Cock, Peter J. A.; Antao, Tiago; Chang, Jeffrey T.; Chapman, Brad A.; Cox, Cymon J.; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J. L.

2009-01-01

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk. PMID:19304878

Software Products - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You astronomy. Available as Fortran, C, or Python source code. Current version: 3.1 Software Products by Our computer or programmable calculator. Standards Of Fundamental Astronomy (SOFA) Libraries The International

DecouplingModes: Passive modes amplitudes

NASA Astrophysics Data System (ADS)

Shaw, J. Richard; Lewis, Antony

2018-01-01

DecouplingModes calculates the amplitude of the passive modes, which requires solving the Einstein equations on superhorizon scales sourced by the anisotropic stress from the magnetic fields (prior to neutrino decoupling), and the magnetic and neutrino stress (after decoupling). The code is available as a Mathematica notebook.

Operational rate-distortion performance for joint source and channel coding of images.

PubMed

Ruf, M J; Modestino, J W

1999-01-01

This paper describes a methodology for evaluating the operational rate-distortion behavior of combined source and channel coding schemes with particular application to images. In particular, we demonstrate use of the operational rate-distortion function to obtain the optimum tradeoff between source coding accuracy and channel error protection under the constraint of a fixed transmission bandwidth for the investigated transmission schemes. Furthermore, we develop information-theoretic bounds on performance for specific source and channel coding systems and demonstrate that our combined source-channel coding methodology applied to different schemes results in operational rate-distortion performance which closely approach these theoretical limits. We concentrate specifically on a wavelet-based subband source coding scheme and the use of binary rate-compatible punctured convolutional (RCPC) codes for transmission over the additive white Gaussian noise (AWGN) channel. Explicit results for real-world images demonstrate the efficacy of this approach.

A new Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, Hannes; Dutta, Rishabh; Jónsson, Sigurjón; Mai, Martin

2017-04-01

Modern earthquake source estimation studies increasingly use non-linear optimization strategies to estimate kinematic rupture parameters, often considering geodetic and seismic data jointly. However, the optimization process is complex and consists of several steps that need to be followed in the earthquake parameter estimation procedure. These include pre-describing or modeling the fault geometry, calculating the Green's Functions (often assuming a layered elastic half-space), and estimating the distributed final slip and possibly other kinematic source parameters. Recently, Bayesian inference has become popular for estimating posterior distributions of earthquake source model parameters given measured/estimated/assumed data and model uncertainties. For instance, some research groups consider uncertainties of the layered medium and propagate these to the source parameter uncertainties. Other groups make use of informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed that efficiently explore the often high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational demands of these methods are high and estimation codes are rarely distributed along with the published results. Even if codes are made available, it is often difficult to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in earthquake source estimations, we undertook the effort of producing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package is build on top of the pyrocko seismological toolbox (www.pyrocko.org) and makes use of the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat) and we encourage and solicit contributions to the project. In this contribution, we present our strategy for developing BEAT, show application examples, and discuss future developments.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2014-01-01

pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Continuation of research into language concepts for the mission support environment: Source code

NASA Technical Reports Server (NTRS)

Barton, Timothy J.; Ratner, Jeremiah M.

1991-01-01

Research into language concepts for the Mission Control Center is presented. A computer code for source codes is presented. The file contains the routines which allow source code files to be created and compiled. The build process assumes that all elements and the COMP exist in the current directory. The build process places as much code generation as possible on the preprocessor as possible. A summary is given of the source files as used and/or manipulated by the build routine.

[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.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

PubMed

Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

2015-01-15

Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Open source tools and toolkits for bioinformatics: significance, and where are we?

PubMed

Stajich, Jason E; Lapp, Hilmar

2006-09-01

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

Idaho National Engineering Laboratory code assessment of the Rocky Flats transuranic waste

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

NONE

1995-07-01

This report is an assessment of the content codes associated with transuranic waste shipped from the Rocky Flats Plant in Golden, Colorado, to INEL. The primary objective of this document is to characterize and describe the transuranic wastes shipped to INEL from Rocky Flats by item description code (IDC). This information will aid INEL in determining if the waste meets the waste acceptance criteria (WAC) of the Waste Isolation Pilot Plant (WIPP). The waste covered by this content code assessment was shipped from Rocky Flats between 1985 and 1989. These years coincide with the dates for information available in themore » Rocky Flats Solid Waste Information Management System (SWIMS). The majority of waste shipped during this time was certified to the existing WIPP WAC. This waste is referred to as precertified waste. Reassessment of these precertified waste containers is necessary because of changes in the WIPP WAC. To accomplish this assessment, the analytical and process knowledge available on the various IDCs used at Rocky Flats were evaluated. Rocky Flats sources for this information include employee interviews, SWIMS, Transuranic Waste Certification Program, Transuranic Waste Inspection Procedure, Backlog Waste Baseline Books, WIPP Experimental Waste Characterization Program (headspace analysis), and other related documents, procedures, and programs. Summaries are provided of: (a) certification information, (b) waste description, (c) generation source, (d) recovery method, (e) waste packaging and handling information, (f) container preparation information, (g) assay information, (h) inspection information, (i) analytical data, and (j) RCRA characterization.« less

Measuring diagnoses: ICD code accuracy.

PubMed

O'Malley, Kimberly J; Cook, Karon F; Price, Matt D; Wildes, Kimberly Raiford; Hurdle, John F; Ashton, Carol M

2005-10-01

To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. Main error sources along the "patient trajectory" include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the "paper trail" include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways.

Insights Gained from Forensic Analysis with MELCOR of the Fukushima-Daiichi Accidents.

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

Andrews, Nathan C.; Gauntt, Randall O.

Since the accidents at Fukushima-Daiichi, Sandia National Laboratories has been modeling these accident scenarios using the severe accident analysis code, MELCOR. MELCOR is a widely used computer code developed at Sandia National Laboratories since ~1982 for the U.S. Nuclear Regulatory Commission. Insights from the modeling of these accidents is being used to better inform future code development and potentially improved accident management. To date, our necessity to better capture in-vessel thermal-hydraulic and ex-vessel melt coolability and concrete interactions has led to the implementation of new models. The most recent analyses, presented in this paper, have been in support of themore » of the Organization for Economic Cooperation and Development Nuclear Energy Agency’s (OECD/NEA) Benchmark Study of the Accident at the Fukushima Daiichi Nuclear Power Station (BSAF) Project. The goal of this project is to accurately capture the source term from all three releases and then model the atmospheric dispersion. In order to do this, a forensic approach is being used in which available plant data and release timings is being used to inform the modeled MELCOR accident scenario. For example, containment failures, core slumping events and lower head failure timings are all enforced parameters in these analyses. This approach is fundamentally different from a blind code assessment analysis often used in standard problem exercises. The timings of these events are informed by representative spikes or decreases in plant data. The combination of improvements to the MELCOR source code resulting from analysis previous accident analysis and this forensic approach has allowed Sandia to generate representative and plausible source terms for all three accidents at Fukushima Daiichi out to three weeks after the accident to capture both early and late releases. In particular, using the source terms developed by MELCOR, the MACCS software code, which models atmospheric dispersion and deposition, we are able to reasonably capture the deposition of radionuclides to the northwest of the reactor site.« less

A Need for a Theory of Visual Literacy.

ERIC Educational Resources Information Center

Hortin, John A.

1982-01-01

Examines sources available for developing a theory of visual literacy and attempts to clarify the meaning of the term. Suggests that visual thinking, a concept supported by recent research on mental imagery, visualization, and dual coding, ought to be the emphasis for future theory development. (FL)

Menu-driven cloud computing and resource sharing for R and Bioconductor

PubMed Central

Bolouri, Hamid; Angerman, Michael

2011-01-01

Summary: We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. Availability and Implementation: CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. Contact: hbolouri@fhcrc.org PMID:21685055

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association.

PubMed

Ma, Jian; Casey, Cameron P; Zheng, Xueyun; Ibrahim, Yehia M; Wilkins, Christopher S; Renslow, Ryan S; Thomas, Dennis G; Payne, Samuel H; Monroe, Matthew E; Smith, Richard D; Teeguarden, Justin G; Baker, Erin S; Metz, Thomas O

2017-09-01

Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library . erin.baker@pnnl.gov or thomas.metz@pnnl.gov. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Critical evaluation of reverse engineering tool Imagix 4D!

PubMed

Yadav, Rashmi; Patel, Ravindra; Kothari, Abhay

2016-01-01

The comprehension of legacy codes is difficult to understand. Various commercial reengineering tools are available that have unique working styles, and are equipped with their inherent capabilities and shortcomings. The focus of the available tools is in visualizing static behavior not the dynamic one. Therefore, it is difficult for people who work in software product maintenance, code understanding reengineering/reverse engineering. Consequently, the need for a comprehensive reengineering/reverse engineering tool arises. We found the usage of Imagix 4D to be good as it generates the maximum pictorial representations in the form of flow charts, flow graphs, class diagrams, metrics and, to a partial extent, dynamic visualizations. We evaluated Imagix 4D with the help of a case study involving a few samples of source code. The behavior of the tool was analyzed on multiple small codes and a large code gcc C parser. Large code evaluation was performed to uncover dead code, unstructured code, and the effect of not including required files at preprocessing level. The utility of Imagix 4D to prepare decision density and complexity metrics for a large code was found to be useful in getting to know how much reengineering is required. At the outset, Imagix 4D offered limitations in dynamic visualizations, flow chart separation (large code) and parsing loops. The outcome of evaluation will eventually help in upgrading Imagix 4D and posed a need of full featured tools in the area of software reengineering/reverse engineering. It will also help the research community, especially those who are interested in the realm of software reengineering tool building.

RICH: OPEN-SOURCE HYDRODYNAMIC SIMULATION ON A MOVING VORONOI MESH

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

Yalinewich, Almog; Steinberg, Elad; Sari, Re’em

2015-02-01

We present here RICH, a state-of-the-art two-dimensional hydrodynamic code based on Godunov’s method, on an unstructured moving mesh (the acronym stands for Racah Institute Computational Hydrodynamics). This code is largely based on the code AREPO. It differs from AREPO in the interpolation and time-advancement schemeS as well as a novel parallelization scheme based on Voronoi tessellation. Using our code, we study the pros and cons of a moving mesh (in comparison to a static mesh). We also compare its accuracy to other codes. Specifically, we show that our implementation of external sources and time-advancement scheme is more accurate and robustmore » than is AREPO when the mesh is allowed to move. We performed a parameter study of the cell rounding mechanism (Lloyd iterations) and its effects. We find that in most cases a moving mesh gives better results than a static mesh, but it is not universally true. In the case where matter moves in one way and a sound wave is traveling in the other way (such that relative to the grid the wave is not moving) a static mesh gives better results than a moving mesh. We perform an analytic analysis for finite difference schemes that reveals that a Lagrangian simulation is better than a Eulerian simulation in the case of a highly supersonic flow. Moreover, we show that Voronoi-based moving mesh schemes suffer from an error, which is resolution independent, due to inconsistencies between the flux calculation and the change in the area of a cell. Our code is publicly available as open source and designed in an object-oriented, user-friendly way that facilitates incorporation of new algorithms and physical processes.« less

Quasi-experimental study designs series-paper 9: collecting data from quasi-experimental studies.

PubMed

Aloe, Ariel M; Becker, Betsy Jane; Duvendack, Maren; Valentine, Jeffrey C; Shemilt, Ian; Waddington, Hugh

2017-09-01

To identify variables that must be coded when synthesizing primary studies that use quasi-experimental designs. All quasi-experimental (QE) designs. When designing a systematic review of QE studies, potential sources of heterogeneity-both theory-based and methodological-must be identified. We outline key components of inclusion criteria for syntheses of quasi-experimental studies. We provide recommendations for coding content-relevant and methodological variables and outlined the distinction between bivariate effect sizes and partial (i.e., adjusted) effect sizes. Designs used and controls used are viewed as of greatest importance. Potential sources of bias and confounding are also addressed. Careful consideration must be given to inclusion criteria and the coding of theoretical and methodological variables during the design phase of a synthesis of quasi-experimental studies. The success of the meta-regression analysis relies on the data available to the meta-analyst. Omission of critical moderator variables (i.e., effect modifiers) will undermine the conclusions of a meta-analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

DREAM-3D and the importance of model inputs and boundary conditions

NASA Astrophysics Data System (ADS)

Friedel, Reiner; Tu, Weichao; Cunningham, Gregory; Jorgensen, Anders; Chen, Yue

2015-04-01

Recent work on radiation belt 3D diffusion codes such as the Los Alamos "DREAM-3D" code have demonstrated the ability of such codes to reproduce realistic magnetospheric storm events in the relativistic electron dynamics - as long as sufficient "event-oriented" boundary conditions and code inputs such as wave powers, low energy boundary conditions, background plasma densities, and last closed drift shell (outer boundary) are available. In this talk we will argue that the main limiting factor in our modeling ability is no longer our inability to represent key physical processes that govern the dynamics of the radiation belts (radial, pitch angle and energy diffusion) but rather our limitations in specifying accurate boundary conditions and code inputs. We use here DREAM-3D runs to show the sensitivity of the modeled outcomes to these boundary conditions and inputs, and also discuss alternate "proxy" approaches to obtain the required inputs from other (ground-based) sources.

MetaJC++: A flexible and automatic program transformation technique using meta framework

NASA Astrophysics Data System (ADS)

Beevi, Nadera S.; Reghu, M.; Chitraprasad, D.; Vinodchandra, S. S.

2014-09-01

Compiler is a tool to translate abstract code containing natural language terms to machine code. Meta compilers are available to compile more than one languages. We have developed a meta framework intends to combine two dissimilar programming languages, namely C++ and Java to provide a flexible object oriented programming platform for the user. Suitable constructs from both the languages have been combined, thereby forming a new and stronger Meta-Language. The framework is developed using the compiler writing tools, Flex and Yacc to design the front end of the compiler. The lexer and parser have been developed to accommodate the complete keyword set and syntax set of both the languages. Two intermediate representations have been used in between the translation of the source program to machine code. Abstract Syntax Tree has been used as a high level intermediate representation that preserves the hierarchical properties of the source program. A new machine-independent stack-based byte-code has also been devised to act as a low level intermediate representation. The byte-code is essentially organised into an output class file that can be used to produce an interpreted output. The results especially in the spheres of providing C++ concepts in Java have given an insight regarding the potential strong features of the resultant meta-language.

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.

Recent and Planned Developments in the CARI Program

DTIC Science & Technology

2013-04-01

software are available from the Radiobiology Research Team Website. The source code is available upon request. CARI-6 is based on the last major... Research Team at its newly founded Civil Aeromedical Research Institute (now called the Civil Aerospace Medical Institute, i.e., CAMI) to investigate...Administration, Office of Aerospace Medicine. Re- port DOT/FAA/AM-11/09, 2011. Online at: www. faa.gov/data_ research / research /med_humanfacs/ oamtechreports

COSMOS: Python library for massively parallel workflows

PubMed Central

Gafni, Erik; Luquette, Lovelace J.; Lancaster, Alex K.; Hawkins, Jared B.; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P.; Tonellato, Peter J.

2014-01-01

Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Availability and implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. Contact: dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24982428

Automated Concurrent Blackboard System Generation in C++

NASA Technical Reports Server (NTRS)

Kaplan, J. A.; McManus, J. W.; Bynum, W. L.

1999-01-01

In his 1992 Ph.D. thesis, "Design and Analysis Techniques for Concurrent Blackboard Systems", John McManus defined several performance metrics for concurrent blackboard systems and developed a suite of tools for creating and analyzing such systems. These tools allow a user to analyze a concurrent blackboard system design and predict the performance of the system before any code is written. The design can be modified until simulated performance is satisfactory. Then, the code generator can be invoked to generate automatically all of the code required for the concurrent blackboard system except for the code implementing the functionality of each knowledge source. We have completed the port of the source code generator and a simulator for a concurrent blackboard system. The source code generator generates the necessary C++ source code to implement the concurrent blackboard system using Parallel Virtual Machine (PVM) running on a heterogeneous network of UNIX(trademark) workstations. The concurrent blackboard simulator uses the blackboard specification file to predict the performance of the concurrent blackboard design. The only part of the source code for the concurrent blackboard system that the user must supply is the code implementing the functionality of the knowledge sources.

Calculated Research on the Energetic Characteristic of TN in Composite Solid Propellant,

DTIC Science & Technology

1986-01-06

TEST CHART NATK)AAL BIREAU Of SIANDARN D %3 A F..• ,*’" ..... . . . L,.•...... . . . . . . . . FTD-ID(RS)T-0905-85 (0 FOREIGN TECHNOLOGY DIVISION...English pages: 12 Source: Yuhang Xuebao, Nr. 2, 1984, pp. 84-90 Country of origin: China Translated by: SCITRAN F33657-84- D -0165 Requester: FTD/TQTA...best quality copy available. Accesston 7i VTIS GT A&l DTIC TAB justif i,,Lltion- Distr-ibution/ Availability Codes Avail and/or D i t Special ft

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

PubMed

Hosny, Abdelrahman; Vera-Licona, Paola; Laubenbacher, Reinhard; Favre, Thibauld

2016-08-01

There is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies. The approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun laubenbacher@uchc.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.

You've Written a Cool Astronomy Code! Now What Do You Do with It?

NASA Astrophysics Data System (ADS)

Allen, Alice; Accomazzi, A.; Berriman, G. B.; DuPrie, K.; Hanisch, R. J.; Mink, J. D.; Nemiroff, R. J.; Shamir, L.; Shortridge, K.; Taylor, M. B.; Teuben, P. J.; Wallin, J. F.

2014-01-01

Now that you've written a useful astronomy code for your soon-to-be-published research, you have to figure out what you want to do with it. Our suggestion? Share it! This presentation highlights the means and benefits of sharing your code. Make your code citable -- submit it to the Astrophysics Source Code Library and have it indexed by ADS! The Astrophysics Source Code Library (ASCL) is a free online registry of source codes of interest to astronomers and astrophysicists. With over 700 codes, it is continuing its rapid growth, with an average of 17 new codes a month. The editors seek out codes for inclusion; indexing by ADS improves the discoverability of codes and provides a way to cite codes as separate entries, especially codes without papers that describe them.

Viewstamped Replication for Highly Available Distributed Systems

DTIC Science & Technology

1988-08-01

IDENTIFICATION NUMBER ORGANIZATION (if amocable ) DARPA/DOD I c. ADDRESS (City, State, and ZIP Code) 10. SOURCE OF FUNDING NUMBERS 1400 Wilson Blvd...several managers at once will slow things down, since there will be more message traffic, but the slowdown will be slight. We can, however, avoid these

Computational Fluids Domain Reduction to a Simplified Fluid Network

DTIC Science & Technology

2012-04-19

readily available read/ write software library. Code components from the open source projects OpenFoam and Paraview were explored for their adaptability...to the project. Both Paraview and OpenFoam read polyhedral mesh. OpenFoam does not read results data. Paraview actually allows for user “filters

Toys for Special Children.

ERIC Educational Resources Information Center

Przybocki, Mary, Ed.; Miller, Stephanie A., Ed.

1984-01-01

The guide presents information on approximately 150 toys useful for infants and children with sensory impairments. The toys listed are available from stores found nation-wide and the list is organized according to age level (infants, toddlers, and elementary levels). A brief description, price, source, and coding of types of skills the toys may…

Monte Carlo simulation of liver cancer treatment with 166Ho-loaded glass microspheres

NASA Astrophysics Data System (ADS)

da Costa Guimarães, Carla; Moralles, Maurício; Roberto Martinelli, José

2014-02-01

Microspheres loaded with pure beta-emitter radioisotopes are used in the treatment of some types of liver cancer. The Instituto de Pesquisas Energéticas e Nucleares (IPEN) is developing 166Ho-loaded glass microspheres as an alternative to the commercially available 90Y microspheres. This work describes the implementation of a Monte Carlo code to simulate both the irradiation effects and the imaging of 166Ho and 90Y sources localized in different parts of the liver. Results obtained with the code and perspectives for the future are discussed.

RNAcentral: an international database of ncRNA sequences

DOE PAGES

Williams, Kelly Porter

2014-10-28

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

A Comparison of Source Code Plagiarism Detection Engines

NASA Astrophysics Data System (ADS)

Lancaster, Thomas; Culwin, Fintan

2004-06-01

Automated techniques for finding plagiarism in student source code submissions have been in use for over 20 years and there are many available engines and services. This paper reviews the literature on the major modern detection engines, providing a comparison of them based upon the metrics and techniques they deploy. Generally the most common and effective techniques are seen to involve tokenising student submissions then searching pairs of submissions for long common substrings, an example of what is defined to be a paired structural metric. Computing academics are recommended to use one of the two Web-based detection engines, MOSS and JPlag. It is shown that whilst detection is well established there are still places where further research would be useful, particularly where visual support of the investigation process is possible.

Matrix factorization-based data fusion for the prediction of lncRNA-disease associations.

PubMed

Fu, Guangyuan; Wang, Jun; Domeniconi, Carlotta; Yu, Guoxian

2018-05-01

Long non-coding RNAs (lncRNAs) play crucial roles in complex disease diagnosis, prognosis, prevention and treatment, but only a small portion of lncRNA-disease associations have been experimentally verified. Various computational models have been proposed to identify lncRNA-disease associations by integrating heterogeneous data sources. However, existing models generally ignore the intrinsic structure of data sources or treat them as equally relevant, while they may not be. To accurately identify lncRNA-disease associations, we propose a Matrix Factorization based LncRNA-Disease Association prediction model (MFLDA in short). MFLDA decomposes data matrices of heterogeneous data sources into low-rank matrices via matrix tri-factorization to explore and exploit their intrinsic and shared structure. MFLDA can select and integrate the data sources by assigning different weights to them. An iterative solution is further introduced to simultaneously optimize the weights and low-rank matrices. Next, MFLDA uses the optimized low-rank matrices to reconstruct the lncRNA-disease association matrix and thus to identify potential associations. In 5-fold cross validation experiments to identify verified lncRNA-disease associations, MFLDA achieves an area under the receiver operating characteristic curve (AUC) of 0.7408, at least 3% higher than those given by state-of-the-art data fusion based computational models. An empirical study on identifying masked lncRNA-disease associations again shows that MFLDA can identify potential associations more accurately than competing models. A case study on identifying lncRNAs associated with breast, lung and stomach cancers show that 38 out of 45 (84%) associations predicted by MFLDA are supported by recent biomedical literature and further proves the capability of MFLDA in identifying novel lncRNA-disease associations. MFLDA is a general data fusion framework, and as such it can be adopted to predict associations between other biological entities. The source code for MFLDA is available at: http://mlda.swu.edu.cn/codes.php? name = MFLDA. gxyu@swu.edu.cn. Supplementary data are available at Bioinformatics online.

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

PubMed

Goloborodko, Anton A; Levitsky, Lev I; Ivanov, Mark V; Gorshkov, Mikhail V

2013-02-01

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

PubMed Central

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E.; Rost, Burkhard; Goldberg, Tatyana

2016-01-01

Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: msa@bio.sh PMID:27412096

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.

PubMed

Curtis, Darren S; Phillips, Aaron R; Callister, Stephen J; Conlan, Sean; McCue, Lee Ann

2013-10-15

At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

Apollo: a community resource for genome annotation editing

PubMed Central

Ed, Lee; Nomi, Harris; Mark, Gibson; Raymond, Chetty; Suzanna, Lewis

2009-01-01

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Availability: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo. Contact: elee@berkeleybop.org PMID:19439563

PDB file parser and structure class implemented in Python.

PubMed

Hamelryck, Thomas; Manderick, Bernard

2003-11-22

The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

NSSDC Data listing

NASA Technical Reports Server (NTRS)

1981-01-01

A convenient reference to space science and supportive data available from the National Space Science Data Center (NSSDC) is provided. Satellite data are organized by NSSDC spacecraft common name. The launch date and NSSDC ID are given. Experiments are listed alphabetically by the principal investigator or team leader. The experiment name and NSSDC ID, data set ID, data set name, data form code, quantity of data, and the time span of the data as verified by NSSDC are shown. Ground-based data, models, computer routines, and composite spacecraft data that are available from NSSDC are listed alphabetically by discipline, source, data type, data content, and data set. The data set name, data form code, quantity of data, and the time span covered where appropriate are included.

Saint: a lightweight integration environment for model annotation.

PubMed

Lister, Allyson L; Pocock, Matthew; Taschuk, Morgan; Wipat, Anil

2009-11-15

Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources. Saint is freely available for use on the web at http://www.cisban.ac.uk/saint. The web application is implemented in Google Web Toolkit and Tomcat, with all major browsers supported. The Java source code is freely available for download at http://saint-annotate.sourceforge.net. The Saint web server requires an installation of libSBML and has been tested on Linux (32-bit Ubuntu 8.10 and 9.04).

Multiple description distributed image coding with side information for mobile wireless transmission

NASA Astrophysics Data System (ADS)

Wu, Min; Song, Daewon; Chen, Chang Wen

2005-03-01

Multiple description coding (MDC) is a source coding technique that involves coding the source information into multiple descriptions, and then transmitting them over different channels in packet network or error-prone wireless environment to achieve graceful degradation if parts of descriptions are lost at the receiver. In this paper, we proposed a multiple description distributed wavelet zero tree image coding system for mobile wireless transmission. We provide two innovations to achieve an excellent error resilient capability. First, when MDC is applied to wavelet subband based image coding, it is possible to introduce correlation between the descriptions in each subband. We consider using such a correlation as well as potentially error corrupted description as side information in the decoding to formulate the MDC decoding as a Wyner Ziv decoding problem. If only part of descriptions is lost, however, their correlation information is still available, the proposed Wyner Ziv decoder can recover the description by using the correlation information and the error corrupted description as side information. Secondly, in each description, single bitstream wavelet zero tree coding is very vulnerable to the channel errors. The first bit error may cause the decoder to discard all subsequent bits whether or not the subsequent bits are correctly received. Therefore, we integrate the multiple description scalar quantization (MDSQ) with the multiple wavelet tree image coding method to reduce error propagation. We first group wavelet coefficients into multiple trees according to parent-child relationship and then code them separately by SPIHT algorithm to form multiple bitstreams. Such decomposition is able to reduce error propagation and therefore improve the error correcting capability of Wyner Ziv decoder. Experimental results show that the proposed scheme not only exhibits an excellent error resilient performance but also demonstrates graceful degradation over the packet loss rate.

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2017-06-02

RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. Polyhedral compilation techniques have proven to be a powerful tool for optimization of dense array codes. However, classical affine loop nest transformations used with these techniques do not optimize effectively codes of dynamic programming of RNA structure predictions. The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related code. This effect is achieved due to improving code locality and calculation parallelization. In order to improve code locality, we apply our previously published technique of automatic loop nest tiling to all the three loops of the Nussinov loop nest. This approach first forms original rectangular 3D tiles and then corrects them to establish their validity by means of applying the transitive closure of a dependence graph. To produce parallel code, we apply the loop skewing technique to a tiled Nussinov loop nest. The technique is implemented as a part of the publicly available polyhedral source-to-source TRACO compiler. Generated code was run on modern Intel multi-core processors and coprocessors. We present the speed-up factor of generated Nussinov RNA parallel code and demonstrate that it is considerably faster than related codes in which only the two outer loops of the Nussinov loop nest are tiled.

Ray-tracing 3D dust radiative transfer with DART-Ray: code upgrade and public release

NASA Astrophysics Data System (ADS)

Natale, Giovanni; Popescu, Cristina C.; Tuffs, Richard J.; Clarke, Adam J.; Debattista, Victor P.; Fischera, Jörg; Pasetto, Stefano; Rushton, Mark; Thirlwall, Jordan J.

2017-11-01

We present an extensively updated version of the purely ray-tracing 3D dust radiation transfer code DART-Ray. The new version includes five major upgrades: 1) a series of optimizations for the ray-angular density and the scattered radiation source function; 2) the implementation of several data and task parallelizations using hybrid MPI+OpenMP schemes; 3) the inclusion of dust self-heating; 4) the ability to produce surface brightness maps for observers within the models in HEALPix format; 5) the possibility to set the expected numerical accuracy already at the start of the calculation. We tested the updated code with benchmark models where the dust self-heating is not negligible. Furthermore, we performed a study of the extent of the source influence volumes, using galaxy models, which are critical in determining the efficiency of the DART-Ray algorithm. The new code is publicly available, documented for both users and developers, and accompanied by several programmes to create input grids for different model geometries and to import the results of N-body and SPH simulations. These programmes can be easily adapted to different input geometries, and for different dust models or stellar emission libraries.

General Mission Analysis Tool (GMAT): Mission, Vision, and Business Case

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

The Goal of the GMAT project is to develop new space trajectory optimization and mission design technology by working inclusively with ordinary people, universities businesses and other government organizations; and to share that technology in an open and unhindered way. GMAT's a free and open source software system; free for anyone to use in development of new mission concepts or to improve current missions, freely available in source code form for enhancement or future technology development.

A database of natural products and chemical entities from marine habitat

PubMed Central

Babu, Padavala Ajay; Puppala, Suma Sree; Aswini, Satyavarapu Lakshmi; Vani, Metta Ramya; Kumar, Chinta Narasimha; Prasanna, Tallapragada

2008-01-01

Marine compound database consists of marine natural products and chemical entities, collected from various literature sources, which are known to possess bioactivity against human diseases. The database is constructed using html code. The 12 categories of 182 compounds are provided with the source, compound name, 2-dimensional structure, bioactivity and clinical trial information. The database is freely available online and can be accessed at http://www.progenebio.in/mcdb/index.htm PMID:19238254

Approaches in highly parameterized inversion—PEST++ Version 3, a Parameter ESTimation and uncertainty analysis software suite optimized for large environmental models

USGS Publications Warehouse

Welter, David E.; White, Jeremy T.; Hunt, Randall J.; Doherty, John E.

2015-09-18

The PEST++ Version 3 software suite can be compiled for Microsoft Windows®4 and Linux®5 operating systems; the source code is available in a Microsoft Visual Studio®6 2013 solution; Linux Makefiles are also provided. PEST++ Version 3 continues to build a foundation for an open-source framework capable of producing robust and efficient parameter estimation tools for large environmental models.

[Fatal occupational accidents: updating of data from a mortality register].

PubMed

Mantero, Silvia; Baldasseroni, A; Chellini, Elisabetta; Giovanetti, Lucia

2005-01-01

In Italy, almost one thousand deaths due to occupational accidents are usually registered by INAIL each year. Case registration by INAIL has merely administrative purposes and therefore it is necessary to use other sources for case ascertainment in order to better estimate the real number of deaths related to occupational accidents, as shown also by previous papers. Evaluation of the contribution of another data source, namely the Tuscany Regional Mortality Registry, to obtain the correct figure for occupational accident deaths through the use of a place-of-occurrence notation on the death certificate. Cases that occurred in residents in Tuscany in 2000-2001 were considered. They were identified from : a) the Tuscany Regional Mortality Registry (RMR) using the E code of the ICD LX code of death, the year and place of occurrence; b) the INAIL archive using the year of event, the type of definition and management. The INAIL source was without doubt the most informative but was only 51% complete, whereas the RMR source, although less informative, was more complete (82.4%) and allowed identification of cases not registered by INAIL, that had occurred for instance in the Armed Forces and in the National Railway Company. However, the vast majority of RMR extra-cases occurred in subjects aged 65+, in agriculture and in the building industry. It is currently possible to plan a systematic linkage of the two sources due to the new possibilities that are available: the place-of-occurrence in the death certificate and the availability of individual data in the INAIL source.

The random energy model in a magnetic field and joint source channel coding

NASA Astrophysics Data System (ADS)

Merhav, Neri

2008-09-01

We demonstrate that there is an intimate relationship between the magnetic properties of Derrida’s random energy model (REM) of spin glasses and the problem of joint source-channel coding in Information Theory. In particular, typical patterns of erroneously decoded messages in the coding problem have “magnetization” properties that are analogous to those of the REM in certain phases, where the non-uniformity of the distribution of the source in the coding problem plays the role of an external magnetic field applied to the REM. We also relate the ensemble performance (random coding exponents) of joint source-channel codes to the free energy of the REM in its different phases.

User Manual and Source Code for a LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)

DTIC Science & Technology

2014-06-01

User Manual and Source Code for a LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E) by James P. Larentzos...Laboratory Aberdeen Proving Ground, MD 21005-5069 ARL-SR-290 June 2014 User Manual and Source Code for a LAMMPS Implementation of Constant...3. DATES COVERED (From - To) September 2013–February 2014 4. TITLE AND SUBTITLE User Manual and Source Code for a LAMMPS Implementation of

Pre-calculated protein structure alignments at the RCSB PDB website.

PubMed

Prlic, Andreas; Bliven, Spencer; Rose, Peter W; Bluhm, Wolfgang F; Bizon, Chris; Godzik, Adam; Bourne, Philip E

2010-12-01

With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org andreas@sdsc.edu; pbourne@ucsd.edu.

NicoLase—An open-source diode laser combiner, fiber launch, and sequencing controller for fluorescence microscopy

PubMed Central

Walsh, James; Böcking, Till; Gaus, Katharina

2017-01-01

Modern fluorescence microscopy requires software-controlled illumination sources with high power across a wide range of wavelengths. Diode lasers meet the power requirements and combining multiple units into a single fiber launch expands their capability across the required spectral range. We present the NicoLase, an open-source diode laser combiner, fiber launch, and software sequence controller for fluorescence microscopy and super-resolution microscopy applications. Two configurations are described, giving four or six output wavelengths and one or two single-mode fiber outputs, with all CAD files, machinist drawings, and controller source code openly available. PMID:28301563

Encrypted optical storage with wavelength-key and random phase codes.

PubMed

Matoba, O; Javidi, B

1999-11-10

An encrypted optical memory system that uses a wavelength code as well as input and Fourier-plane random phase codes is proposed. Original data are illuminated by a coherent light source with a specified wavelength and are then encrypted with two random phase codes before being stored holographically in a photorefractive material. Successful decryption requires the use of a readout beam with the same wavelength as that used in the recording, in addition to the correct phase key in the Fourier plane. The wavelength selectivity of the proposed system is evaluated numerically. We show that the number of available wavelength keys depends on the correlation length of the phase key in the Fourier plane. Preliminary experiments of encryption and decryption of optical memory in a LiNbO(3):Fe photorefractive crystal are demonstrated.

Phylowood: interactive web-based animations of biogeographic and phylogeographic histories.

PubMed

Landis, Michael J; Bedford, Trevor

2014-01-01

Phylowood is a web service that uses JavaScript to generate in-browser animations of biogeographic and phylogeographic histories from annotated phylogenetic input. The animations are interactive, allowing the user to adjust spatial and temporal resolution, and highlight phylogenetic lineages of interest. All documentation and source code for Phylowood is freely available at https://github.com/mlandis/phylowood, and a live web application is available at https://mlandis.github.io/phylowood.

Astronomy education and the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; Nemiroff, Robert J.

2016-01-01

The Astrophysics Source Code Library (ASCL) is an online registry of source codes used in refereed astrophysics research. It currently lists nearly 1,200 codes and covers all aspects of computational astrophysics. How can this resource be of use to educators and to the graduate students they mentor? The ASCL serves as a discovery tool for codes that can be used for one's own research. Graduate students can also investigate existing codes to see how common astronomical problems are approached numerically in practice, and use these codes as benchmarks for their own solutions to these problems. Further, they can deepen their knowledge of software practices and techniques through examination of others' codes.

NSDann2BS, a neutron spectrum unfolding code based on neural networks technology and two bonner spheres

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

Ortiz-Rodriguez, J. M.; Reyes Alfaro, A.; Reyes Haro, A.

In this work a neutron spectrum unfolding code, based on artificial intelligence technology is presented. The code called ''Neutron Spectrometry and Dosimetry with Artificial Neural Networks and two Bonner spheres'', (NSDann2BS), was designed in a graphical user interface under the LabVIEW programming environment. The main features of this code are to use an embedded artificial neural network architecture optimized with the ''Robust design of artificial neural networks methodology'' and to use two Bonner spheres as the only piece of information. In order to build the code here presented, once the net topology was optimized and properly trained, knowledge stored atmore » synaptic weights was extracted and using a graphical framework build on the LabVIEW programming environment, the NSDann2BS code was designed. This code is friendly, intuitive and easy to use for the end user. The code is freely available upon request to authors. To demonstrate the use of the neural net embedded in the NSDann2BS code, the rate counts of {sup 252}Cf, {sup 241}AmBe and {sup 239}PuBe neutron sources measured with a Bonner spheres system.« less

NSDann2BS, a neutron spectrum unfolding code based on neural networks technology and two bonner spheres

NASA Astrophysics Data System (ADS)

Ortiz-Rodríguez, J. M.; Reyes Alfaro, A.; Reyes Haro, A.; Solís Sánches, L. O.; Miranda, R. Castañeda; Cervantes Viramontes, J. M.; Vega-Carrillo, H. R.

2013-07-01

In this work a neutron spectrum unfolding code, based on artificial intelligence technology is presented. The code called "Neutron Spectrometry and Dosimetry with Artificial Neural Networks and two Bonner spheres", (NSDann2BS), was designed in a graphical user interface under the LabVIEW programming environment. The main features of this code are to use an embedded artificial neural network architecture optimized with the "Robust design of artificial neural networks methodology" and to use two Bonner spheres as the only piece of information. In order to build the code here presented, once the net topology was optimized and properly trained, knowledge stored at synaptic weights was extracted and using a graphical framework build on the LabVIEW programming environment, the NSDann2BS code was designed. This code is friendly, intuitive and easy to use for the end user. The code is freely available upon request to authors. To demonstrate the use of the neural net embedded in the NSDann2BS code, the rate counts of 252Cf, 241AmBe and 239PuBe neutron sources measured with a Bonner spheres system.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

JBioWH: an open-source Java framework for bioinformatics data integration

PubMed Central

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh PMID:23846595

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

JBioWH: an open-source Java framework for bioinformatics data integration.

PubMed

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

A convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography.

PubMed

Yang, Xiaogang; De Carlo, Francesco; Phatak, Charudatta; Gürsoy, Dogˇa

2017-03-01

This paper presents an algorithm to calibrate the center-of-rotation for X-ray tomography by using a machine learning approach, the Convolutional Neural Network (CNN). The algorithm shows excellent accuracy from the evaluation of synthetic data with various noise ratios. It is further validated with experimental data of four different shale samples measured at the Advanced Photon Source and at the Swiss Light Source. The results are as good as those determined by visual inspection and show better robustness than conventional methods. CNN has also great potential for reducing or removing other artifacts caused by instrument instability, detector non-linearity, etc. An open-source toolbox, which integrates the CNN methods described in this paper, is freely available through GitHub at tomography/xlearn and can be easily integrated into existing computational pipelines available at various synchrotron facilities. Source code, documentation and information on how to contribute are also provided.

A new chapter in environmental sensing: The Open-Source Published Environmental Sensing (OPENS) laboratory

NASA Astrophysics Data System (ADS)

Selker, J. S.; Roques, C.; Higgins, C. W.; Good, S. P.; Hut, R.; Selker, A.

2015-12-01

The confluence of 3-Dimensional printing, low-cost solid-state-sensors, low-cost, low-power digital controllers (e.g., Arduinos); and open-source publishing (e.g., Github) is poised to transform environmental sensing. The Open-Source Published Environmental Sensing (OPENS) laboratory has launched and is available for all to use. OPENS combines cutting edge technologies and makes them available to the global environmental sensing community. OPENS includes a Maker lab space where people may collaborate in person or virtually via on-line forum for the publication and discussion of environmental sensing technology (Corvallis, Oregon, USA, please feel free to request a free reservation for space and equipment use). The physical lab houses a test-bed for sensors, as well as a complete classical machine shop, 3-D printers, electronics development benches, and workstations for code development. OPENS will provide a web-based formal publishing framework wherein global students and scientists can peer-review publish (with DOI) novel and evolutionary advancements in environmental sensor systems. This curated and peer-reviewed digital collection will include complete sets of "printable" parts and operating computer code for sensing systems. The physical lab will include all of the machines required to produce these sensing systems. These tools can be addressed in person or virtually, creating a truly global venue for advancement in monitoring earth's environment and agricultural systems. In this talk we will present an example of the process of design and publication the design and data from the OPENS-Permeameter. The publication includes 3-D printing code, Arduino (or other control/logging platform) operational code; sample data sets, and a full discussion of the design set in the scientific context of previous related devices. Editors for the peer-review process are currently sought - contact John.Selker@Oregonstate.edu or Clement.Roques@Oregonstate.edu.

Design Pattern Mining Using Distributed Learning Automata and DNA Sequence Alignment

PubMed Central

Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

2014-01-01

Context Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. Objective This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. Method The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. Results The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. Conclusion The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns. PMID:25243670

Data processing with microcode designed with source coding

DOEpatents

McCoy, James A; Morrison, Steven E

2013-05-07

Programming for a data processor to execute a data processing application is provided using microcode source code. The microcode source code is assembled to produce microcode that includes digital microcode instructions with which to signal the data processor to execute the data processing application.

A review of high-speed, convective, heat-transfer computation methods

NASA Technical Reports Server (NTRS)

Tauber, Michael E.

1989-01-01

The objective of this report is to provide useful engineering formulations and to instill a modest degree of physical understanding of the phenomena governing convective aerodynamic heating at high flight speeds. Some physical insight is not only essential to the application of the information presented here, but also to the effective use of computer codes which may be available to the reader. A discussion is given of cold-wall, laminar boundary layer heating. A brief presentation of the complex boundary layer transition phenomenon follows. Next, cold-wall turbulent boundary layer heating is discussed. This topic is followed by a brief coverage of separated flow-region and shock-interaction heating. A review of heat protection methods follows, including the influence of mass addition on laminar and turbulent boundary layers. Also discussed are a discussion of finite-difference computer codes and a comparison of some results from these codes. An extensive list of references is also provided from sources such as the various AIAA journals and NASA reports which are available in the open literature.

A review of high-speed, convective, heat-transfer computation methods

NASA Technical Reports Server (NTRS)

Tauber, Michael E.

1989-01-01

The objective is to provide useful engineering formulations and to instill a modest degree of physical understanding of the phenomena governing convective aerodynamic heating at high flight speeds. Some physical insight is not only essential to the application of the information presented here, but also to the effective use of computer codes which may be available to the reader. Given first is a discussion of cold-wall, laminar boundary layer heating. A brief presentation of the complex boundary layer transition phenomenon follows. Next, cold-wall turbulent boundary layer heating is discussed. This topic is followed by a brief coverage of separated flow-region and shock-interaction heating. A review of heat protection methods follows, including the influence of mass addition on laminar and turbulent boundary layers. Next is a discussion of finite-difference computer codes and a comparison of some results from these codes. An extensive list of references is also provided from sources such as the various AIAA journals and NASA reports which are available in the open literature.

CRITICA: coding region identification tool invoking comparative analysis

NASA Technical Reports Server (NTRS)

Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

1999-01-01

Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

The Application of Function Points to Predict Source Lines of Code for Software Development

DTIC Science & Technology

1992-09-01

there are some disadvantages. Software estimating tools are expensive. A single tool may cost more than $15,000 due to the high market value of the...term and Lang variables simultaneously onlN added marginal improvements over models with these terms included singularly. Using all the available

Development of an IHE MRRT-compliant open-source web-based reporting platform.

PubMed

Pinto Dos Santos, Daniel; Klos, G; Kloeckner, R; Oberle, R; Dueber, C; Mildenberger, P

2017-01-01

To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. • A platform for structured reporting using IHE MRRT-compliant templates is presented. • Incorporating structured reporting into clinical routine is feasible. • Full source code will be provided upon request under a free license.

jFuzz: A Concolic Whitebox Fuzzer for Java

NASA Technical Reports Server (NTRS)

Jayaraman, Karthick; Harvison, David; Ganesh, Vijay; Kiezun, Adam

2009-01-01

We present jFuzz, a automatic testing tool for Java programs. jFuzz is a concolic whitebox fuzzer, built on the NASA Java PathFinder, an explicit-state Java model checker, and a framework for developing reliability and analysis tools for Java. Starting from a seed input, jFuzz automatically and systematically generates inputs that exercise new program paths. jFuzz uses a combination of concrete and symbolic execution, and constraint solving. Time spent on solving constraints can be significant. We implemented several well-known optimizations and name-independent caching, which aggressively normalizes the constraints to reduce the number of calls to the constraint solver. We present preliminary results due to the optimizations, and demonstrate the effectiveness of jFuzz in creating good test inputs. The source code of jFuzz is available as part of the NASA Java PathFinder. jFuzz is intended to be a research testbed for investigating new testing and analysis techniques based on concrete and symbolic execution. The source code of jFuzz is available as part of the NASA Java PathFinder.

Parameter Measurement Methods for Interfacing Hydraulic Systems with Microelectronic Instruments and Controllers.

DTIC Science & Technology

1983-11-01

successfully. I- Accession For NTIS -GO iiiONa DTIC TAB t Unannounced - Justificatio Distribution/ I Availability Codes vail and/or DIst Special IA-11...terms of initial signal power. An active sensor must be excited externally. Such a sensor receives its power from an external source and merely modulates...electrons in the material to gain L enough energy to be emitted. The voltage source causes a positive potential to be felt on the collector, thus causing the

Adaptive distributed source coding.

PubMed

Varodayan, David; Lin, Yao-Chung; Girod, Bernd

2012-05-01

We consider distributed source coding in the presence of hidden variables that parameterize the statistical dependence among sources. We derive the Slepian-Wolf bound and devise coding algorithms for a block-candidate model of this problem. The encoder sends, in addition to syndrome bits, a portion of the source to the decoder uncoded as doping bits. The decoder uses the sum-product algorithm to simultaneously recover the source symbols and the hidden statistical dependence variables. We also develop novel techniques based on density evolution (DE) to analyze the coding algorithms. We experimentally confirm that our DE analysis closely approximates practical performance. This result allows us to efficiently optimize parameters of the algorithms. In particular, we show that the system performs close to the Slepian-Wolf bound when an appropriate doping rate is selected. We then apply our coding and analysis techniques to a reduced-reference video quality monitoring system and show a bit rate saving of about 75% compared with fixed-length coding.

Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

PubMed

Campbell, J R; Carpenter, P; Sneiderman, C; Cohn, S; Chute, C G; Warren, J

1997-01-01

To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity. No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. Is suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record.

The Particle Accelerator Simulation Code PyORBIT

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

Gorlov, Timofey V; Holmes, Jeffrey A; Cousineau, Sarah M

2015-01-01

The particle accelerator simulation code PyORBIT is presented. The structure, implementation, history, parallel and simulation capabilities, and future development of the code are discussed. The PyORBIT code is a new implementation and extension of algorithms of the original ORBIT code that was developed for the Spallation Neutron Source accelerator at the Oak Ridge National Laboratory. The PyORBIT code has a two level structure. The upper level uses the Python programming language to control the flow of intensive calculations performed by the lower level code implemented in the C++ language. The parallel capabilities are based on MPI communications. The PyORBIT ismore » an open source code accessible to the public through the Google Open Source Projects Hosting service.« less

Psynteract: A flexible, cross-platform, open framework for interactive experiments.

PubMed

Henninger, Felix; Kieslich, Pascal J; Hilbig, Benjamin E

2017-10-01

We introduce a novel platform for interactive studies, that is, any form of study in which participants' experiences depend not only on their own responses, but also on those of other participants who complete the same study in parallel, for example a prisoner's dilemma or an ultimatum game. The software thus especially serves the rapidly growing field of strategic interaction research within psychology and behavioral economics. In contrast to all available software packages, our platform does not handle stimulus display and response collection itself. Instead, we provide a mechanism to extend existing experimental software to incorporate interactive functionality. This approach allows us to draw upon the capabilities already available, such as accuracy of temporal measurement, integration with auxiliary hardware such as eye-trackers or (neuro-)physiological apparatus, and recent advances in experimental software, for example capturing response dynamics through mouse-tracking. Through integration with OpenSesame, an open-source graphical experiment builder, studies can be assembled via a drag-and-drop interface requiring little or no further programming skills. In addition, by using the same communication mechanism across software packages, we also enable interoperability between systems. Our source code, which provides support for all major operating systems and several popular experimental packages, can be freely used and distributed under an open source license. The communication protocols underlying its functionality are also well documented and easily adapted to further platforms. Code and documentation are available at https://github.com/psynteract/ .

Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules

PubMed Central

Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M.; Lange, Oliver F.; Thompson, James; Jacak, Ron; Kaufman, Kristian; Renfrew, P. Douglas; Smith, Colin A.; Sheffler, Will; Davis, Ian W.; Cooper, Seth; Treuille, Adrien; Mandell, Daniel J.; Richter, Florian; Ban, Yih-En Andrew; Fleishman, Sarel J.; Corn, Jacob E.; Kim, David E.; Lyskov, Sergey; Berrondo, Monica; Mentzer, Stuart; Popović, Zoran; Havranek, James J.; Karanicolas, John; Das, Rhiju; Meiler, Jens; Kortemme, Tanja; Gray, Jeffrey J.; Kuhlman, Brian; Baker, David; Bradley, Philip

2013-01-01

We have recently completed a full re-architecturing of the Rosetta molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy to use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as Rosetta3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This document describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform. PMID:21187238

Impacts of DNAPL Source Treatment: Experimental and Modeling Assessment of the Benefits of Partial DNAPL Source Removal

DTIC Science & Technology

2009-09-01

nuclear industry for conducting performance assessment calculations. The analytical FORTRAN code for the DNAPL source function, REMChlor, was...project. The first was to apply existing deterministic codes , such as T2VOC and UTCHEM, to the DNAPL source zone to simulate the remediation processes...but describe the spatial variability of source zones unlike one-dimensional flow and transport codes that assume homogeneity. The Lagrangian models

ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration

PubMed Central

Bottolo, Leonardo; Langley, Sarah R.; Petretto, Enrico; Tiret, Laurence; Tregouet, David; Richardson, Sylvia

2011-01-01

Summary: ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the ‘large p, small n’ case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few responses simultaneously. The core engine of ESS++ for the selection of relevant predictors is based on Evolutionary Monte Carlo. Our implementation is open source, allowing community-based alterations and improvements. Availability: C++ source code and documentation including compilation instructions are available under GNU licence at http://bgx.org.uk/software/ESS.html. Contact: l.bottolo@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21233165

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

Chaste: An Open Source C++ Library for Computational Physiology and Biology

PubMed Central

Mirams, Gary R.; Arthurs, Christopher J.; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Corrias, Alberto; Davit, Yohan; Dunn, Sara-Jane; Fletcher, Alexander G.; Harvey, Daniel G.; Marsh, Megan E.; Osborne, James M.; Pathmanathan, Pras; Pitt-Francis, Joe; Southern, James; Zemzemi, Nejib; Gavaghan, David J.

2013-01-01

Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials. PMID:23516352

Phase II Evaluation of Clinical Coding Schemes

PubMed Central

Campbell, James R.; Carpenter, Paul; Sneiderman, Charles; Cohn, Simon; Chute, Christopher G.; Warren, Judith

1997-01-01

Abstract Objective: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). Methods: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for “parent” and “child” codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. Results: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p <.00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56; UMLS 3.17; READ 2.14, *p <.005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p <. 00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p <. 004) associated with a loss of clarity. Conclusion: No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. It suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record. PMID:9147343

GALARIO: a GPU accelerated library for analysing radio interferometer observations

NASA Astrophysics Data System (ADS)

Tazzari, Marco; Beaujean, Frederik; Testi, Leonardo

2018-06-01

We present GALARIO, a computational library that exploits the power of modern graphical processing units (GPUs) to accelerate the analysis of observations from radio interferometers like Atacama Large Millimeter and sub-millimeter Array or the Karl G. Jansky Very Large Array. GALARIO speeds up the computation of synthetic visibilities from a generic 2D model image or a radial brightness profile (for axisymmetric sources). On a GPU, GALARIO is 150 faster than standard PYTHON and 10 times faster than serial C++ code on a CPU. Highly modular, easy to use, and to adopt in existing code, GALARIO comes as two compiled libraries, one for Nvidia GPUs and one for multicore CPUs, where both have the same functions with identical interfaces. GALARIO comes with PYTHON bindings but can also be directly used in C or C++. The versatility and the speed of GALARIO open new analysis pathways that otherwise would be prohibitively time consuming, e.g. fitting high-resolution observations of large number of objects, or entire spectral cubes of molecular gas emission. It is a general tool that can be applied to any field that uses radio interferometer observations. The source code is available online at http://github.com/mtazzari/galario under the open source GNU Lesser General Public License v3.

: A Scalable and Transparent System for Simulating MPI Programs

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

Perumalla, Kalyan S

2010-01-01

is a scalable, transparent system for experimenting with the execution of parallel programs on simulated computing platforms. The level of simulated detail can be varied for application behavior as well as for machine characteristics. Unique features of are repeatability of execution, scalability to millions of simulated (virtual) MPI ranks, scalability to hundreds of thousands of host (real) MPI ranks, portability of the system to a variety of host supercomputing platforms, and the ability to experiment with scientific applications whose source-code is available. The set of source-code interfaces supported by is being expanded to support a wider set of applications, andmore » MPI-based scientific computing benchmarks are being ported. In proof-of-concept experiments, has been successfully exercised to spawn and sustain very large-scale executions of an MPI test program given in source code form. Low slowdowns are observed, due to its use of purely discrete event style of execution, and due to the scalability and efficiency of the underlying parallel discrete event simulation engine, sik. In the largest runs, has been executed on up to 216,000 cores of a Cray XT5 supercomputer, successfully simulating over 27 million virtual MPI ranks, each virtual rank containing its own thread context, and all ranks fully synchronized by virtual time.« less

The Open Spectral Database: an open platform for sharing and searching spectral data.

PubMed

Chalk, Stuart J

2016-01-01

A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers.

Development of an open-source web-based intervention for Brazilian smokers - Viva sem Tabaco.

PubMed

Gomide, H P; Bernardino, H S; Richter, K; Martins, L F; Ronzani, T M

2016-08-02

Web-based interventions for smoking cessation available in Portuguese do not adhere to evidence-based treatment guidelines. Besides, all existing web-based interventions are built on proprietary platforms that developing countries often cannot afford. We aimed to describe the development of "Viva sem Tabaco", an open-source web-based intervention. The development of the intervention included the selection of content from evidence-based guidelines for smoking cessation, the design of the first layout, conduction of 2 focus groups to identify potential features, refinement of the layout based on focus groups and correction of content based on feedback provided by specialists on smoking cessation. At the end, we released the source-code and intervention on the Internet and translated it into Spanish and English. The intervention developed fills gaps in the information available in Portuguese and the lack of open-source interventions for smoking cessation. The open-source licensing format and its translation system may help researchers from different countries deploying evidence-based interventions for smoking cessation.

Inverse identification of unknown finite-duration air pollutant release from a point source in urban environment

NASA Astrophysics Data System (ADS)

Kovalets, Ivan V.; Efthimiou, George C.; Andronopoulos, Spyros; Venetsanos, Alexander G.; Argyropoulos, Christos D.; Kakosimos, Konstantinos E.

2018-05-01

In this work, we present an inverse computational method for the identification of the location, start time, duration and quantity of emitted substance of an unknown air pollution source of finite time duration in an urban environment. We considered a problem of transient pollutant dispersion under stationary meteorological fields, which is a reasonable assumption for the assimilation of available concentration measurements within 1 h from the start of an incident. We optimized the calculation of the source-receptor function by developing a method which requires integrating as many backward adjoint equations as the available measurement stations. This resulted in high numerical efficiency of the method. The source parameters are computed by maximizing the correlation function of the simulated and observed concentrations. The method has been integrated into the CFD code ADREA-HF and it has been tested successfully by performing a series of source inversion runs using the data of 200 individual realizations of puff releases, previously generated in a wind tunnel experiment.

Doclet To Synthesize UML

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

The RoseDoclet computer program extends the capability of Java doclet software to automatically synthesize Unified Modeling Language (UML) content from Java language source code. [Doclets are Java-language programs that use the doclet application programming interface (API) to specify the content and format of the output of Javadoc. Javadoc is a program, originally designed to generate API documentation from Java source code, now also useful as an extensible engine for processing Java source code.] RoseDoclet takes advantage of Javadoc comments and tags already in the source code to produce a UML model of that code. RoseDoclet applies the doclet API to create a doclet passed to Javadoc. The Javadoc engine applies the doclet to the source code, emitting the output format specified by the doclet. RoseDoclet emits a Rose model file and populates it with fully documented packages, classes, methods, variables, and class diagrams identified in the source code. The way in which UML models are generated can be controlled by use of new Javadoc comment tags that RoseDoclet provides. The advantage of using RoseDoclet is that Javadoc documentation becomes leveraged for two purposes: documenting the as-built API and keeping the design documentation up to date.

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

PubMed

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

2010-06-15

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

shiftNMFk 1.1: Robust Nonnegative matrix factorization with kmeans clustering and signal shift, for allocation of unknown physical sources, toy version for open sourcing with publications

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

Alexandrov, Boian S.; Lliev, Filip L.; Stanev, Valentin G.

This code is a toy (short) version of CODE-2016-83. From a general perspective, the code represents an unsupervised adaptive machine learning algorithm that allows efficient and high performance de-mixing and feature extraction of a multitude of non-negative signals mixed and recorded by a network of uncorrelated sensor arrays. The code identifies the number of the mixed original signals and their locations. Further, the code also allows deciphering of signals that have been delayed in regards to the mixing process in each sensor. This code is high customizable and it can be efficiently used for a fast macro-analyses of data. Themore » code is applicable to a plethora of distinct problems: chemical decomposition, pressure transient decomposition, unknown sources/signal allocation, EM signal decomposition. An additional procedure for allocation of the unknown sources is incorporated in the code.« less

Joint Source-Channel Decoding of Variable-Length Codes with Soft Information: A Survey

NASA Astrophysics Data System (ADS)

Guillemot, Christine; Siohan, Pierre

2005-12-01

Multimedia transmission over time-varying wireless channels presents a number of challenges beyond existing capabilities conceived so far for third-generation networks. Efficient quality-of-service (QoS) provisioning for multimedia on these channels may in particular require a loosening and a rethinking of the layer separation principle. In that context, joint source-channel decoding (JSCD) strategies have gained attention as viable alternatives to separate decoding of source and channel codes. A statistical framework based on hidden Markov models (HMM) capturing dependencies between the source and channel coding components sets the foundation for optimal design of techniques of joint decoding of source and channel codes. The problem has been largely addressed in the research community, by considering both fixed-length codes (FLC) and variable-length source codes (VLC) widely used in compression standards. Joint source-channel decoding of VLC raises specific difficulties due to the fact that the segmentation of the received bitstream into source symbols is random. This paper makes a survey of recent theoretical and practical advances in the area of JSCD with soft information of VLC-encoded sources. It first describes the main paths followed for designing efficient estimators for VLC-encoded sources, the key component of the JSCD iterative structure. It then presents the main issues involved in the application of the turbo principle to JSCD of VLC-encoded sources as well as the main approaches to source-controlled channel decoding. This survey terminates by performance illustrations with real image and video decoding systems.

GeNN: a code generation framework for accelerated brain simulations

NASA Astrophysics Data System (ADS)

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations.

PubMed

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-07

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations

PubMed Central

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/. PMID:26740369

Make Movies out of Your Dynamical Simulations with OGRE!

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Douglas, R. W.; Ge, H. W.; Burns, J. A.

2013-10-01

We have developed OGRE, the Orbital GRaphics Environment, an open-source project comprising a graphical user interface that allows the user to view the output from several dynamical integrators (e.g., SWIFT) that are commonly used for academic work. One can interactively vary the display speed, rotate the view and zoom the camera. This makes OGRE a great tool for students or the general public to explore accurate orbital histories that may display interesting dynamical features, e.g. the destabilization of Solar System orbits under the Nice model, or interacting pairs of exoplanets. Furthermore, OGRE allows the user to choreograph sequences of transformations as the simulation is played to generate movies for use in public talks or professional presentations. The graphical user interface is coded using Qt to ensure portability across different operating systems. OGRE will run on Linux and Mac OS X. The program is available as a self-contained executable, or as source code that the user can compile. We are continually updating the code, and hope that people who find it useful will contribute to the development of new features.

Make Movies out of Your Dynamical Simulations with OGRE!

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Douglas, R. W.; Ge, H. W.; Burns, J. A.

2014-01-01

We have developed OGRE, the Orbital GRaphics Environment, an open-source project comprising a graphical user interface that allows the user to view the output from several dynamical integrators (e.g., SWIFT) that are commonly used for academic work. One can interactively vary the display speed, rotate the view and zoom the camera. This makes OGRE a great tool for students or the general public to explore accurate orbital histories that may display interesting dynamical features, e.g. the destabilization of Solar System orbits under the Nice model, or interacting pairs of exoplanets. Furthermore, OGRE allows the user to choreograph sequences of transformations as the simulation is played to generate movies for use in public talks or professional presentations. The graphical user interface is coded using Qt to ensure portability across different operating systems. OGRE will run on Linux and Mac OS X. The program is available as a self-contained executable, or as source code that the user can compile. We are continually updating the code, and hope that people who find it useful will contribute to the development of new features.

Multidimensional incremental parsing for universal source coding.

PubMed

Bae, Soo Hyun; Juang, Biing-Hwang

2008-10-01

A multidimensional incremental parsing algorithm (MDIP) for multidimensional discrete sources, as a generalization of the Lempel-Ziv coding algorithm, is investigated. It consists of three essential component schemes, maximum decimation matching, hierarchical structure of multidimensional source coding, and dictionary augmentation. As a counterpart of the longest match search in the Lempel-Ziv algorithm, two classes of maximum decimation matching are studied. Also, an underlying behavior of the dictionary augmentation scheme for estimating the source statistics is examined. For an m-dimensional source, m augmentative patches are appended into the dictionary at each coding epoch, thus requiring the transmission of a substantial amount of information to the decoder. The property of the hierarchical structure of the source coding algorithm resolves this issue by successively incorporating lower dimensional coding procedures in the scheme. In regard to universal lossy source coders, we propose two distortion functions, the local average distortion and the local minimax distortion with a set of threshold levels for each source symbol. For performance evaluation, we implemented three image compression algorithms based upon the MDIP; one is lossless and the others are lossy. The lossless image compression algorithm does not perform better than the Lempel-Ziv-Welch coding, but experimentally shows efficiency in capturing the source structure. The two lossy image compression algorithms are implemented using the two distortion functions, respectively. The algorithm based on the local average distortion is efficient at minimizing the signal distortion, but the images by the one with the local minimax distortion have a good perceptual fidelity among other compression algorithms. Our insights inspire future research on feature extraction of multidimensional discrete sources.

Landlab: an Open-Source Python Library for Modeling Earth Surface Dynamics

NASA Astrophysics Data System (ADS)

Gasparini, N. M.; Adams, J. M.; Hobley, D. E. J.; Hutton, E.; Nudurupati, S. S.; Istanbulluoglu, E.; Tucker, G. E.

2016-12-01

Landlab is an open-source Python modeling library that enables users to easily build unique models to explore earth surface dynamics. The Landlab library provides a number of tools and functionalities that are common to many earth surface models, thus eliminating the need for a user to recode fundamental model elements each time she explores a new problem. For example, Landlab provides a gridding engine so that a user can build a uniform or nonuniform grid in one line of code. The library has tools for setting boundary conditions, adding data to a grid, and performing basic operations on the data, such as calculating gradients and curvature. The library also includes a number of process components, which are numerical implementations of physical processes. To create a model, a user creates a grid and couples together process components that act on grid variables. The current library has components for modeling a diverse range of processes, from overland flow generation to bedrock river incision, from soil wetting and drying to vegetation growth, succession and death. The code is freely available for download (https://github.com/landlab/landlab) or can be installed as a Python package. Landlab models can also be built and run on Hydroshare (www.hydroshare.org), an online collaborative environment for sharing hydrologic data, models, and code. Tutorials illustrating a wide range of Landlab capabilities such as building a grid, setting boundary conditions, reading in data, plotting, using components and building models are also available (https://github.com/landlab/tutorials). The code is also comprehensively documented both online and natively in Python. In this presentation, we illustrate the diverse capabilities of Landlab. We highlight existing functionality by illustrating outcomes from a range of models built with Landlab - including applications that explore landscape evolution and ecohydrology. Finally, we describe the range of resources available for new users.

Seismic Canvas: Evolution as a Data Exploration and Analysis Tool

NASA Astrophysics Data System (ADS)

Kroeger, G. C.

2015-12-01

SeismicCanvas, originally developed as a prototype interactive waveform display and printing application for educational use has evolved to include significant data exploration and analysis functionality. The most recent version supports data import from a variety of standard file formats including SAC and mini-SEED, as well as search and download capabilities via IRIS/FDSN Web Services. Data processing tools now include removal of means and trends, interactive windowing, filtering, smoothing, tapering, resampling. Waveforms can be displayed in a free-form canvas or as a record section based on angular or great circle distance, azimuth or back azimuth. Integrated tau-p code allows the calculation and display of theoretical phase arrivals from a variety of radial Earth models. Waveforms can be aligned by absolute time, event time, picked or theoretical arrival times and can be stacked after alignment. Interactive measurements include means, amplitudes, time delays, ray parameters and apparent velocities. Interactive picking of an arbitrary list of seismic phases is supported. Bode plots of amplitude and phase spectra and spectrograms can be created from multiple seismograms or selected windows of seismograms. Direct printing is implemented on all supported platforms along with output of high-resolution pdf files. With these added capabilities, the application is now being used as a data exploration tool for research. Coded in C++ and using the cross-platform Qt framework, the most recent version is available as a 64-bit application for Windows 7-10, Mac OS X 10.6-10.11, and most distributions of Linux, and a 32-bit version for Windows XP and 7. With the latest improvements and refactoring of trace display classes, the 64-bit versions have been tested with over 250 million samples and remain responsive in interactive operations. The source code is available under a LPGLv3 license and both source and executables are available through the IRIS SeisCode repository.

PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.

PubMed

Kruger, Felix A; Gaulton, Anna; Nowotka, Michal; Overington, John P

2015-03-01

PPDMs is a resource that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein families. Small molecule bioactivities mapped to protein domains add important precision to approaches that use protein sequence searches alignments to assist applications in computational drug discovery and systems and chemical biology. We have previously proposed a mapping heuristic for a subset of bioactivities stored in ChEMBL with the Pfam-A domain most likely to mediate small molecule binding. We have since refined this mapping using a manual procedure. Here, we present a resource that provides up-to-date mappings and the possibility to review assigned mappings as well as to participate in their assignment and curation. We also describe how mappings provided through the PPDMs resource are made accessible through the main schema of the ChEMBL database. The PPDMs resource and curation interface is available at https://www.ebi.ac.uk/chembl/research/ppdms/pfam_maps. The source-code for PPDMs is available under the Apache license at https://github.com/chembl/pfam_maps. Source code is available at https://github.com/chembl/pfam_map_loader to demonstrate the integration process with the main schema of ChEMBL. © The Author 2014. Published by Oxford University Press.

Implementation of GenePattern within the Stanford Microarray Database.

PubMed

Hubble, Jeremy; Demeter, Janos; Jin, Heng; Mao, Maria; Nitzberg, Michael; Reddy, T B K; Wymore, Farrell; Zachariah, Zachariah K; Sherlock, Gavin; Ball, Catherine A

2009-01-01

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

An Efficient Variable Length Coding Scheme for an IID Source

NASA Technical Reports Server (NTRS)

Cheung, K. -M.

1995-01-01

A scheme is examined for using two alternating Huffman codes to encode a discrete independent and identically distributed source with a dominant symbol. This combined strategy, or alternating runlength Huffman (ARH) coding, was found to be more efficient than ordinary coding in certain circumstances.

Pteros: fast and easy to use open-source C++ library for molecular analysis.

PubMed

Yesylevskyy, Semen O

2012-07-15

An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

Source Code Plagiarism--A Student Perspective

ERIC Educational Resources Information Center

Joy, M.; Cosma, G.; Yau, J. Y.-K.; Sinclair, J.

2011-01-01

This paper considers the problem of source code plagiarism by students within the computing disciplines and reports the results of a survey of students in Computing departments in 18 institutions in the U.K. This survey was designed to investigate how well students understand the concept of source code plagiarism and to discover what, if any,…

Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark.

PubMed

Klein, Max; Sharma, Rati; Bohrer, Chris H; Avelis, Cameron M; Roberts, Elijah

2017-01-15

Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology. Source code is licensed under the Apache 2.0 open source license and is available at the project website: https://www.assembla.com/spaces/roberts-lab-public/wiki/Biospark CONTACT: eroberts@jhu.eduSupplementary information: 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.

Recent advances in coding theory for near error-free communications

NASA Technical Reports Server (NTRS)

Cheung, K.-M.; Deutsch, L. J.; Dolinar, S. J.; Mceliece, R. J.; Pollara, F.; Shahshahani, M.; Swanson, L.

1991-01-01

Channel and source coding theories are discussed. The following subject areas are covered: large constraint length convolutional codes (the Galileo code); decoder design (the big Viterbi decoder); Voyager's and Galileo's data compression scheme; current research in data compression for images; neural networks for soft decoding; neural networks for source decoding; finite-state codes; and fractals for data compression.

Hybrid concatenated codes and iterative decoding

NASA Technical Reports Server (NTRS)

Divsalar, Dariush (Inventor); Pollara, Fabrizio (Inventor)

2000-01-01

Several improved turbo code apparatuses and methods. The invention encompasses several classes: (1) A data source is applied to two or more encoders with an interleaver between the source and each of the second and subsequent encoders. Each encoder outputs a code element which may be transmitted or stored. A parallel decoder provides the ability to decode the code elements to derive the original source information d without use of a received data signal corresponding to d. The output may be coupled to a multilevel trellis-coded modulator (TCM). (2) A data source d is applied to two or more encoders with an interleaver between the source and each of the second and subsequent encoders. Each of the encoders outputs a code element. In addition, the original data source d is output from the encoder. All of the output elements are coupled to a TCM. (3) At least two data sources are applied to two or more encoders with an interleaver between each source and each of the second and subsequent encoders. The output may be coupled to a TCM. (4) At least two data sources are applied to two or more encoders with at least two interleavers between each source and each of the second and subsequent encoders. (5) At least one data source is applied to one or more serially linked encoders through at least one interleaver. The output may be coupled to a TCM. The invention includes a novel way of terminating a turbo coder.

HitWalker2: visual analytics for precision medicine and beyond.

PubMed

Bottomly, Daniel; McWeeney, Shannon K; Wilmot, Beth

2016-04-15

The lack of visualization frameworks to guide interpretation and facilitate discovery is a potential bottleneck for precision medicine, systems genetics and other studies. To address this we have developed an interactive, reproducible, web-based prioritization approach that builds on our earlier work. HitWalker2 is highly flexible and can utilize many data types and prioritization methods based upon available data and desired questions, allowing it to be utilized in a diverse range of studies such as cancer, infectious disease and psychiatric disorders. Source code is freely available at https://github.com/biodev/HitWalker2 and implemented using Python/Django, Neo4j and Javascript (D3.js and jQuery). We support major open source browsers (e.g. Firefox and Chromium/Chrome). wilmotb@ohsu.edu Supplementary data are available at Bioinformatics online. Additional information/instructions are available at https://github.com/biodev/HitWalker2/wiki. © The Author 2015. Published by Oxford University Press.

42 CFR 482.41 - Condition of participation: Physical environment.

Code of Federal Regulations, 2011 CFR

2011-10-01

... pharmaceutical, food preparation, and other appropriate areas. [51 FR 22042, June 17, 1986, as amended at 53 FR... rooms, and stairwells. In all other areas not serviced by the emergency supply source, battery lamps and.... 552(a) and 1 CFR part 51. A copy of the Code is available for inspection at the CMS Information...

42 CFR 482.41 - Condition of participation: Physical environment.

Code of Federal Regulations, 2012 CFR

2012-10-01

... pharmaceutical, food preparation, and other appropriate areas. [51 FR 22042, June 17, 1986, as amended at 53 FR... rooms, and stairwells. In all other areas not serviced by the emergency supply source, battery lamps and.... 552(a) and 1 CFR part 51. A copy of the Code is available for inspection at the CMS Information...

Performing aggressive code optimization with an ability to rollback changes made by the aggressive optimizations

DOEpatents

Gschwind, Michael K

2013-07-23

Mechanisms for aggressively optimizing computer code are provided. With these mechanisms, a compiler determines an optimization to apply to a portion of source code and determines if the optimization as applied to the portion of source code will result in unsafe optimized code that introduces a new source of exceptions being generated by the optimized code. In response to a determination that the optimization is an unsafe optimization, the compiler generates an aggressively compiled code version, in which the unsafe optimization is applied, and a conservatively compiled code version in which the unsafe optimization is not applied. The compiler stores both versions and provides them for execution. Mechanisms are provided for switching between these versions during execution in the event of a failure of the aggressively compiled code version. Moreover, predictive mechanisms are provided for predicting whether such a failure is likely.

Observations and Thermochemical Calculations for Hot-Jupiter Atmospheres

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver; Cubillos, Patricio; Stemm, Madison

2015-01-01

I present Spitzer eclipse observations for WASP-14b and WASP-43b, an open source tool for thermochemical equilibrium calculations, and components of an open source tool for atmospheric parameter retrieval from spectroscopic data. WASP-14b is a planet that receives high irradiation from its host star, yet, although theory does not predict it, the planet hosts a thermal inversion. The WASP-43b eclipses have signal-to-noise ratios of ~25, one of the largest among exoplanets. To assess these planets' atmospheric composition and thermal structure, we developed an open-source Bayesian Atmospheric Radiative Transfer (BART) code. My dissertation tasks included developing a Thermochemical Equilibrium Abundances (TEA) code, implementing the eclipse geometry calculation in BART's radiative transfer module, and generating parameterized pressure and temperature profiles so the radiative-transfer module can be driven by the statistical module.To initialize the radiative-transfer calculation in BART, TEA calculates the equilibrium abundances of gaseous molecular species at a given temperature and pressure. It uses the Gibbs-free-energy minimization method with an iterative Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. The code is tested against the original method developed by White at al. (1958), the analytic method developed by Burrows and Sharp (1999), and the Newton-Raphson method implemented in the open-source Chemical Equilibrium with Applications (CEA) code. TEA, written in Python, is modular, documented, and available to the community via the open-source development site GitHub.com.Support for this work was provided by NASA Headquarters under the NASA Earth and Space Science Fellowship Program, grant NNX12AL83H, by NASA through an award issued by JPL/Caltech, and through the Science Mission Directorate's Planetary Atmospheres Program, grant NNX12AI69G.

Inventory of Data Sources for Estimating Health Care Costs in the United States

PubMed Central

Lund, Jennifer L.; Yabroff, K. Robin; Ibuka, Yoko; Russell, Louise B.; Barnett, Paul G.; Lipscomb, Joseph; Lawrence, William F.; Brown, Martin L.

2011-01-01

Objective To develop an inventory of data sources for estimating health care costs in the United States and provide information to aid researchers in identifying appropriate data sources for their specific research questions. Methods We identified data sources for estimating health care costs using 3 approaches: (1) a review of the 18 articles included in this supplement, (2) an evaluation of websites of federal government agencies, non profit foundations, and related societies that support health care research or provide health care services, and (3) a systematic review of the recently published literature. Descriptive information was abstracted from each data source, including sponsor, website, lowest level of data aggregation, type of data source, population included, cross-sectional or longitudinal data capture, source of diagnosis information, and cost of obtaining the data source. Details about the cost elements available in each data source were also abstracted. Results We identified 88 data sources that can be used to estimate health care costs in the United States. Most data sources were sponsored by government agencies, national or nationally representative, and cross-sectional. About 40% were surveys, followed by administrative or linked administrative data, fee or cost schedules, discharges, and other types of data. Diagnosis information was available in most data sources through procedure or diagnosis codes, self-report, registry, or chart review. Cost elements included inpatient hospitalizations (42.0%), physician and other outpatient services (45.5%), outpatient pharmacy or laboratory (28.4%), out-of-pocket (22.7%), patient time and other direct nonmedical costs (35.2%), and wages (13.6%). About half were freely available for downloading or available for a nominal fee, and the cost of obtaining the remaining data sources varied by the scope of the project. Conclusions Available data sources vary in population included, type of data source, scope, and accessibility, and have different strengths and weaknesses for specific research questions. PMID:19536009

Intrinsic Radiation Source Generation with the ISC Package: Data Comparisons and Benchmarking

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

Solomon, Clell J. Jr.

The characterization of radioactive emissions from unstable isotopes (intrinsic radiation) is necessary for shielding and radiological-dose calculations from radioactive materials. While most radiation transport codes, e.g., MCNP [X-5 Monte Carlo Team, 2003], provide the capability to input user prescribed source definitions, such as radioactive emissions, they do not provide the capability to calculate the correct radioactive-source definition given the material compositions. Special modifications to MCNP have been developed in the past to allow the user to specify an intrinsic source, but these modification have not been implemented into the primary source base [Estes et al., 1988]. To facilitate the descriptionmore » of the intrinsic radiation source from a material with a specific composition, the Intrinsic Source Constructor library (LIBISC) and MCNP Intrinsic Source Constructor (MISC) utility have been written. The combination of LIBISC and MISC will be herein referred to as the ISC package. LIBISC is a statically linkable C++ library that provides the necessary functionality to construct the intrinsic-radiation source generated by a material. Furthermore, LIBISC provides the ability use different particle-emission databases, radioactive-decay databases, and natural-abundance databases allowing the user flexibility in the specification of the source, if one database is preferred over others. LIBISC also provides functionality for aging materials and producing a thick-target bremsstrahlung photon source approximation from the electron emissions. The MISC utility links to LIBISC and facilitates the description of intrinsic-radiation sources into a format directly usable with the MCNP transport code. Through a series of input keywords and arguments the MISC user can specify the material, age the material if desired, and produce a source description of the radioactive emissions from the material in an MCNP readable format. Further details of using the MISC utility can be obtained from the user guide [Solomon, 2012]. The remainder of this report presents a discussion of the databases available to LIBISC and MISC, a discussion of the models employed by LIBISC, a comparison of the thick-target bremsstrahlung model employed, a benchmark comparison to plutonium and depleted-uranium spheres, and a comparison of the available particle-emission databases.« less

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks

PubMed Central

Pang, Chao; van Enckevort, David; de Haan, Mark; Kelpin, Fleur; Jetten, Jonathan; Hendriksen, Dennis; de Boer, Tommy; Charbon, Bart; Winder, Erwin; van der Velde, K. Joeri; Doiron, Dany; Fortier, Isabel; Hillege, Hans

2016-01-01

Motivation: While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. Results: To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Availability and Implementation: Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect. Contact: m.a.swertz@rug.nl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153686

SU-E-T-212: Comparison of TG-43 Dosimetric Parameters of Low and High Energy Brachytherapy Sources Obtained by MCNP Code Versions of 4C, X and 5

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

Zehtabian, M; Zaker, N; Sina, S

2015-06-15

Purpose: Different versions of MCNP code are widely used for dosimetry purposes. The purpose of this study is to compare different versions of the MCNP codes in dosimetric evaluation of different brachytherapy sources. Methods: The TG-43 parameters such as dose rate constant, radial dose function, and anisotropy function of different brachytherapy sources, i.e. Pd-103, I-125, Ir-192, and Cs-137 were calculated in water phantom. The results obtained by three versions of Monte Carlo codes (MCNP4C, MCNPX, MCNP5) were compared for low and high energy brachytherapy sources. Then the cross section library of MCNP4C code was changed to ENDF/B-VI release 8 whichmore » is used in MCNP5 and MCNPX codes. Finally, the TG-43 parameters obtained using the MCNP4C-revised code, were compared with other codes. Results: The results of these investigations indicate that for high energy sources, the differences in TG-43 parameters between the codes are less than 1% for Ir-192 and less than 0.5% for Cs-137. However for low energy sources like I-125 and Pd-103, large discrepancies are observed in the g(r) values obtained by MCNP4C and the two other codes. The differences between g(r) values calculated using MCNP4C and MCNP5 at the distance of 6cm were found to be about 17% and 28% for I-125 and Pd-103 respectively. The results obtained with MCNP4C-revised and MCNPX were similar. However, the maximum difference between the results obtained with the MCNP5 and MCNP4C-revised codes was 2% at 6cm. Conclusion: The results indicate that using MCNP4C code for dosimetry of low energy brachytherapy sources can cause large errors in the results. Therefore it is recommended not to use this code for low energy sources, unless its cross section library is changed. Since the results obtained with MCNP4C-revised and MCNPX were similar, it is concluded that the difference between MCNP4C and MCNPX is their cross section libraries.« less

Synthesis of Arbitrary Quantum Circuits to Topological Assembly: Systematic, Online and Compact.

PubMed

Paler, Alexandru; Fowler, Austin G; Wille, Robert

2017-09-05

It is challenging to transform an arbitrary quantum circuit into a form protected by surface code quantum error correcting codes (a variant of topological quantum error correction), especially if the goal is to minimise overhead. One of the issues is the efficient placement of magic state distillation sub circuits, so-called distillation boxes, in the space-time volume that abstracts the computation's required resources. This work presents a general, systematic, online method for the synthesis of such circuits. Distillation box placement is controlled by so-called schedulers. The work introduces a greedy scheduler generating compact box placements. The implemented software, whose source code is available at www.github.com/alexandrupaler/tqec, is used to illustrate and discuss synthesis examples. Synthesis and optimisation improvements are proposed.

EUPDF-II: An Eulerian Joint Scalar Monte Carlo PDF Module : User's Manual

NASA Technical Reports Server (NTRS)

Raju, M. S.; Liu, Nan-Suey (Technical Monitor)

2004-01-01

EUPDF-II provides the solution for the species and temperature fields based on an evolution equation for PDF (Probability Density Function) and it is developed mainly for application with sprays, combustion, parallel computing, and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase CFD and spray solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type. The manual provides the user with an understanding of the various models involved in the PDF formulation, its code structure and solution algorithm, and various other issues related to parallelization and its coupling with other solvers. The source code of EUPDF-II will be available with National Combustion Code (NCC) as a complete package.

The inverse of winnowing: a FORTRAN subroutine and discussion of unwinnowing discrete data

USGS Publications Warehouse

Bracken, Robert E.

2004-01-01

This report describes an unwinnowing algorithm that utilizes a discrete Fourier transform, and a resulting Fortran subroutine that winnows or unwinnows a 1-dimensional stream of discrete data; the source code is included. The unwinnowing algorithm effectively increases (by integral factors) the number of available data points while maintaining the original frequency spectrum of a data stream. This has utility when an increased data density is required together with an availability of higher order derivatives that honor the original data.

Process Model Improvement for Source Code Plagiarism Detection in Student Programming Assignments

ERIC Educational Resources Information Center

Kermek, Dragutin; Novak, Matija

2016-01-01

In programming courses there are various ways in which students attempt to cheat. The most commonly used method is copying source code from other students and making minimal changes in it, like renaming variable names. Several tools like Sherlock, JPlag and Moss have been devised to detect source code plagiarism. However, for larger student…

WISE Photometry for 400 million SDSS sources

DOE PAGES

Lang, Dustin; Hogg, David W.; Schlegel, David J.

2016-01-28

Here, we present photometry of images from the Wide-Field Infrared Survey Explorer (WISE) of over 400 million sources detected by the Sloan Digital Sky Survey (SDSS). We also use a "forced photometry" technique, using measured SDSS source positions, star-galaxy classification, and galaxy profiles to define the sources whose fluxes are to be measured in the WISE images. We perform photometry with The Tractor image modeling code, working on our "unWISE" coaddds and taking account of the WISE point-spread function and a noise model. The result is a measurement of the flux of each SDSS source in each WISE band. Manymore » sources have little flux in the WISE bands, so often the measurements we report are consistent with zero given our uncertainties. But, for many sources we get 3σ or 4σ measurements; these sources would not be reported by the "official" WISE pipeline and will not appear in the WISE catalog, yet they can be highly informative for some scientific questions. In addition, these small-signal measurements can be used in stacking analyses at the catalog level. The forced photometry approach has the advantage that we measure a consistent set of sources between SDSS and WISE, taking advantage of the resolution and depth of the SDSS images to interpret the WISE images; objects that are resolved in SDSS but blended together in WISE still have accurate measurements in our photometry. Our results, and the code used to produce them, are publicly available at http://unwise.me.« less

Finding Resolution for the Responsible Transparency of Economic Models in Health and Medicine.

PubMed

Padula, William V; McQueen, Robert Brett; Pronovost, Peter J

2017-11-01

The Second Panel on Cost-Effectiveness in Health and Medicine recommendations for conduct, methodological practices, and reporting of cost-effectiveness analyses has a number of questions unanswered with respect to the implementation of transparent, open source code interface for economic models. The possibility of making economic model source code could be positive and progressive for the field; however, several unintended consequences of this system should be first considered before complete implementation of this model. First, there is the concern regarding intellectual property rights that modelers have to their analyses. Second, the open source code could make analyses more accessible to inexperienced modelers, leading to inaccurate or misinterpreted results. We propose several resolutions to these concerns. The field should establish a licensing system of open source code such that the model originators maintain control of the code use and grant permissions to other investigators who wish to use it. The field should also be more forthcoming towards the teaching of cost-effectiveness analysis in medical and health services education so that providers and other professionals are familiar with economic modeling and able to conduct analyses with open source code. These types of unintended consequences need to be fully considered before the field's preparedness to move forward into an era of model transparency with open source code.

RD Optimized, Adaptive, Error-Resilient Transmission of MJPEG2000-Coded Video over Multiple Time-Varying Channels

NASA Astrophysics Data System (ADS)

Bezan, Scott; Shirani, Shahram

2006-12-01

To reliably transmit video over error-prone channels, the data should be both source and channel coded. When multiple channels are available for transmission, the problem extends to that of partitioning the data across these channels. The condition of transmission channels, however, varies with time. Therefore, the error protection added to the data at one instant of time may not be optimal at the next. In this paper, we propose a method for adaptively adding error correction code in a rate-distortion (RD) optimized manner using rate-compatible punctured convolutional codes to an MJPEG2000 constant rate-coded frame of video. We perform an analysis on the rate-distortion tradeoff of each of the coding units (tiles and packets) in each frame and adapt the error correction code assigned to the unit taking into account the bandwidth and error characteristics of the channels. This method is applied to both single and multiple time-varying channel environments. We compare our method with a basic protection method in which data is either not transmitted, transmitted with no protection, or transmitted with a fixed amount of protection. Simulation results show promising performance for our proposed method.

mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

PubMed Central

Karpievitch, Yuliya V; Almeida, Jonas S

2006-01-01

Background Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. Results mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Conclusion Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet. PMID:16539707

mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.

PubMed

Karpievitch, Yuliya V; Almeida, Jonas S

2006-03-15

Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet.

40 CFR 51.50 - What definitions apply to this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... accuracy description (MAD) codes means a set of six codes used to define the accuracy of latitude/longitude data for point sources. The six codes and their definitions are: (1) Coordinate Data Source Code: The... physical piece of or a closely related set of equipment. The EPA's reporting format for a given inventory...

The Astrophysics Source Code Library by the numbers

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter; Berriman, G. Bruce; DuPrie, Kimberly; Mink, Jessica; Nemiroff, Robert; Ryan, PW; Schmidt, Judy; Shamir, Lior; Shortridge, Keith; Wallin, John; Warmels, Rein

2018-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) was founded in 1999 by Robert Nemiroff and John Wallin. ASCL editors seek both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and add entries for the found codes to the library. Software authors can submit their codes to the ASCL as well. This ensures a comprehensive listing covering a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL is indexed by both NASA’s Astrophysics Data System (ADS) and Web of Science, making software used in research more discoverable. This presentation covers the growth in the ASCL’s number of entries, the number of citations to its entries, and in which journals those citations appear. It also discusses what changes have been made to the ASCL recently, and what its plans are for the future.

Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, A.; DuPrie, K.; Berriman, B.; Hanisch, R. J.; Mink, J.; Teuben, P. J.

2013-10-01

The Astrophysics Source Code Library (ASCL), founded in 1999, is a free on-line registry for source codes of interest to astronomers and astrophysicists. The library is housed on the discussion forum for Astronomy Picture of the Day (APOD) and can be accessed at http://ascl.net. The ASCL has a comprehensive listing that covers a significant number of the astrophysics source codes used to generate results published in or submitted to refereed journals and continues to grow. The ASCL currently has entries for over 500 codes; its records are citable and are indexed by ADS. The editors of the ASCL and members of its Advisory Committee were on hand at a demonstration table in the ADASS poster room to present the ASCL, accept code submissions, show how the ASCL is starting to be used by the astrophysics community, and take questions on and suggestions for improving the resource.

Generating code adapted for interlinking legacy scalar code and extended vector code

DOEpatents

Gschwind, Michael K

2013-06-04

Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

PubMed Central

Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H.A.; Hlavacek, William S.; Posner, Richard G.

2016-01-01

Summary: Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. Availability and implementation: BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary information: Supplementary data are available at Bioinformatics online. Contact: bionetgen.help@gmail.com PMID:26556387

The IntAct molecular interaction database in 2012

PubMed Central

Kerrien, Samuel; Aranda, Bruno; Breuza, Lionel; Bridge, Alan; Broackes-Carter, Fiona; Chen, Carol; Duesbury, Margaret; Dumousseau, Marine; Feuermann, Marc; Hinz, Ursula; Jandrasits, Christine; Jimenez, Rafael C.; Khadake, Jyoti; Mahadevan, Usha; Masson, Patrick; Pedruzzi, Ivo; Pfeiffenberger, Eric; Porras, Pablo; Raghunath, Arathi; Roechert, Bernd; Orchard, Sandra; Hermjakob, Henning

2012-01-01

IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275 000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact. PMID:22121220

COSMOS: Python library for massively parallel workflows.

PubMed

Gafni, Erik; Luquette, Lovelace J; Lancaster, Alex K; Hawkins, Jared B; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P; Tonellato, Peter J

2014-10-15

Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

CHEMICAL STORAGE: MYTHS VERSUS REALITY

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

Simmons, F

A large number of resources explaining proper chemical storage are available. These resources include books, databases/tables, and articles that explain various aspects of chemical storage including compatible chemical storage, signage, and regulatory requirements. Another source is the chemical manufacturer or distributor who provides storage information in the form of icons or color coding schemes on container labels. Despite the availability of these resources, chemical accidents stemming from improper storage, according to recent reports (1) (2), make up almost 25% of all chemical accidents. This relatively high percentage of chemical storage accidents suggests that these publications and color coding schemes althoughmore » helpful, still provide incomplete information that may not completely mitigate storage risks. This manuscript will explore some ways published storage information may be incomplete, examine the associated risks, and suggest methods to help further eliminate chemical storage risks.« less

A multiphysics and multiscale software environment for modeling astrophysical systems

NASA Astrophysics Data System (ADS)

Portegies Zwart, Simon; McMillan, Steve; Harfst, Stefan; Groen, Derek; Fujii, Michiko; Nualláin, Breanndán Ó.; Glebbeek, Evert; Heggie, Douglas; Lombardi, James; Hut, Piet; Angelou, Vangelis; Banerjee, Sambaran; Belkus, Houria; Fragos, Tassos; Fregeau, John; Gaburov, Evghenii; Izzard, Rob; Jurić, Mario; Justham, Stephen; Sottoriva, Andrea; Teuben, Peter; van Bever, Joris; Yaron, Ofer; Zemp, Marcel

2009-05-01

We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a "Noah's Ark" milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multiscale and multiphysics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe three examples calculated using MUSE: the merger of two galaxies, the merger of two evolving stars, and a hybrid N-body simulation. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.

Status and future of MUSE

NASA Astrophysics Data System (ADS)

Harfst, S.; Portegies Zwart, S.; McMillan, S.

2008-12-01

We present MUSE, a software framework for combining existing computational tools from different astrophysical domains into a single multi-physics, multi-scale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly-coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a ``Noah's Ark'' milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multi-scale and multi-physics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe two examples calculated using MUSE: the merger of two galaxies and an N-body simulation with live stellar evolution. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.

Public domain optical character recognition

NASA Astrophysics Data System (ADS)

Garris, Michael D.; Blue, James L.; Candela, Gerald T.; Dimmick, Darrin L.; Geist, Jon C.; Grother, Patrick J.; Janet, Stanley A.; Wilson, Charles L.

1995-03-01

A public domain document processing system has been developed by the National Institute of Standards and Technology (NIST). The system is a standard reference form-based handprint recognition system for evaluating optical character recognition (OCR), and it is intended to provide a baseline of performance on an open application. The system's source code, training data, performance assessment tools, and type of forms processed are all publicly available. The system recognizes the handprint entered on handwriting sample forms like the ones distributed with NIST Special Database 1. From these forms, the system reads hand-printed numeric fields, upper and lowercase alphabetic fields, and unconstrained text paragraphs comprised of words from a limited-size dictionary. The modular design of the system makes it useful for component evaluation and comparison, training and testing set validation, and multiple system voting schemes. The system contains a number of significant contributions to OCR technology, including an optimized probabilistic neural network (PNN) classifier that operates a factor of 20 times faster than traditional software implementations of the algorithm. The source code for the recognition system is written in C and is organized into 11 libraries. In all, there are approximately 19,000 lines of code supporting more than 550 subroutines. Source code is provided for form registration, form removal, field isolation, field segmentation, character normalization, feature extraction, character classification, and dictionary-based postprocessing. The recognition system has been successfully compiled and tested on a host of UNIX workstations. This paper gives an overview of the recognition system's software architecture, including descriptions of the various system components along with timing and accuracy statistics.

JETSPIN: A specific-purpose open-source software for simulations of nanofiber electrospinning

NASA Astrophysics Data System (ADS)

Lauricella, Marco; Pontrelli, Giuseppe; Coluzza, Ivan; Pisignano, Dario; Succi, Sauro

2015-12-01

We present the open-source computer program JETSPIN, specifically designed to simulate the electrospinning process of nanofibers. Its capabilities are shown with proper reference to the underlying model, as well as a description of the relevant input variables and associated test-case simulations. The various interactions included in the electrospinning model implemented in JETSPIN are discussed in detail. The code is designed to exploit different computational architectures, from single to parallel processor workstations. This paper provides an overview of JETSPIN, focusing primarily on its structure, parallel implementations, functionality, performance, and availability.

Cytoscape.js: a graph theory library for visualisation and analysis.

PubMed

Franz, Max; Lopes, Christian T; Huck, Gerardo; Dong, Yue; Sumer, Onur; Bader, Gary D

2016-01-15

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. gary.bader@utoronto.ca. © The Author 2015. Published by Oxford University Press.

GLACiAR, an Open-Source Python Tool for Simulations of Source Recovery and Completeness in Galaxy Surveys

NASA Astrophysics Data System (ADS)

Carrasco, D.; Trenti, M.; Mutch, S.; Oesch, P. A.

2018-06-01

The luminosity function is a fundamental observable for characterising how galaxies form and evolve throughout the cosmic history. One key ingredient to derive this measurement from the number counts in a survey is the characterisation of the completeness and redshift selection functions for the observations. In this paper, we present GLACiAR, an open python tool available on GitHub to estimate the completeness and selection functions in galaxy surveys. The code is tailored for multiband imaging surveys aimed at searching for high-redshift galaxies through the Lyman-break technique, but it can be applied broadly. The code generates artificial galaxies that follow Sérsic profiles with different indexes and with customisable size, redshift, and spectral energy distribution properties, adds them to input images, and measures the recovery rate. To illustrate this new software tool, we apply it to quantify the completeness and redshift selection functions for J-dropouts sources (redshift z 10 galaxies) in the Hubble Space Telescope Brightest of Reionizing Galaxies Survey. Our comparison with a previous completeness analysis on the same dataset shows overall agreement, but also highlights how different modelling assumptions for the artificial sources can impact completeness estimates.

Data compression for satellite images

NASA Technical Reports Server (NTRS)

Chen, P. H.; Wintz, P. A.

1976-01-01

An efficient data compression system is presented for satellite pictures and two grey level pictures derived from satellite pictures. The compression techniques take advantages of the correlation between adjacent picture elements. Several source coding methods are investigated. Double delta coding is presented and shown to be the most efficient. Both predictive differential quantizing technique and double delta coding can be significantly improved by applying a background skipping technique. An extension code is constructed. This code requires very little storage space and operates efficiently. Simulation results are presented for various coding schemes and source codes.

Layered video transmission over multirate DS-CDMA wireless systems

NASA Astrophysics Data System (ADS)

Kondi, Lisimachos P.; Srinivasan, Deepika; Pados, Dimitris A.; Batalama, Stella N.

2003-05-01

n this paper, we consider the transmission of video over wireless direct-sequence code-division multiple access (DS-CDMA) channels. A layered (scalable) video source codec is used and each layer is transmitted over a different CDMA channel. Spreading codes with different lengths are allowed for each CDMA channel (multirate CDMA). Thus, a different number of chips per bit can be used for the transmission of each scalable layer. For a given fixed energy value per chip and chip rate, the selection of a spreading code length affects the transmitted energy per bit and bit rate for each scalable layer. An MPEG-4 source encoder is used to provide a two-layer SNR scalable bitstream. Each of the two layers is channel-coded using Rate-Compatible Punctured Convolutional (RCPC) codes. Then, the data are interleaved, spread, carrier-modulated and transmitted over the wireless channel. A multipath Rayleigh fading channel is assumed. At the other end, we assume the presence of an antenna array receiver. After carrier demodulation, multiple-access-interference suppressing despreading is performed using space-time auxiliary vector (AV) filtering. The choice of the AV receiver is dictated by realistic channel fading rates that limit the data record available for receiver adaptation and redesign. Indeed, AV filter short-data-record estimators have been shown to exhibit superior bit-error-rate performance in comparison with LMS, RLS, SMI, or 'multistage nested Wiener' adaptive filter implementations. Our experimental results demonstrate the effectiveness of multirate DS-CDMA systems for wireless video transmission.

Parallelisation study of a three-dimensional environmental flow model

NASA Astrophysics Data System (ADS)

O'Donncha, Fearghal; Ragnoli, Emanuele; Suits, Frank

2014-03-01

There are many simulation codes in the geosciences that are serial and cannot take advantage of the parallel computational resources commonly available today. One model important for our work in coastal ocean current modelling is EFDC, a Fortran 77 code configured for optimal deployment on vector computers. In order to take advantage of our cache-based, blade computing system we restructured EFDC from serial to parallel, thereby allowing us to run existing models more quickly, and to simulate larger and more detailed models that were previously impractical. Since the source code for EFDC is extensive and involves detailed computation, it is important to do such a port in a manner that limits changes to the files, while achieving the desired speedup. We describe a parallelisation strategy involving surgical changes to the source files to minimise error-prone alteration of the underlying computations, while allowing load-balanced domain decomposition for efficient execution on a commodity cluster. The use of conjugate gradient posed particular challenges due to implicit non-local communication posing a hindrance to standard domain partitioning schemes; a number of techniques are discussed to address this in a feasible, computationally efficient manner. The parallel implementation demonstrates good scalability in combination with a novel domain partitioning scheme that specifically handles mixed water/land regions commonly found in coastal simulations. The approach presented here represents a practical methodology to rejuvenate legacy code on a commodity blade cluster with reasonable effort; our solution has direct application to other similar codes in the geosciences.

Sandia National Laboratories environmental fluid dynamics code. Marine Hydrokinetic Module User's Manual

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

James, Scott Carlton; Roberts, Jesse D.

2014-03-01

This document describes the marine hydrokinetic (MHK) input file and subroutines for the Sandia National Laboratories Environmental Fluid Dynamics Code (SNL-EFDC), which is a combined hydrodynamic, sediment transport, and water quality model based on the Environmental Fluid Dynamics Code (EFDC) developed by John Hamrick [1], formerly sponsored by the U.S. Environmental Protection Agency, and now maintained by Tetra Tech, Inc. SNL-EFDC has been previously enhanced with the incorporation of the SEDZLJ sediment dynamics model developed by Ziegler, Lick, and Jones [2-4]. SNL-EFDC has also been upgraded to more accurately simulate algae growth with specific application to optimizing biomass in anmore » open-channel raceway for biofuels production [5]. A detailed description of the input file containing data describing the MHK device/array is provided, along with a description of the MHK FORTRAN routine. Both a theoretical description of the MHK dynamics as incorporated into SNL-EFDC and an explanation of the source code are provided. This user manual is meant to be used in conjunction with the original EFDC [6] and sediment dynamics SNL-EFDC manuals [7]. Through this document, the authors provide information for users who wish to model the effects of an MHK device (or array of devices) on a flow system with EFDC and who also seek a clear understanding of the source code, which is available from staff in the Water Power Technologies Department at Sandia National Laboratories, Albuquerque, New Mexico.« less

Distributed Joint Source-Channel Coding in Wireless Sensor Networks

PubMed Central

Zhu, Xuqi; Liu, Yu; Zhang, Lin

2009-01-01

Considering the fact that sensors are energy-limited and the wireless channel conditions in wireless sensor networks, there is an urgent need for a low-complexity coding method with high compression ratio and noise-resisted features. This paper reviews the progress made in distributed joint source-channel coding which can address this issue. The main existing deployments, from the theory to practice, of distributed joint source-channel coding over the independent channels, the multiple access channels and the broadcast channels are introduced, respectively. To this end, we also present a practical scheme for compressing multiple correlated sources over the independent channels. The simulation results demonstrate the desired efficiency. PMID:22408560

State-Chart Autocoder

NASA Technical Reports Server (NTRS)

Clark, Kenneth; Watney, Garth; Murray, Alexander; Benowitz, Edward

2007-01-01

A computer program translates Unified Modeling Language (UML) representations of state charts into source code in the C, C++, and Python computing languages. ( State charts signifies graphical descriptions of states and state transitions of a spacecraft or other complex system.) The UML representations constituting the input to this program are generated by using a UML-compliant graphical design program to draw the state charts. The generated source code is consistent with the "quantum programming" approach, which is so named because it involves discrete states and state transitions that have features in common with states and state transitions in quantum mechanics. Quantum programming enables efficient implementation of state charts, suitable for real-time embedded flight software. In addition to source code, the autocoder program generates a graphical-user-interface (GUI) program that, in turn, generates a display of state transitions in response to events triggered by the user. The GUI program is wrapped around, and can be used to exercise the state-chart behavior of, the generated source code. Once the expected state-chart behavior is confirmed, the generated source code can be augmented with a software interface to the rest of the software with which the source code is required to interact.

radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar.

PubMed

Taylor, Philip D; Brzustowski, John M; Matkovich, Carolyn; Peckford, Michael L; Wilson, Dave

2010-10-26

Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets.

radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar

PubMed Central

2010-01-01

Background Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Results Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Conclusions Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets. PMID:20977735

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

PubMed

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

2016-11-15

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online. msa@bio.sh. © The Author 2016. Published by Oxford University Press.

ProtVista: visualization of protein sequence annotations.

PubMed

Watkins, Xavier; Garcia, Leyla J; Pundir, Sangya; Martin, Maria J

2017-07-01

ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations. ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uniprot.github.io/ProtVista/ . martin@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data

PubMed Central

Linderman, Michael D.; Simonds, Erin F.; Qiu, Peng; Bruggner, Robert V.; Sheode, Ketaki; Meng, Teresa H.; Plevritis, Sylvia K.; Nolan, Garry P.

2012-01-01

Motivation: Recent advances in flow cytometry enable simultaneous single-cell measurement of 30+ surface and intracellular proteins. CytoSPADE is a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events algorithm for tree-based analysis and visualization of this high-dimensional cytometry data. Availability: Source code and binaries are freely available at http://cytospade.org and via Bioconductor version 2.10 onwards for Linux, OSX and Windows. CytoSPADE is implemented in R, C++ and Java. Contact: michael.linderman@mssm.edu Supplementary Information: Additional documentation available at http://cytospade.org. PMID:22782546

The National Transport Code Collaboration Module Library

NASA Astrophysics Data System (ADS)

Kritz, A. H.; Bateman, G.; Kinsey, J.; Pankin, A.; Onjun, T.; Redd, A.; McCune, D.; Ludescher, C.; Pletzer, A.; Andre, R.; Zakharov, L.; Lodestro, L.; Pearlstein, L. D.; Jong, R.; Houlberg, W.; Strand, P.; Wiley, J.; Valanju, P.; John, H. St.; Waltz, R.; Mandrekas, J.; Mau, T. K.; Carlsson, J.; Braams, B.

2004-12-01

This paper reports on the progress in developing a library of code modules under the auspices of the National Transport Code Collaboration (NTCC). Code modules are high quality, fully documented software packages with a clearly defined interface. The modules provide a variety of functions, such as implementing numerical physics models; performing ancillary functions such as I/O or graphics; or providing tools for dealing with common issues in scientific programming such as portability of Fortran codes. Researchers in the plasma community submit code modules, and a review procedure is followed to insure adherence to programming and documentation standards. The review process is designed to provide added confidence with regard to the use of the modules and to allow users and independent reviews to validate the claims of the modules' authors. All modules include source code; clear instructions for compilation of binaries on a variety of target architectures; and test cases with well-documented input and output. All the NTCC modules and ancillary information, such as current standards and documentation, are available from the NTCC Module Library Website http://w3.pppl.gov/NTCC. The goal of the project is to develop a resource of value to builders of integrated modeling codes and to plasma physics researchers generally. Currently, there are more than 40 modules in the module library.

Residential Segregation and the Availability of Primary Care Physicians

PubMed Central

Gaskin, Darrell J; Dinwiddie, Gniesha Y; Chan, Kitty S; McCleary, Rachael R

2012-01-01

Objective To examine the association between residential segregation and geographic access to primary care physicians (PCPs) in metropolitan statistical areas (MSAs). Data Sources We combined zip code level data on primary care physicians from the 2006 American Medical Association master file with demographic, socioeconomic, and segregation measures from the 2000 U.S. Census. Our sample consisted of 15,465 zip codes located completely or partially in an MSA. Methods We defined PCP shortage areas as those zip codes with no PCP or a population to PCP ratio of >3,500. Using logistic regressions, we estimated the association between a zip code's odds of being a PCP shortage area and its minority composition and degree of segregation in its MSA. Principal Findings We found that odds of being a PCP shortage area were 67 percent higher for majority African American zip codes but 27 percent lower for majority Hispanic zip codes. The association varied with the degree of segregation. As the degree of segregation increased, the odds of being a PCP shortage area increased for majority African American zip codes; however, the converse was true for majority Hispanic and Asian zip codes. Conclusions Efforts to address PCP shortages should target African American communities especially in segregated MSAs. PMID:22524264

An automated workflow for parallel processing of large multiview SPIM recordings

PubMed Central

Schmied, Christopher; Steinbach, Peter; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel

2016-01-01

Summary: Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster. Here, we introduce an automated workflow for processing large multiview, multichannel, multiillumination time-lapse SPIM data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it. Availability and implementation: The code is distributed free and open source under the MIT license http://opensource.org/licenses/MIT. The source code can be downloaded from github: https://github.com/mpicbg-scicomp/snakemake-workflows. Documentation can be found here: http://fiji.sc/Automated_workflow_for_parallel_Multiview_Reconstruction. Contact: schmied@mpi-cbg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26628585

Computational modeling in cognitive science: a manifesto for change.

PubMed

Addyman, Caspar; French, Robert M

2012-07-01

Computational modeling has long been one of the traditional pillars of cognitive science. Unfortunately, the computer models of cognition being developed today have not kept up with the enormous changes that have taken place in computer technology and, especially, in human-computer interfaces.  For all intents and purposes, modeling is still done today as it was 25, or even 35, years ago. Everyone still programs in his or her own favorite programming language, source code is rarely made available, accessibility of models to non-programming researchers is essentially non-existent, and even for other modelers, the profusion of source code in a multitude of programming languages, written without programming guidelines, makes it almost impossible to access, check, explore, re-use, or continue to develop. It is high time to change this situation, especially since the tools are now readily available to do so. We propose that the modeling community adopt three simple guidelines that would ensure that computational models would be accessible to the broad range of researchers in cognitive science. We further emphasize the pivotal role that journal editors must play in making computational models accessible to readers of their journals. Copyright © 2012 Cognitive Science Society, Inc.

A convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography

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

Yang, Xiaogang; De Carlo, Francesco; Phatak, Charudatta

This paper presents an algorithm to calibrate the center-of-rotation for X-ray tomography by using a machine learning approach, the Convolutional Neural Network (CNN). The algorithm shows excellent accuracy from the evaluation of synthetic data with various noise ratios. It is further validated with experimental data of four different shale samples measured at the Advanced Photon Source and at the Swiss Light Source. The results are as good as those determined by visual inspection and show better robustness than conventional methods. CNN has also great potential forreducing or removingother artifacts caused by instrument instability, detector non-linearity,etc. An open-source toolbox, which integratesmore » the CNN methods described in this paper, is freely available through GitHub at tomography/xlearn and can be easily integrated into existing computational pipelines available at various synchrotron facilities. Source code, documentation and information on how to contribute are also provided.« less

W-026, Waste Receiving and Processing Facility data management system validation and verification report

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

Palmer, M.E.

1997-12-05

This V and V Report includes analysis of two revisions of the DMS [data management system] System Requirements Specification (SRS) and the Preliminary System Design Document (PSDD); the source code for the DMS Communication Module (DMSCOM) messages; the source code for selected DMS Screens, and the code for the BWAS Simulator. BDM Federal analysts used a series of matrices to: compare the requirements in the System Requirements Specification (SRS) to the specifications found in the System Design Document (SDD), to ensure the design supports the business functions, compare the discreet parts of the SDD with each other, to ensure thatmore » the design is consistent and cohesive, compare the source code of the DMS Communication Module with the specifications, to ensure that the resultant messages will support the design, compare the source code of selected screens to the specifications to ensure that resultant system screens will support the design, compare the source code of the BWAS simulator with the requirements to interface with DMS messages and data transfers relating to the BWAS operations.« less

Earth Global Reference Atmospheric Model (GRAM99): Short Course

NASA Technical Reports Server (NTRS)

Leslie, Fred W.; Justus, C. G.

2007-01-01

Earth-GRAM is a FORTRAN software package that can run on a variety of platforms including PC's. For any time and location in the Earth's atmosphere, Earth-GRAM provides values of atmospheric quantities such as temperature, pressure, density, winds, constituents, etc.. Dispersions (perturbations) of these parameters are also provided and have realistic correlations, means, and variances - useful for Monte Carlo analysis. Earth-GRAM is driven by observations including a tropospheric database available from the National Climatic Data Center. Although Earth-GRAM can be run in a "stand-alone" mode, many users incorporate it into their trajectory codes. The source code is distributed free-of-charge to eligible recipients.

Apollo: a community resource for genome annotation editing.

PubMed

Lee, Ed; Harris, Nomi; Gibson, Mark; Chetty, Raymond; Lewis, Suzanna

2009-07-15

Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.

PMAnalyzer: a new web interface for bacterial growth curve analysis.

PubMed

Cuevas, Daniel A; Edwards, Robert A

2017-06-15

Bacterial growth curves are essential representations for characterizing bacteria metabolism within a variety of media compositions. Using high-throughput, spectrophotometers capable of processing tens of 96-well plates, quantitative phenotypic information can be easily integrated into the current data structures that describe a bacterial organism. The PMAnalyzer pipeline performs a growth curve analysis to parameterize the unique features occurring within microtiter wells containing specific growth media sources. We have expanded the pipeline capabilities and provide a user-friendly, online implementation of this automated pipeline. PMAnalyzer version 2.0 provides fast automatic growth curve parameter analysis, growth identification and high resolution figures of sample-replicate growth curves and several statistical analyses. PMAnalyzer v2.0 can be found at https://edwards.sdsu.edu/pmanalyzer/ . Source code for the pipeline can be found on GitHub at https://github.com/dacuevas/PMAnalyzer . Source code for the online implementation can be found on GitHub at https://github.com/dacuevas/PMAnalyzerWeb . dcuevas08@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

The IRAS Minor Planet Survey

NASA Technical Reports Server (NTRS)

Tedesco, Edward F.; Veeder, Glenn J.; Fowler, John W.; Chillemi, Joseph R.

1992-01-01

This report documents the program and data used to identify known asteroids observed by the Infrared Astronomical Satellite (IRAS) and to compute albedos and diameters from their IRAS fluxes. It also presents listings of the results obtained. These results supplant those in the IRAS Asteroid and Comet Survey, 1986. The present version used new and improved asteroid orbital elements for 4679 numbered asteroids and 2632 additional asteroids for which at least two-opposition elements were available as of mid-1991. It employed asteroid absolute magnitudes on the International Astronomical Union system adopted in 1991. In addition, the code was modified to increase the reliability of associating asteroids with IRAS sources and rectify several shortcomings in the final data products released in 1986. Association reliability was improved by decreasing the position difference between an IRAS source and a predicted asteroid position required for an association. The shortcomings addressed included the problem of flux overestimation for low SNR sources and the systematic difference in albedos and diameters among the three wavelength bands (12, 25, and 60 micrometers). Several minor bugs in the original code were also corrected.

Web-based network analysis and visualization using CellMaps

PubMed Central

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-01-01

Summary: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. Availability and Implementation: The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps. The client is implemented in JavaScript and the server in C and Java. Contact: jdopazo@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27296979

Authorship attribution of source code by using back propagation neural network based on particle swarm optimization

PubMed Central

Xu, Guoai; Li, Qi; Guo, Yanhui; Zhang, Miao

2017-01-01

Authorship attribution is to identify the most likely author of a given sample among a set of candidate known authors. It can be not only applied to discover the original author of plain text, such as novels, blogs, emails, posts etc., but also used to identify source code programmers. Authorship attribution of source code is required in diverse applications, ranging from malicious code tracking to solving authorship dispute or software plagiarism detection. This paper aims to propose a new method to identify the programmer of Java source code samples with a higher accuracy. To this end, it first introduces back propagation (BP) neural network based on particle swarm optimization (PSO) into authorship attribution of source code. It begins by computing a set of defined feature metrics, including lexical and layout metrics, structure and syntax metrics, totally 19 dimensions. Then these metrics are input to neural network for supervised learning, the weights of which are output by PSO and BP hybrid algorithm. The effectiveness of the proposed method is evaluated on a collected dataset with 3,022 Java files belong to 40 authors. Experiment results show that the proposed method achieves 91.060% accuracy. And a comparison with previous work on authorship attribution of source code for Java language illustrates that this proposed method outperforms others overall, also with an acceptable overhead. PMID:29095934

The mathematical theory of signal processing and compression-designs

NASA Astrophysics Data System (ADS)

Feria, Erlan H.

2006-05-01

The mathematical theory of signal processing, named processor coding, will be shown to inherently arise as the computational time dual of Shannon's mathematical theory of communication which is also known as source coding. Source coding is concerned with signal source memory space compression while processor coding deals with signal processor computational time compression. Their combination is named compression-designs and referred as Conde in short. A compelling and pedagogically appealing diagram will be discussed highlighting Conde's remarkable successful application to real-world knowledge-aided (KA) airborne moving target indicator (AMTI) radar.

Accurate Modeling of Ionospheric Electromagnetic Fields Generated by a Low-Altitude VLF Transmitter

DTIC Science & Technology

2007-08-31

latitude) for 3 different grid spacings. 14 8. Low-altitude fields produced by a 10-kHz source computed using the FD and TD codes. The agreement is...excellent, validating the new FD code. 16 9. High-altitude fields produced by a 10-kHz source computed using the FD and TD codes. The agreement is...again excellent. 17 10. Low-altitude fields produced by a 20-k.Hz source computed using the FD and TD codes. 17 11. High-altitude fields produced

Modelling the phase curve and occultation of WASP-43b with SPIDERMAN

NASA Astrophysics Data System (ADS)

Louden, Tom

2017-06-01

Presenting SPIDERMAN, a fast code for calculating exoplanet phase curves and secondary eclipses with arbitrary two dimensional surface brightness distributions. SPIDERMAN uses an exact geometric algorithm to calculate the area of sub-regions of the planet that are occulted by the star, with no loss in numerical precision. The speed of this calculation makes it possible to run MCMCs to marginalise effectively over the underlying parameters controlling the brightness distribution of exoplanets. The code is fully open source and available over Github. We apply the code to the phase curve of WASP-43b using an analytical surface brightness distribution, and find an excellent fit to the data. We are able to place direct constraints on the physics of heat transport in the atmosphere, such as the ratio between advective and radiative timescales at different altitudes.

GridMan: A grid manipulation system

NASA Technical Reports Server (NTRS)

Eiseman, Peter R.; Wang, Zhu

1992-01-01

GridMan is an interactive grid manipulation system. It operates on grids to produce new grids which conform to user demands. The input grids are not constrained to come from any particular source. They may be generated by algebraic methods, elliptic methods, hyperbolic methods, parabolic methods, or some combination of methods. The methods are included in the various available structured grid generation codes. These codes perform the basic assembly function for the various elements of the initial grid. For block structured grids, the assembly can be quite complex due to a large number of clock corners, edges, and faces for which various connections and orientations must be properly identified. The grid generation codes are distinguished among themselves by their balance between interactive and automatic actions and by their modest variations in control. The basic form of GridMan provides a much more substantial level of grid control and will take its input from any of the structured grid generation codes. The communication link to the outside codes is a data file which contains the grid or section of grid.

Monte Carlo dose calculations of beta-emitting sources for intravascular brachytherapy: a comparison between EGS4, EGSnrc, and MCNP.

PubMed

Wang, R; Li, X A

2001-02-01

The dose parameters for the beta-particle emitting 90Sr/90Y source for intravascular brachytherapy (IVBT) have been calculated by different investigators. At a distant distance from the source, noticeable differences are seen in these parameters calculated using different Monte Carlo codes. The purpose of this work is to quantify as well as to understand these differences. We have compared a series of calculations using an EGS4, an EGSnrc, and the MCNP Monte Carlo codes. Data calculated and compared include the depth dose curve for a broad parallel beam of electrons, and radial dose distributions for point electron sources (monoenergetic or polyenergetic) and for a real 90Sr/90Y source. For the 90Sr/90Y source, the doses at the reference position (2 mm radial distance) calculated by the three code agree within 2%. However, the differences between the dose calculated by the three codes can be over 20% in the radial distance range interested in IVBT. The difference increases with radial distance from source, and reaches 30% at the tail of dose curve. These differences may be partially attributed to the different multiple scattering theories and Monte Carlo models for electron transport adopted in these three codes. Doses calculated by the EGSnrc code are more accurate than those by the EGS4. The two calculations agree within 5% for radial distance <6 mm.

The SAMI Galaxy Survey: A prototype data archive for Big Science exploration

NASA Astrophysics Data System (ADS)

Konstantopoulos, I. S.; Green, A. W.; Foster, C.; Scott, N.; Allen, J. T.; Fogarty, L. M. R.; Lorente, N. P. F.; Sweet, S. M.; Hopkins, A. M.; Bland-Hawthorn, J.; Bryant, J. J.; Croom, S. M.; Goodwin, M.; Lawrence, J. S.; Owers, M. S.; Richards, S. N.

2015-11-01

We describe the data archive and database for the SAMI Galaxy Survey, an ongoing observational program that will cover ≈3400 galaxies with integral-field (spatially-resolved) spectroscopy. Amounting to some three million spectra, this is the largest sample of its kind to date. The data archive and built-in query engine use the versatile Hierarchical Data Format (HDF5), which precludes the need for external metadata tables and hence the setup and maintenance overhead those carry. The code produces simple outputs that can easily be translated to plots and tables, and the combination of these tools makes for a light system that can handle heavy data. This article acts as a contextual companion to the SAMI Survey Database source code repository, samiDB, which is freely available online and written entirely in Python. We also discuss the decisions related to the selection of tools and the creation of data visualisation modules. It is our aim that the work presented in this article-descriptions, rationale, and source code-will be of use to scientists looking to set up a maintenance-light data archive for a Big Science data load.

Source Authentication for Code Dissemination Supporting Dynamic Packet Size in Wireless Sensor Networks.

PubMed

Kim, Daehee; Kim, Dongwan; An, Sunshin

2016-07-09

Code dissemination in wireless sensor networks (WSNs) is a procedure for distributing a new code image over the air in order to update programs. Due to the fact that WSNs are mostly deployed in unattended and hostile environments, secure code dissemination ensuring authenticity and integrity is essential. Recent works on dynamic packet size control in WSNs allow enhancing the energy efficiency of code dissemination by dynamically changing the packet size on the basis of link quality. However, the authentication tokens attached by the base station become useless in the next hop where the packet size can vary according to the link quality of the next hop. In this paper, we propose three source authentication schemes for code dissemination supporting dynamic packet size. Compared to traditional source authentication schemes such as μTESLA and digital signatures, our schemes provide secure source authentication under the environment, where the packet size changes in each hop, with smaller energy consumption.

Source Authentication for Code Dissemination Supporting Dynamic Packet Size in Wireless Sensor Networks †

PubMed Central

Kim, Daehee; Kim, Dongwan; An, Sunshin

2016-01-01

Code dissemination in wireless sensor networks (WSNs) is a procedure for distributing a new code image over the air in order to update programs. Due to the fact that WSNs are mostly deployed in unattended and hostile environments, secure code dissemination ensuring authenticity and integrity is essential. Recent works on dynamic packet size control in WSNs allow enhancing the energy efficiency of code dissemination by dynamically changing the packet size on the basis of link quality. However, the authentication tokens attached by the base station become useless in the next hop where the packet size can vary according to the link quality of the next hop. In this paper, we propose three source authentication schemes for code dissemination supporting dynamic packet size. Compared to traditional source authentication schemes such as μTESLA and digital signatures, our schemes provide secure source authentication under the environment, where the packet size changes in each hop, with smaller energy consumption. PMID:27409616

Model-Based Least Squares Reconstruction of Coded Source Neutron Radiographs: Integrating the ORNL HFIR CG1D Source Model

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

Santos-Villalobos, Hector J; Gregor, Jens; Bingham, Philip R

2014-01-01

At the present, neutron sources cannot be fabricated small and powerful enough in order to achieve high resolution radiography while maintaining an adequate flux. One solution is to employ computational imaging techniques such as a Magnified Coded Source Imaging (CSI) system. A coded-mask is placed between the neutron source and the object. The system resolution is increased by reducing the size of the mask holes and the flux is increased by increasing the size of the coded-mask and/or the number of holes. One limitation of such system is that the resolution of current state-of-the-art scintillator-based detectors caps around 50um. Tomore » overcome this challenge, the coded-mask and object are magnified by making the distance from the coded-mask to the object much smaller than the distance from object to detector. In previous work, we have shown via synthetic experiments that our least squares method outperforms other methods in image quality and reconstruction precision because of the modeling of the CSI system components. However, the validation experiments were limited to simplistic neutron sources. In this work, we aim to model the flux distribution of a real neutron source and incorporate such a model in our least squares computational system. We provide a full description of the methodology used to characterize the neutron source and validate the method with synthetic experiments.« less

Streamlined Genome Sequence Compression using Distributed Source Coding

PubMed Central

Wang, Shuang; Jiang, Xiaoqian; Chen, Feng; Cui, Lijuan; Cheng, Samuel

2014-01-01

We aim at developing a streamlined genome sequence compression algorithm to support alternative miniaturized sequencing devices, which have limited communication, storage, and computation power. Existing techniques that require heavy client (encoder side) cannot be applied. To tackle this challenge, we carefully examined distributed source coding theory and developed a customized reference-based genome compression protocol to meet the low-complexity need at the client side. Based on the variation between source and reference, our protocol will pick adaptively either syndrome coding or hash coding to compress subsequences of changing code length. Our experimental results showed promising performance of the proposed method when compared with the state-of-the-art algorithm (GRS). PMID:25520552

The FORTRAN static source code analyzer program (SAP) system description

NASA Technical Reports Server (NTRS)

Decker, W.; Taylor, W.; Merwarth, P.; Oneill, M.; Goorevich, C.; Waligora, S.

1982-01-01

A source code analyzer program (SAP) designed to assist personnel in conducting studies of FORTRAN programs is described. The SAP scans FORTRAN source code and produces reports that present statistics and measures of statements and structures that make up a module. The processing performed by SAP and of the routines, COMMON blocks, and files used by SAP are described. The system generation procedure for SAP is also presented.

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

Anthony, Stephen

The Sandia hyperspectral upper-bound spectrum algorithm (hyper-UBS) is a cosmic ray despiking algorithm for hyperspectral data sets. When naturally-occurring, high-energy (gigaelectronvolt) cosmic rays impact the earth’s atmosphere, they create an avalanche of secondary particles which will register as a large, positive spike on any spectroscopic detector they hit. Cosmic ray spikes are therefore an unavoidable spectroscopic contaminant which can interfere with subsequent analysis. A variety of cosmic ray despiking algorithms already exist and can potentially be applied to hyperspectral data matrices, most notably the upper-bound spectrum data matrices (UBS-DM) algorithm by Dongmao Zhang and Dor Ben-Amotz which served as themore » basis for the hyper-UBS algorithm. However, the existing algorithms either cannot be applied to hyperspectral data, require information that is not always available, introduce undesired spectral bias, or have otherwise limited effectiveness for some experimentally relevant conditions. Hyper-UBS is more effective at removing a wider variety of cosmic ray spikes from hyperspectral data without introducing undesired spectral bias. In addition to the core algorithm the Sandia hyper-UBS software package includes additional source code useful in evaluating the effectiveness of the hyper-UBS algorithm. The accompanying source code includes code to generate simulated hyperspectral data contaminated by cosmic ray spikes, several existing despiking algorithms, and code to evaluate the performance of the despiking algorithms on simulated data.« less

MrLavaLoba: A new probabilistic model for the simulation of lava flows as a settling process

NASA Astrophysics Data System (ADS)

de'Michieli Vitturi, Mattia; Tarquini, Simone

2018-01-01

A new code to simulate lava flow spread, MrLavaLoba, is presented. In the code, erupted lava is itemized in parcels having an elliptical shape and prescribed volume. New parcels bud from existing ones according to a probabilistic law influenced by the local steepest slope direction and by tunable input settings. MrLavaLoba must be accounted among the probabilistic codes for the simulation of lava flows, because it is not intended to mimic the actual process of flowing or to provide directly the progression with time of the flow field, but rather to guess the most probable inundated area and final thickness of the lava deposit. The code's flexibility allows it to produce variable lava flow spread and emplacement according to different dynamics (e.g. pahoehoe or channelized-'a'ā). For a given scenario, it is shown that model outputs converge, in probabilistic terms, towards a single solution. The code is applied to real cases in Hawaii and Mt. Etna, and the obtained maps are shown. The model is written in Python and the source code is available at http://demichie.github.io/MrLavaLoba/.

ADPAC v1.0: User's Manual

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Heidegger, Nathan J.; Delaney, Robert A.

1999-01-01

The overall objective of this study was to evaluate the effects of turbulence models in a 3-D numerical analysis on the wake prediction capability. The current version of the computer code resulting from this study is referred to as ADPAC v7 (Advanced Ducted Propfan Analysis Codes -Version 7). This report is intended to serve as a computer program user's manual for the ADPAC code used and modified under Task 15 of NASA Contract NAS3-27394. The ADPAC program is based on a flexible multiple-block and discretization scheme permitting coupled 2-D/3-D mesh block solutions with application to a wide variety of geometries. Aerodynamic calculations are based on a four-stage Runge-Kutta time-marching finite volume solution technique with added numerical dissipation. Steady flow predictions are accelerated by a multigrid procedure. Turbulence models now available in the ADPAC code are: a simple mixing-length model, the algebraic Baldwin-Lomax model with user defined coefficients, the one-equation Spalart-Allmaras model, and a two-equation k-R model. The consolidated ADPAC code is capable of executing in either a serial or parallel computing mode from a single source code.

Automated UMLS-Based Comparison of Medical Forms

PubMed Central

Dugas, Martin; Fritz, Fleur; Krumm, Rainer; Breil, Bernhard

2013-01-01

Medical forms are very heterogeneous: on a European scale there are thousands of data items in several hundred different systems. To enable data exchange for clinical care and research purposes there is a need to develop interoperable documentation systems with harmonized forms for data capture. A prerequisite in this harmonization process is comparison of forms. So far – to our knowledge – an automated method for comparison of medical forms is not available. A form contains a list of data items with corresponding medical concepts. An automatic comparison needs data types, item names and especially item with these unique concept codes from medical terminologies. The scope of the proposed method is a comparison of these items by comparing their concept codes (coded in UMLS). Each data item is represented by item name, concept code and value domain. Two items are called identical, if item name, concept code and value domain are the same. Two items are called matching, if only concept code and value domain are the same. Two items are called similar, if their concept codes are the same, but the value domains are different. Based on these definitions an open-source implementation for automated comparison of medical forms in ODM format with UMLS-based semantic annotations was developed. It is available as package compareODM from http://cran.r-project.org. To evaluate this method, it was applied to a set of 7 real medical forms with 285 data items from a large public ODM repository with forms for different medical purposes (research, quality management, routine care). Comparison results were visualized with grid images and dendrograms. Automated comparison of semantically annotated medical forms is feasible. Dendrograms allow a view on clustered similar forms. The approach is scalable for a large set of real medical forms. PMID:23861827

An X-Ray Analysis Database of Photoionization Cross Sections Including Variable Ionization

NASA Technical Reports Server (NTRS)

Wang, Ping; Cohen, David H.; MacFarlane, Joseph J.; Cassinelli, Joseph P.

1997-01-01

Results of research efforts in the following areas are discussed: review of the major theoretical and experimental data of subshell photoionization cross sections and ionization edges of atomic ions to assess the accuracy of the data, and to compile the most reliable of these data in our own database; detailed atomic physics calculations to complement the database for all ions of 17 cosmically abundant elements; reconciling the data from various sources and our own calculations; and fitting cross sections with functional approximations and incorporating these functions into a compact computer code.Also, efforts included adapting an ionization equilibrium code, tabulating results, and incorporating them into the overall program and testing the code (both ionization equilibrium and opacity codes) with existing observational data. The background and scientific applications of this work are discussed. Atomic physics cross section models and calculations are described. Calculation results are compared with available experimental data and other theoretical data. The functional approximations used for fitting cross sections are outlined and applications of the database are discussed.

Data integration of structured and unstructured sources for assigning clinical codes to patient stays

PubMed Central

Luyckx, Kim; Luyten, Léon; Daelemans, Walter; Van den Bulcke, Tim

2016-01-01

Objective Enormous amounts of healthcare data are becoming increasingly accessible through the large-scale adoption of electronic health records. In this work, structured and unstructured (textual) data are combined to assign clinical diagnostic and procedural codes (specifically ICD-9-CM) to patient stays. We investigate whether integrating these heterogeneous data types improves prediction strength compared to using the data types in isolation. Methods Two separate data integration approaches were evaluated. Early data integration combines features of several sources within a single model, and late data integration learns a separate model per data source and combines these predictions with a meta-learner. This is evaluated on data sources and clinical codes from a broad set of medical specialties. Results When compared with the best individual prediction source, late data integration leads to improvements in predictive power (eg, overall F-measure increased from 30.6% to 38.3% for International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnostic codes), while early data integration is less consistent. The predictive strength strongly differs between medical specialties, both for ICD-9-CM diagnostic and procedural codes. Discussion Structured data provides complementary information to unstructured data (and vice versa) for predicting ICD-9-CM codes. This can be captured most effectively by the proposed late data integration approach. Conclusions We demonstrated that models using multiple electronic health record data sources systematically outperform models using data sources in isolation in the task of predicting ICD-9-CM codes over a broad range of medical specialties. PMID:26316458

MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.

PubMed

Bunk, Boyke; Kucklick, Martin; Jonas, Rochus; Münch, Richard; Schobert, Max; Jahn, Dieter; Hiller, Karsten

2006-12-01

MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual intervention. The integration of a self-acting calibration function allows the parallel and fast calibration for several metabolites simultaneously. Finally, MetaQuant is able to import GC/MS data in the common NetCDF format and to export the results of the quantification into Systems Biology Markup Language (SBML), Comma Separated Values (CSV) or Microsoft Excel (XLS) format. MetaQuant is written in Java and is available under an open source license. Precompiled packages for the installation on Windows or Linux operating systems are freely available for download. The source code as well as the installation packages are available at http://bioinformatics.org/metaquant

Software Attribution for Geoscience Applications in the Computational Infrastructure for Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, L.; Dumit, J.; Fish, A.; Soito, L.; Kellogg, L. H.; Smith, M.

2015-12-01

Scientific software is largely developed by individual scientists and represents a significant intellectual contribution to the field. As the scientific culture and funding agencies move towards an expectation that software be open-source, there is a corresponding need for mechanisms to cite software, both to provide credit and recognition to developers, and to aid in discoverability of software and scientific reproducibility. We assess the geodynamic modeling community's current citation practices by examining more than 300 predominantly self-reported publications utilizing scientific software in the past 5 years that is available through the Computational Infrastructure for Geodynamics (CIG). Preliminary results indicate that authors cite and attribute software either through citing (in rank order) peer-reviewed scientific publications, a user's manual, and/or a paper describing the software code. Attributions maybe found directly in the text, in acknowledgements, in figure captions, or in footnotes. What is considered citable varies widely. Citations predominantly lack software version numbers or persistent identifiers to find the software package. Versioning may be implied through reference to a versioned user manual. Authors sometimes report code features used and whether they have modified the code. As an open-source community, CIG requests that researchers contribute their modifications to the repository. However, such modifications may not be contributed back to a repository code branch, decreasing the chances of discoverability and reproducibility. Survey results through CIG's Software Attribution for Geoscience Applications (SAGA) project suggest that lack of knowledge, tools, and workflows to cite codes are barriers to effectively implement the emerging citation norms. Generated on-demand attributions on software landing pages and a prototype extensible plug-in to automatically generate attributions in codes are the first steps towards reproducibility.

GPU-accelerated atmospheric chemical kinetics in the ECHAM/MESSy (EMAC) Earth system model (version 2.52)

NASA Astrophysics Data System (ADS)

Alvanos, Michail; Christoudias, Theodoros

2017-10-01

This paper presents an application of GPU accelerators in Earth system modeling. We focus on atmospheric chemical kinetics, one of the most computationally intensive tasks in climate-chemistry model simulations. We developed a software package that automatically generates CUDA kernels to numerically integrate atmospheric chemical kinetics in the global climate model ECHAM/MESSy Atmospheric Chemistry (EMAC), used to study climate change and air quality scenarios. A source-to-source compiler outputs a CUDA-compatible kernel by parsing the FORTRAN code generated by the Kinetic PreProcessor (KPP) general analysis tool. All Rosenbrock methods that are available in the KPP numerical library are supported.Performance evaluation, using Fermi and Pascal CUDA-enabled GPU accelerators, shows achieved speed-ups of 4. 5 × and 20. 4 × , respectively, of the kernel execution time. A node-to-node real-world production performance comparison shows a 1. 75 × speed-up over the non-accelerated application using the KPP three-stage Rosenbrock solver. We provide a detailed description of the code optimizations used to improve the performance including memory optimizations, control code simplification, and reduction of idle time. The accuracy and correctness of the accelerated implementation are evaluated by comparing to the CPU-only code of the application. The median relative difference is found to be less than 0.000000001 % when comparing the output of the accelerated kernel the CPU-only code.The approach followed, including the computational workload division, and the developed GPU solver code can potentially be used as the basis for hardware acceleration of numerous geoscientific models that rely on KPP for atmospheric chemical kinetics applications.

EPA Office of Water (OW): SDWIS - HUC12 Densities for Public Surface Water and Groundwater Sources

EPA Pesticide Factsheets

Public Water System location points, based on information from the Safe Drinking Water Act Information System (SDWIS/Federal) for a 2010 third quarter (SDWIS_2010Q3) baseline period, were applied to relate system latitude and longitude coordinates (LatLongs) to Watershed Boundary Dataset subwatershed polygons (HUC12s). This HUC12 table can be mapped through setting up appropriate table relationships on the attribute HUC_12 with the HUC12 GIS layer that is part of EPA's Reach Address Database (RAD) Version 3. At the present time, the RAD Version 3 contains HUC12 polygons for the conterminous United States (CONUS), Hawaii, Puerto Rico, and the U.S. Virgin Islands (materials for Alaska or for other territories and dependencies are not available as of February, 2010). The records in this table are based on a special QUERY created by the EPA Office of Ground Water and Drinking Water (OGWDW) from the primary SDWIS/FED information to provide a robust point representation for a PWS system. PWS points are selected based on the following prioritization: 1. If the system has a treatment plant with LatLongs and MAD codes; 2. If the system has a treatment plant with LatLongs but without MAD codes; 3. If the system has a well with LatLongs and MAD codes; 4. If the system has a well with LatLongs but without MAD codes; 5. If the system has an intake with LatLongs and MAD codes; 6. If the system has an intake with LatLongs but without MAD codes; 7. If the system has any source

Python-Assisted MODFLOW Application and Code Development

NASA Astrophysics Data System (ADS)

Langevin, C.

2013-12-01

The U.S. Geological Survey (USGS) has a long history of developing and maintaining free, open-source software for hydrological investigations. The MODFLOW program is one of the most popular hydrologic simulation programs released by the USGS, and it is considered to be the most widely used groundwater flow simulation code. MODFLOW was written using a modular design and a procedural FORTRAN style, which resulted in code that could be understood, modified, and enhanced by many hydrologists. The code is fast, and because it uses standard FORTRAN it can be run on most operating systems. Most MODFLOW users rely on proprietary graphical user interfaces for constructing models and viewing model results. Some recent efforts, however, have focused on construction of MODFLOW models using open-source Python scripts. Customizable Python packages, such as FloPy (https://code.google.com/p/flopy), can be used to generate input files, read simulation results, and visualize results in two and three dimensions. Automating this sequence of steps leads to models that can be reproduced directly from original data and rediscretized in space and time. Python is also being used in the development and testing of new MODFLOW functionality. New packages and numerical formulations can be quickly prototyped and tested first with Python programs before implementation in MODFLOW. This is made possible by the flexible object-oriented design capabilities available in Python, the ability to call FORTRAN code from Python, and the ease with which linear systems of equations can be solved using SciPy, for example. Once new features are added to MODFLOW, Python can then be used to automate comprehensive regression testing and ensure reliability and accuracy of new versions prior to release.

WISE PHOTOMETRY FOR 400 MILLION SDSS SOURCES

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

Lang, Dustin; Hogg, David W.; Schlegel, David J., E-mail: dstndstn@gmail.com

2016-02-15

We present photometry of images from the Wide-Field Infrared Survey Explorer (WISE) of over 400 million sources detected by the Sloan Digital Sky Survey (SDSS). We use a “forced photometry” technique, using measured SDSS source positions, star–galaxy classification, and galaxy profiles to define the sources whose fluxes are to be measured in the WISE images. We perform photometry with The Tractor image modeling code, working on our “unWISE” coaddds and taking account of the WISE point-spread function and a noise model. The result is a measurement of the flux of each SDSS source in each WISE band. Many sources havemore » little flux in the WISE bands, so often the measurements we report are consistent with zero given our uncertainties. However, for many sources we get 3σ or 4σ measurements; these sources would not be reported by the “official” WISE pipeline and will not appear in the WISE catalog, yet they can be highly informative for some scientific questions. In addition, these small-signal measurements can be used in stacking analyses at the catalog level. The forced photometry approach has the advantage that we measure a consistent set of sources between SDSS and WISE, taking advantage of the resolution and depth of the SDSS images to interpret the WISE images; objects that are resolved in SDSS but blended together in WISE still have accurate measurements in our photometry. Our results, and the code used to produce them, are publicly available at http://unwise.me.« less

Entropy-Based Bounds On Redundancies Of Huffman Codes

NASA Technical Reports Server (NTRS)

Smyth, Padhraic J.

1992-01-01

Report presents extension of theory of redundancy of binary prefix code of Huffman type which includes derivation of variety of bounds expressed in terms of entropy of source and size of alphabet. Recent developments yielded bounds on redundancy of Huffman code in terms of probabilities of various components in source alphabet. In practice, redundancies of optimal prefix codes often closer to 0 than to 1.

40 CFR Appendix A to Subpart A of... - Tables

Code of Federal Regulations, 2010 CFR

2010-07-01

... phone number ✓ ✓ (6) FIPS code ✓ ✓ (7) Facility ID codes ✓ ✓ (8) Unit ID code ✓ ✓ (9) Process ID code... for Reporting on Emissions From Nonpoint Sources and Nonroad Mobile Sources, Where Required by 40 CFR... start date ✓ ✓ (3) Inventory end date ✓ ✓ (4) Contact name ✓ ✓ (5) Contact phone number ✓ ✓ (6) FIPS...

SOURCELESS STARTUP. A MACHINE CODE FOR COMPUTING LOW-SOURCE REACTOR STARTUPS

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

MacMillan, D.B.

1960-06-01

>A revision to the sourceless start-up code is presented. The code solves a system of differential equations encountered in computing the probability distribution of activity at an observed power level during reactor start-up from a very low source level. (J.R.D.)

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2011 CFR

2011-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2012 CFR

2012-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2014 CFR

2014-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2010 CFR

2010-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar data produced for...

Menu-driven cloud computing and resource sharing for R and Bioconductor.

PubMed

Bolouri, Hamid; Dulepet, Rajiv; Angerman, Michael

2011-08-15

We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. hbolouri@fhcrc.org.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

canvasDesigner: A versatile interactive high-resolution scientific multi-panel visualization toolkit.

PubMed

Zhang, Baohong; Zhao, Shanrong; Neuhaus, Isaac

2018-05-03

We present a bioinformatics and systems biology visualization toolkit harmonizing real time interactive exploring and analyzing of big data, full-fledged customizing of look-n-feel, and producing multi-panel publication-ready figures in PDF format simultaneously. Source code and detailed user guides are available at http://canvasxpress.org, https://baohongz.github.io/canvasDesigner, and https://baohongz.github.io/canvasDesigner/demo_video.html. isaac.neuhaus@bms.com, baohong.zhang@pfizer.com, shanrong.zhao@pfizer.com. Supplementary materials are available at https://goo.gl/1uQygs.

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Asai, Kiyoshi; Frith, Martin C

2017-03-15

LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. the source code is freely available at http://last.cbrc.jp/. mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies.

PubMed

Tregouet, D A; Garelle, V

2007-04-15

THESIAS (Testing Haplotype EffectS In Association Studies) is a popular software for carrying haplotype association analysis in unrelated individuals. In addition to the command line interface, a graphical JAVA interface is now proposed allowing one to run THESIAS in a user-friendly manner. Besides, new functionalities have been added to THESIAS including the possibility to analyze polychotomous phenotype and X-linked polymorphisms. The software package including documentation and example data files is freely available at http://genecanvas.ecgene.net. The source codes are also available upon request.

Handling of Atomic Data

NASA Astrophysics Data System (ADS)

Rauch, T.; Deetjen, J. L.

2003-01-01

State-of-the-art NLTE model atmosphere codes have arrived at a high level of ``numerical'' sophistication and are an adequate tool to analyze the available high-quality spectra from the infrared to the X-ray wavelength range. The computational capacities allow the calculation which include all elements from hydrogen up to the iron group and the lack of reliable atomic data has become a crucial problem for further progress. We summarize briefly the available sources of atomic data and how these are implemented in the Tübingen Model Atmosphere Package (TMAP).

LDPC-based iterative joint source-channel decoding for JPEG2000.

PubMed

Pu, Lingling; Wu, Zhenyu; Bilgin, Ali; Marcellin, Michael W; Vasic, Bane

2007-02-01

A framework is proposed for iterative joint source-channel decoding of JPEG2000 codestreams. At the encoder, JPEG2000 is used to perform source coding with certain error-resilience (ER) modes, and LDPC codes are used to perform channel coding. During decoding, the source decoder uses the ER modes to identify corrupt sections of the codestream and provides this information to the channel decoder. Decoding is carried out jointly in an iterative fashion. Experimental results indicate that the proposed method requires fewer iterations and improves overall system performance.

Porting plasma physics simulation codes to modern computing architectures using the libmrc framework

NASA Astrophysics Data System (ADS)

Germaschewski, Kai; Abbott, Stephen

2015-11-01

Available computing power has continued to grow exponentially even after single-core performance satured in the last decade. The increase has since been driven by more parallelism, both using more cores and having more parallelism in each core, e.g. in GPUs and Intel Xeon Phi. Adapting existing plasma physics codes is challenging, in particular as there is no single programming model that covers current and future architectures. We will introduce the open-source libmrc framework that has been used to modularize and port three plasma physics codes: The extended MHD code MRCv3 with implicit time integration and curvilinear grids; the OpenGGCM global magnetosphere model; and the particle-in-cell code PSC. libmrc consolidates basic functionality needed for simulations based on structured grids (I/O, load balancing, time integrators), and also introduces a parallel object model that makes it possible to maintain multiple implementations of computational kernels, on e.g. conventional processors and GPUs. It handles data layout conversions and enables us to port performance-critical parts of a code to a new architecture step-by-step, while the rest of the code can remain unchanged. We will show examples of the performance gains and some physics applications.

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

PubMed

Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

2016-06-15

Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2013 CFR

2013-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... funds; (ii) Studies, analyses, test data, or similar data produced for this contract, when the study...

MDSplus quality improvement project

DOE PAGES

Fredian, Thomas W.; Stillerman, Joshua; Manduchi, Gabriele; ...

2016-05-31

MDSplus is a data acquisition and analysis system used worldwide predominantly in the fusion research community. Development began 29 years ago on the OpenVMS operating system. Since that time there have been many new features added and the code has been ported to many different operating systems. There have been contributions to the MDSplus development from the fusion community in the way of feature suggestions, feature implementations, documentation and porting to different operating systems. The bulk of the development and support of MDSplus, however, has been provided by a relatively small core developer group of three or four members. Givenmore » the size of the development team and the large number of users much more effort was focused on providing new features for the community than on keeping the underlying code and documentation up to date with the evolving software development standards. To ensure that MDSplus will continue to provide the needs of the community in the future, the MDSplus development team along with other members of the MDSplus user community has commenced on a major quality improvement project. The planned improvements include changes to software build scripts to better use GNU Autoconf and Automake tools, refactoring many of the source code modules using new language features available in modern compilers, using GNU MinGW-w64 to create MS Windows distributions, migrating to a more modern source code management system, improvement of source documentation as well as improvements to the www.mdsplus.org web site documentation and layout, and the addition of more comprehensive test suites to apply to MDSplus code builds prior to releasing installation kits to the community. This paper should lead to a much more robust product and establish a framework to maintain stability as more enhancements and features are added. Finally, this paper will describe these efforts that are either in progress or planned for the near future.« less

SolTrace | Concentrating Solar Power | NREL

Science.gov Websites

NREL packaged distribution or from source code at the SolTrace open source project website. NREL Publications Support FAQs SolTrace open source project The code uses Monte-Carlo ray-tracing methodology. The -tracing capabilities. With the release of the SolTrace open source project, the software has adopted

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

PubMed Central

Carter, Hannah; Diekhans, Mark; Ryan, Michael C.; Karchin, Rachel

2011-01-01

Summary: Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. Availability and Implementation: MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM. Contact: karchin@jhu.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21685053

Fostering Team Awareness in Earth System Modeling Communities

NASA Astrophysics Data System (ADS)

Easterbrook, S. M.; Lawson, A.; Strong, S.

2009-12-01

Existing Global Climate Models are typically managed and controlled at a single site, with varied levels of participation by scientists outside the core lab. As these models evolve to encompass a wider set of earth systems, this central control of the modeling effort becomes a bottleneck. But such models cannot evolve to become fully distributed open source projects unless they address the imbalance in the availability of communication channels: scientists at the core site have access to regular face-to-face communication with one another, while those at remote sites have access to only a subset of these conversations - e.g. formally scheduled teleconferences and user meetings. Because of this imbalance, critical decision making can be hidden from many participants, their code contributions can interact in unanticipated ways, and the community loses awareness of who knows what. We have documented some of these problems in a field study at one climate modeling centre, and started to develop tools to overcome these problems. We report on one such tool, TracSNAP, which analyzes the social network of the scientists contributing code to the model by extracting the data in an existing project code repository. The tool presents the results of this analysis to modelers and model users in a number of ways: recommendation for who has expertise on particular code modules, suggestions for code sections that are related to files being worked on, and visualizations of team communication patterns. The tool is currently available as a plugin for the Trac bug tracking system.

nRC: non-coding RNA Classifier based on structural features.

PubMed

Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

2017-01-01

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

BioBlend: automating pipeline analyses within Galaxy and CloudMan.

PubMed

Sloggett, Clare; Goonasekera, Nuwan; Afgan, Enis

2013-07-01

We present BioBlend, a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs. BioBlend makes it easy for bioinformaticians to automate end-to-end large data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provide the required infrastructure and automate complex analyses over large datasets within the familiar Galaxy environment. http://bioblend.readthedocs.org/. Automated installation of BioBlend is available via PyPI (e.g. pip install bioblend). Alternatively, the source code is available from the GitHub repository (https://github.com/afgane/bioblend) under the MIT open source license. The library has been tested and is working on Linux, Macintosh and Windows-based systems.

Web-based network analysis and visualization using CellMaps.

PubMed

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-10-01

: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps The client is implemented in JavaScript and the server in C and Java. jdopazo@cipf.es Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

PyPanda: a Python package for gene regulatory network reconstruction.

PubMed

van IJzendoorn, David G P; Glass, Kimberly; Quackenbush, John; Kuijjer, Marieke L

2016-11-01

PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of 'omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis. The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda CONTACT: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl. © The Author 2016. Published by Oxford University Press.

Pharmer: efficient and exact pharmacophore search.

PubMed

Koes, David Ryan; Camacho, Carlos J

2011-06-27

Pharmacophore search is a key component of many drug discovery efforts. Pharmer is a new computational approach to pharmacophore search that scales with the breadth and complexity of the query, not the size of the compound library being screened. Two novel methods for organizing pharmacophore data, the Pharmer KDB-tree and Bloom fingerprints, enable Pharmer to perform an exact pharmacophore search of almost two million structures in less than a minute. In general, Pharmer is more than an order of magnitude faster than existing technologies. The complete source code is available under an open-source license at http://pharmer.sourceforge.net .

Neutrons Flux Distributions of the Pu-Be Source and its Simulation by the MCNP-4B Code

NASA Astrophysics Data System (ADS)

Faghihi, F.; Mehdizadeh, S.; Hadad, K.

Neutron Fluence rate of a low intense Pu-Be source is measured by Neutron Activation Analysis (NAA) of 197Au foils. Also, the neutron fluence rate distribution versus energy is calculated using the MCNP-4B code based on ENDF/B-V library. Theoretical simulation as well as our experimental performance are a new experience for Iranians to make reliability with the code for further researches. In our theoretical investigation, an isotropic Pu-Be source with cylindrical volume distribution is simulated and relative neutron fluence rate versus energy is calculated using MCNP-4B code. Variation of the fast and also thermal neutrons fluence rate, which are measured by NAA method and MCNP code, are compared.

Two-terminal video coding.

PubMed

Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

2009-03-01

Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

Comparison of TG-43 dosimetric parameters of brachytherapy sources obtained by three different versions of MCNP codes.

PubMed

Zaker, Neda; Zehtabian, Mehdi; Sina, Sedigheh; Koontz, Craig; Meigooni, Ali S

2016-03-08

Monte Carlo simulations are widely used for calculation of the dosimetric parameters of brachytherapy sources. MCNP4C2, MCNP5, MCNPX, EGS4, EGSnrc, PTRAN, and GEANT4 are among the most commonly used codes in this field. Each of these codes utilizes a cross-sectional library for the purpose of simulating different elements and materials with complex chemical compositions. The accuracies of the final outcomes of these simulations are very sensitive to the accuracies of the cross-sectional libraries. Several investigators have shown that inaccuracies of some of the cross section files have led to errors in 125I and 103Pd parameters. The purpose of this study is to compare the dosimetric parameters of sample brachytherapy sources, calculated with three different versions of the MCNP code - MCNP4C, MCNP5, and MCNPX. In these simulations for each source type, the source and phantom geometries, as well as the number of the photons, were kept identical, thus eliminating the possible uncertainties. The results of these investigations indicate that for low-energy sources such as 125I and 103Pd there are discrepancies in gL(r) values. Discrepancies up to 21.7% and 28% are observed between MCNP4C and other codes at a distance of 6 cm for 103Pd and 10 cm for 125I from the source, respectively. However, for higher energy sources, the discrepancies in gL(r) values are less than 1.1% for 192Ir and less than 1.2% for 137Cs between the three codes.

M2Lite: An Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool.

PubMed

Aiyetan, Paul; Zhang, Bai; Chen, Lily; Zhang, Zhen; Zhang, Hui

2014-04-28

Proteome Discoverer is one of many tools used for protein database search and peptide to spectrum assignment in mass spectrometry-based proteomics. However, the inadequacy of conversion tools makes it challenging to compare and integrate its results to those of other analytical tools. Here we present M2Lite, an open-source, light-weight, easily pluggable and fast conversion tool. M2Lite converts proteome discoverer derived MSF files to the proteomics community defined standard - the mzIdentML file format. M2Lite's source code is available as open-source at https://bitbucket.org/paiyetan/m2lite/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/m2lite/downloads.

AMPA: an automated web server for prediction of protein antimicrobial regions.

PubMed

Torrent, Marc; Di Tommaso, Paolo; Pulido, David; Nogués, M Victòria; Notredame, Cedric; Boix, Ester; Andreu, David

2012-01-01

AMPA is a web application for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptide-based drugs against pathogens. Results are shown in a user-friendly graphical interface and can be downloaded as raw data for later examination. AMPA is freely available on the web at http://tcoffee.crg.cat/apps/ampa. The source code is also available in the web. marc.torrent@upf.edu; david.andreu@upf.edu Supplementary data are available at Bioinformatics online.

The Mystro system: A comprehensive translator toolkit

NASA Technical Reports Server (NTRS)

Collins, W. R.; Noonan, R. E.

1985-01-01

Mystro is a system that facilities the construction of compilers, assemblers, code generators, query interpretors, and similar programs. It provides features to encourage the use of iterative enhancement. Mystro was developed in response to the needs of NASA Langley Research Center (LaRC) and enjoys a number of advantages over similar systems. There are other programs available that can be used in building translators. These typically build parser tables, usually supply the source of a parser and parts of a lexical analyzer, but provide little or no aid for code generation. In general, only the front end of the compiler is addressed. Mystro, on the other hand, emphasizes tools for both ends of a compiler.

MELCOR/CONTAIN LMR Implementation Report - FY16 Progress.

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

Louie, David; Humphries, Larry L.

2016-11-01

This report describes the progress of the CONTAIN - LMR sodium physics and chemistry models to be implemented in MELCOR 2.1. In the past three years , the implementation included the addition of sodium equations of state and sodium properties from two different sources. The first source is based on the previous work done by Idaho National Laboratory by modifying MELCOR to include liquid lithium equation of state as a working fluid to model the nuclear fusion safety research. The second source uses properties generated for the SIMMER code. The implemented modeling has been tested and results are reported inmore » this document. In addition, the CONTAIN - LMR code was derived from an early version of the CONTAIN code, and many physical models that were developed since this early version of CONTAIN are not available in this early code version. Therefore, CONTAIN 2 has been updated with the sodium models in CONTAIN - LMR as CONTAIN2 - LMR, which may be used to provide code-to-code comparison with CONTAIN - LMR and MELCOR when the sodium chemistry models from CONTAIN - LMR have been completed. Both the spray fire and pool fire chemistry routines from CONTAIN - LMR have been integrated into MELCOR 2.1, and debugging and testing are in progress. Because MELCOR only models the equation of state for liquid and gas phases of the coolant, a modeling gap still exists when dealing with experiments or accident conditions that take place when the ambient temperature is below the freezing point of sodium. An alternative method is under investigation to overcome this gap . We are no longer working on the separate branch from the main branch of MELCOR 2.1 since the major modeling of MELCOR 2.1 has been completed. At the current stage, the newly implemented sodium chemistry models will be a part of the main MELCOR release version (MELCOR 2.2). This report will discuss the accomplishments and issues relating to the implementation. Also, we will report on the planned completion of all remaining tasks in the upcoming FY2017, including the atmospheric chemistry model and sodium - concrete interaction model implementation .« less

Mitigation of Earth-asteroid collisions via explosive, intense radiation sources

NASA Astrophysics Data System (ADS)

Miles, Aaron; Sanders, James

2005-10-01

The Universe is continually producing astrophysical explosions that generate intense bursts of electromagnetic and particle radiation. Interaction of this radiation with nearby objects can effect significant changes to their dynamics through a variety of processes including ionization, ablation, and shock generation. The next time a large asteroid or comet is found to be approaching the Earth on an impact trajectory, humans may find it prudent to mimic nature by using the most intense radiation sources available to alter the incoming object's trajectory and avert a catastrophic collision. With this in mind, we consider the effect of nuclear explosives on nearby would-be Earth impactors. Neutrons and x-rays produced in the explosion are deposited in a thin layer of the asteroid's surface, resulting in ablation and shock and thereby imparting a deflection velocity. A Monte Carlo code is used for radiation transport and energy deposition, while the subsequent dynamic evolution of the asteroid is followed with the hydrodynamics code CALE. We consider the dependence of the deflection velocity on the source energy and spectrum, the asteroid or comet composition, and the standoff distance between the target and the source. This work was performed under the auspices of the U. S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

Language-Agnostic Reproducible Data Analysis Using Literate Programming.

PubMed

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir.

Language-Agnostic Reproducible Data Analysis Using Literate Programming

PubMed Central

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir. PMID:27711123

A Flexible Cosmic Ultraviolet Background Model

NASA Astrophysics Data System (ADS)

McQuinn, Matthew

2016-10-01

HST studies of the IGM, of the CGM, and of reionization-era galaxies are all aided by ionizing background models, which are a critical input in modeling the ionization state of diffuse, 10^4 K gas. The ionization state in turn enables the determination of densities and sizes of absorbing clouds and, when applied to the Ly-a forest, the global ionizing emissivity of sources. Unfortunately, studies that use these background models have no way of gauging the amount of uncertainty in the adopted model other than to recompute their results using previous background models with outdated observational inputs. As of yet there has been no systematic study of uncertainties in the background model and there unfortunately is no publicly available ultraviolet background code. A public code would enable users to update the calculation with the latest observational constraints, and it would allow users to experiment with varying the background model's assumptions regarding emissions and absorptions. We propose to develop a publicly available ionizing background code and, as an initial application, quantify the level of uncertainty in the ionizing background spectrum across cosmic time. As the background model improves, so does our understanding of (1) the sources that dominate ionizing emissions across cosmic time and (2) the properties of diffuse gas in the circumgalactic medium, the WHIM, and the Ly-a forest. HST is the primary telescope for studying both the highest redshift galaxies and low-redshift diffuse gas. The proposed program would benefit HST studies of the Universe at z 0 all the way up to z = 10, including of high-z galaxies observed in the HST Frontier Fields.

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples.

PubMed

Yu, Hua; Jiao, Bingke; Lu, Lu; Wang, Pengfei; Chen, Shuangcheng; Liang, Chengzhi; Liu, Wei

2018-01-01

Accurately reconstructing gene co-expression network is of great importance for uncovering the genetic architecture underlying complex and various phenotypes. The recent availability of high-throughput RNA-seq sequencing has made genome-wide detecting and quantifying of the novel, rare and low-abundance transcripts practical. However, its potential merits in reconstructing gene co-expression network have still not been well explored. Using massive-scale RNA-seq samples, we have designed an ensemble pipeline, called NetMiner, for building genome-scale and high-quality Gene Co-expression Network (GCN) by integrating three frequently used inference algorithms. We constructed a RNA-seq-based GCN in one species of monocot rice. The quality of network obtained by our method was verified and evaluated by the curated gene functional association data sets, which obviously outperformed each single method. In addition, the powerful capability of network for associating genes with functions and agronomic traits was shown by enrichment analysis and case studies. In particular, we demonstrated the potential value of our proposed method to predict the biological roles of unknown protein-coding genes, long non-coding RNA (lncRNA) genes and circular RNA (circRNA) genes. Our results provided a valuable and highly reliable data source to select key candidate genes for subsequent experimental validation. To facilitate identification of novel genes regulating important biological processes and phenotypes in other plants or animals, we have published the source code of NetMiner, making it freely available at https://github.com/czllab/NetMiner.

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.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering.

PubMed

Nuñez, Isaac; Matute, Tamara; Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy; Federici, Fernán

2017-01-01

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

PubMed Central

Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy

2017-01-01

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses. PMID:29140977

McSKY: A hybrid Monte-Carlo lime-beam code for shielded gamma skyshine calculations

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

Shultis, J.K.; Faw, R.E.; Stedry, M.H.

1994-07-01

McSKY evaluates skyshine dose from an isotropic, monoenergetic, point photon source collimated into either a vertical cone or a vertical structure with an N-sided polygon cross section. The code assumes an overhead shield of two materials, through the user can specify zero shield thickness for an unshielded calculation. The code uses a Monte-Carlo algorithm to evaluate transport through source shields and the integral line source to describe photon transport through the atmosphere. The source energy must be between 0.02 and 100 MeV. For heavily shielded sources with energies above 20 MeV, McSKY results must be used cautiously, especially at detectormore » locations near the source.« less

Joint design of QC-LDPC codes for coded cooperation system with joint iterative decoding

NASA Astrophysics Data System (ADS)

Zhang, Shunwai; Yang, Fengfan; Tang, Lei; Ejaz, Saqib; Luo, Lin; Maharaj, B. T.

2016-03-01

In this paper, we investigate joint design of quasi-cyclic low-density-parity-check (QC-LDPC) codes for coded cooperation system with joint iterative decoding in the destination. First, QC-LDPC codes based on the base matrix and exponent matrix are introduced, and then we describe two types of girth-4 cycles in QC-LDPC codes employed by the source and relay. In the equivalent parity-check matrix corresponding to the jointly designed QC-LDPC codes employed by the source and relay, all girth-4 cycles including both type I and type II are cancelled. Theoretical analysis and numerical simulations show that the jointly designed QC-LDPC coded cooperation well combines cooperation gain and channel coding gain, and outperforms the coded non-cooperation under the same conditions. Furthermore, the bit error rate performance of the coded cooperation employing jointly designed QC-LDPC codes is better than those of random LDPC codes and separately designed QC-LDPC codes over AWGN channels.

Performance and Architecture Lab Modeling Tool

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

2014-06-19

Analytical application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult. Furthermore, models are frequently expressed in forms that are hard to distribute and validate. The Performance and Architecture Lab Modeling tool, or Palm, is a modeling tool designed to make application modeling easier. Palm provides a source code modeling annotation language. Not only does the modeling language divide the modeling task into sub problems, it formally links an application's source code with its model. This link is important because a model's purpose is to capture application behavior. Furthermore, this linkmore » makes it possible to define rules for generating models according to source code organization. Palm generates hierarchical models according to well-defined rules. Given an application, a set of annotations, and a representative execution environment, Palm will generate the same model. A generated model is a an executable program whose constituent parts directly correspond to the modeled application. Palm generates models by combining top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. A model's hierarchy is defined by static and dynamic source code structure. Because Palm coordinates models and source code, Palm's models are 'first-class' and reproducible. Palm automates common modeling tasks. For instance, Palm incorporates measurements to focus attention, represent constant behavior, and validate models. Palm's workflow is as follows. The workflow's input is source code annotated with Palm modeling annotations. The most important annotation models an instance of a block of code. Given annotated source code, the Palm Compiler produces executables and the Palm Monitor collects a representative performance profile. The Palm Generator synthesizes a model based on the static and dynamic mapping of annotations to program behavior. The model -- an executable program -- is a hierarchical composition of annotation functions, synthesized functions, statistics for runtime values, and performance measurements.« less

Chromaticity calculations and code comparisons for x-ray lithography source XLS and SXLS rings

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

Parsa, Z.

1988-06-16

This note presents the chromaticity calculations and code comparison results for the (x-ray lithography source) XLS (Chasman Green, XUV Cosy lattice) and (2 magnet 4T) SXLS lattices, with the standard beam optic codes, including programs SYNCH88.5, MAD6, PATRICIA88.4, PATPET88.2, DIMAD, BETA, and MARYLIE. This analysis is a part of our ongoing accelerator physics code studies. 4 figs., 10 tabs.

The Astrophysics Source Code Library: Where Do We Go from Here?

NASA Astrophysics Data System (ADS)

Allen, A.; Berriman, B.; DuPrie, K.; Hanisch, R. J.; Mink, J.; Nemiroff, R. J.; Shamir, L.; Shortridge, K.; Taylor, M. B.; Teuben, P.; Wallen, J.

2014-05-01

The Astrophysics Source Code Library1, started in 1999, has in the past three years grown from a repository for 40 codes to a registry of over 700 codes that are now indexed by ADS. What comes next? We examine the future of the , the challenges facing it, the rationale behind its practices, and the need to balance what we might do with what we have the resources to accomplish.

Evaluating Open-Source Full-Text Search Engines for Matching ICD-10 Codes.

PubMed

Jurcău, Daniel-Alexandru; Stoicu-Tivadar, Vasile

2016-01-01

This research presents the results of evaluating multiple free, open-source engines on matching ICD-10 diagnostic codes via full-text searches. The study investigates what it takes to get an accurate match when searching for a specific diagnostic code. For each code the evaluation starts by extracting the words that make up its text and continues with building full-text search queries from the combinations of these words. The queries are then run against all the ICD-10 codes until a match indicates the code in question as a match with the highest relative score. This method identifies the minimum number of words that must be provided in order for the search engines choose the desired entry. The engines analyzed include a popular Java-based full-text search engine, a lightweight engine written in JavaScript which can even execute on the user's browser, and two popular open-source relational database management systems.

Fisher Matrix Preloaded — FISHER4CAST

NASA Astrophysics Data System (ADS)

Bassett, Bruce A.; Fantaye, Yabebal; Hlozek, Renée; Kotze, Jacques

The Fisher Matrix is the backbone of modern cosmological forecasting. We describe the Fisher4Cast software: A general-purpose, easy-to-use, Fisher Matrix framework. It is open source, rigorously designed and tested and includes a Graphical User Interface (GUI) with automated LATEX file creation capability and point-and-click Fisher ellipse generation. Fisher4Cast was designed for ease of extension and, although written in Matlab, is easily portable to open-source alternatives such as Octave and Scilab. Here we use Fisher4Cast to present new 3D and 4D visualizations of the forecasting landscape and to investigate the effects of growth and curvature on future cosmological surveys. Early releases have been available at since mid-2008. The current release of the code is Version 2.2 which is described here. For ease of reference a Quick Start guide and the code used to produce the figures in this paper are included, in the hope that it will be useful to the cosmology and wider scientific communities.

PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

NASA Astrophysics Data System (ADS)

Sibaev, Marat; Crittenden, Deborah L.

2016-06-01

The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

Suite of Benchmark Tests to Conduct Mesh-Convergence Analysis of Nonlinear and Non-constant Coefficient Transport Codes

NASA Astrophysics Data System (ADS)

Zamani, K.; Bombardelli, F. A.

2014-12-01

Verification of geophysics codes is imperative to avoid serious academic as well as practical consequences. In case that access to any given source code is not possible, the Method of Manufactured Solution (MMS) cannot be employed in code verification. In contrast, employing the Method of Exact Solution (MES) has several practical advantages. In this research, we first provide four new one-dimensional analytical solutions designed for code verification; these solutions are able to uncover the particular imperfections of the Advection-diffusion-reaction equation, such as nonlinear advection, diffusion or source terms, as well as non-constant coefficient equations. After that, we provide a solution of Burgers' equation in a novel setup. Proposed solutions satisfy the continuity of mass for the ambient flow, which is a crucial factor for coupled hydrodynamics-transport solvers. Then, we use the derived analytical solutions for code verification. To clarify gray-literature issues in the verification of transport codes, we designed a comprehensive test suite to uncover any imperfection in transport solvers via a hierarchical increase in the level of tests' complexity. The test suite includes hundreds of unit tests and system tests to check vis-a-vis the portions of the code. Examples for checking the suite start by testing a simple case of unidirectional advection; then, bidirectional advection and tidal flow and build up to nonlinear cases. We design tests to check nonlinearity in velocity, dispersivity and reactions. The concealing effect of scales (Peclet and Damkohler numbers) on the mesh-convergence study and appropriate remedies are also discussed. For the cases in which the appropriate benchmarks for mesh convergence study are not available, we utilize symmetry. Auxiliary subroutines for automation of the test suite and report generation are designed. All in all, the test package is not only a robust tool for code verification but it also provides comprehensive insight on the ADR solvers capabilities. Such information is essential for any rigorous computational modeling of ADR equation for surface/subsurface pollution transport. We also convey our experiences in finding several errors which were not detectable with routine verification techniques.

FracPaQ: A MATLAB™ toolbox for the quantification of fracture patterns

NASA Astrophysics Data System (ADS)

Healy, David; Rizzo, Roberto E.; Cornwell, David G.; Farrell, Natalie J. C.; Watkins, Hannah; Timms, Nick E.; Gomez-Rivas, Enrique; Smith, Michael

2017-02-01

The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, and spatial distributions often exhibit some kind of order. In detail, relationships may exist among the different fracture attributes, e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture attributes and patterns. This paper describes FracPaQ, a new open source, cross-platform toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on previously published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity. An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales, rock types and tectonic settings. The implemented methods presented are inherently scale independent, and a key task where applicable is analysing and integrating quantitative fracture pattern data from micro-to macro-scales. The toolbox was developed in MATLAB™ and the source code is publicly available on GitHub™ and the Mathworks™ FileExchange. The code runs on any computer with MATLAB installed, including PCs with Microsoft Windows, Apple Macs with Mac OS X, and machines running different flavours of Linux. The application, source code and sample input files are available in open repositories in the hope that other developers and researchers will optimise and extend the functionality for the benefit of the wider community.

Methods for Coding Tobacco-Related Twitter Data: A Systematic Review

PubMed Central

Unger, Jennifer B; Cruz, Tess Boley; Chu, Kar-Hai

2017-01-01

Background As Twitter has grown in popularity to 313 million monthly active users, researchers have increasingly been using it as a data source for tobacco-related research. Objective The objective of this systematic review was to assess the methodological approaches of categorically coded tobacco Twitter data and make recommendations for future studies. Methods Data sources included PsycINFO, Web of Science, PubMed, ABI/INFORM, Communication Source, and Tobacco Regulatory Science. Searches were limited to peer-reviewed journals and conference proceedings in English from January 2006 to July 2016. The initial search identified 274 articles using a Twitter keyword and a tobacco keyword. One coder reviewed all abstracts and identified 27 articles that met the following inclusion criteria: (1) original research, (2) focused on tobacco or a tobacco product, (3) analyzed Twitter data, and (4) coded Twitter data categorically. One coder extracted data collection and coding methods. Results E-cigarettes were the most common type of Twitter data analyzed, followed by specific tobacco campaigns. The most prevalent data sources were Gnip and Twitter’s Streaming application programming interface (API). The primary methods of coding were hand-coding and machine learning. The studies predominantly coded for relevance, sentiment, theme, user or account, and location of user. Conclusions Standards for data collection and coding should be developed to be able to more easily compare and replicate tobacco-related Twitter results. Additional recommendations include the following: sample Twitter’s databases multiple times, make a distinction between message attitude and emotional tone for sentiment, code images and URLs, and analyze user profiles. Being relatively novel and widely used among adolescents and black and Hispanic individuals, Twitter could provide a rich source of tobacco surveillance data among vulnerable populations. PMID:28363883

A joint source-channel distortion model for JPEG compressed images.

PubMed

Sabir, Muhammad F; Sheikh, Hamid Rahim; Heath, Robert W; Bovik, Alan C

2006-06-01

The need for efficient joint source-channel coding (JSCC) is growing as new multimedia services are introduced in commercial wireless communication systems. An important component of practical JSCC schemes is a distortion model that can predict the quality of compressed digital multimedia such as images and videos. The usual approach in the JSCC literature for quantifying the distortion due to quantization and channel errors is to estimate it for each image using the statistics of the image for a given signal-to-noise ratio (SNR). This is not an efficient approach in the design of real-time systems because of the computational complexity. A more useful and practical approach would be to design JSCC techniques that minimize average distortion for a large set of images based on some distortion model rather than carrying out per-image optimizations. However, models for estimating average distortion due to quantization and channel bit errors in a combined fashion for a large set of images are not available for practical image or video coding standards employing entropy coding and differential coding. This paper presents a statistical model for estimating the distortion introduced in progressive JPEG compressed images due to quantization and channel bit errors in a joint manner. Statistical modeling of important compression techniques such as Huffman coding, differential pulse-coding modulation, and run-length coding are included in the model. Examples show that the distortion in terms of peak signal-to-noise ratio (PSNR) can be predicted within a 2-dB maximum error over a variety of compression ratios and bit-error rates. To illustrate the utility of the proposed model, we present an unequal power allocation scheme as a simple application of our model. Results show that it gives a PSNR gain of around 6.5 dB at low SNRs, as compared to equal power allocation.

Computerized Workstation for Tsunami Hazard Monitoring

NASA Astrophysics Data System (ADS)

Lavrentiev-Jr, Mikhail; Marchuk, Andrey; Romanenko, Alexey; Simonov, Konstantin; Titov, Vasiliy

2010-05-01

We present general structure and functionality of the proposed Computerized Workstation for Tsunami Hazard Monitoring (CWTHM). The tool allows interactive monitoring of hazard, tsunami risk assessment, and mitigation - at all stages, from the period of strong tsunamigenic earthquake preparation to inundation of the defended coastal areas. CWTHM is a software-hardware complex with a set of software applications, optimized to achieve best performance on hardware platforms in use. The complex is calibrated for selected tsunami source zone(s) and coastal zone(s) to be defended. The number of zones (both source and coastal) is determined, or restricted, by available hardware resources. The presented complex performs monitoring of selected tsunami source zone via the Internet. The authors developed original algorithms, which enable detection of the preparation zone of the strong underwater earthquake automatically. For the so-determined zone the event time, magnitude and spatial location of tsunami source are evaluated by means of energy of the seismic precursors (foreshocks) analysis. All the above parameters are updated after each foreshock. Once preparing event is detected, several scenarios are forecasted for wave amplitude parameters as well as the inundation zone. Estimations include the lowest and the highest wave amplitudes and the least and the most inundation zone. In addition to that, the most probable case is calculated. In case of multiple defended coastal zones, forecasts and estimates can be done in parallel. Each time the simulated model wave reaches deep ocean buoys or tidal gauge, expected values of wave parameters and inundation zones are updated with historical events information and pre-calculated scenarios. The Method of Splitting Tsunami (MOST) software package is used for mathematical simulation. The authors suggest code acceleration for deep water wave propagation. As a result, performance is 15 times faster compared to MOST, original version. Performance gain is achieved by compiler options, use of optimized libraries, and advantages of OpenMP parallel technology. Moreover, it is possible to achieve 100 times code acceleration by using modern Graphics Processing Units (GPU). Parallel evaluation of inundation zones for multiple coastal zones is also available. All computer codes can be easily assembled under MS Windows and Unix OS family. Although software is virtually platform independent, the most performance gain is achieved while using the recommended hardware components. When the seismic event occurs, all valuable parameters are updated with seismic data and wave propagation monitoring is enabled. As soon as the wave passes each deep ocean tsunameter, parameters of the initial displacement at source are updated from direct calculations based on original algorithms. For better source reconstruction, a combination of two methods is used: optimal unit source linear combination from preliminary calculated database and direct numerical inversion along the wave ray between real source and particular measurement buoys. Specific dissipation parameter along with the wave ray is also taken into account. During the entire wave propagation process the expected wave parameters and inundation zone(s) characteristics are updated with all available information. If recommended hardware components are used, monitoring results are available in real time. The suggested version of CWTHM has been tested by analyzing seismic precursors (foreshocks) and the measured tsunami waves at North Pacific for the Central Kuril's tsunamigenic earthquake of November 15, 2006.

Performance of Compiler-Assisted Memory Safety Checking

DTIC Science & Technology

2014-08-01

software developer has in mind a particular object to which the pointer should point, the intended referent. A memory access error occurs when an ac...Performance of Compiler-Assisted Memory Safety Checking David Keaton Robert C. Seacord August 2014 TECHNICAL NOTE CMU/SEI-2014-TN...based memory safety checking tool and the performance that can be achieved with two such tools whose source code is freely available. The note then

Statistical Characterization of MP3 Encoders for Steganalysis: ’CHAMP3’

DTIC Science & Technology

2004-04-27

compression exceeds those of typical stegano- graphic tools (e. g., LSB image embedding), the availability of commented source codes for MP3 encoders...developed by testing the approach on known and unknown reference data. 15. SUBJECT TERMS EOARD, Steganography , Digital Watermarking...Pages kbps Kilobits per Second LGPL Lesser General Public License LSB Least Significant Bit MB Megabyte MDCT Modified Discrete Cosine Transformation MP3

Application of Modular Building Block Databus to Air Force Systems

DTIC Science & Technology

1988-06-01

City, State, and ZIP Code) Electronic Systems Division, AFSC Hanscom AFB, MA 01731-5000 10. SOURCE OF FUNDING NUMBERS PROGRAM ELEMENT NO...implement remote monitoring and control of the modules. Computer assistance is available for these processes. Cabinets are independent of the shelter...3 fc to the red databus. Located between the two databuses is the computer sup- porting the technical control position (figure 4) as well as

JSC document index

NASA Technical Reports Server (NTRS)

1988-01-01

The Johnson Space Center (JSC) document index is intended to provide a single source listing of all published JSC-numbered documents their authors, and the designated offices of prime responsibility (OPR's) by mail code at the time of publication. The index contains documents which have been received and processed by the JSC Technical Library as of January 13, 1988. Other JSC-numbered documents which are controlled but not available through the JSC Library are also listed.

Social and Political Event Data to Support Army Requirements: Volume 1

DTIC Science & Technology

2017-11-01

available information . Geographic data at the city level is not enough spatial fidelity for tactical-level analyses. Vi- olent Events Socio-Cultural...analyze and/or visualize the data to produce mission-relevant information . Hand-coded datasets can be more precise, but they require added time and labor...Figure 4. Process to transform event data into mission-relevant information . ................... 35 Tables Table 1. Sources of event data

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Baddourah, Majdi; Qin, Jiangning

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigensolution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization search analysis and domain decomposition. The source code for many of these algorithms is available.

Tailoring a software production environment for a large project

NASA Technical Reports Server (NTRS)

Levine, D. R.

1984-01-01

A software production environment was constructed to meet the specific goals of a particular large programming project. These goals, the specific solutions as implemented, and the experiences on a project of over 100,000 lines of source code are discussed. The base development environment for this project was an ordinary PWB Unix (tm) system. Several important aspects of the development process required support not available in the existing tool set.

NucliTrack: an integrated nuclei tracking application

PubMed Central

Cooper, Sam; Barr, Alexis R.; Glen, Robert; Bakal, Chris

2017-01-01

Abstract Summary Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack’s interactive, graphical interface makes it significantly more user friendly. Availability and implementation NucliTrack is available as a free, cross platform application and open source Python package. Installation details and documentation are at: http://nuclitrack.readthedocs.io/en/latest/ A video guide can be viewed online: https://www.youtube.com/watch?v=J6e0D9F-qSU Source code is available through Github: https://github.com/samocooper/nuclitrack. A Matlab toolbox is also available at: https://uk.mathworks.com/matlabcentral/fileexchange/61479-samocooper-nuclitrack-matlab. Contact sam@socooper.com Supplementary information Supplementary data are available at Bioinformatics online. PMID:28637183

Image authentication using distributed source coding.

PubMed

Lin, Yao-Chung; Varodayan, David; Girod, Bernd

2012-01-01

We present a novel approach using distributed source coding for image authentication. The key idea is to provide a Slepian-Wolf encoded quantized image projection as authentication data. This version can be correctly decoded with the help of an authentic image as side information. Distributed source coding provides the desired robustness against legitimate variations while detecting illegitimate modification. The decoder incorporating expectation maximization algorithms can authenticate images which have undergone contrast, brightness, and affine warping adjustments. Our authentication system also offers tampering localization by using the sum-product algorithm.

Aquarius Project: Research in the System Architecture of Accelerators for the High Performance Execution of Logic Programs.

DTIC Science & Technology

1991-05-31

benchmarks ............ .... . .. .. . . .. 220 Appendix G : Source code of the Aquarius Prolog compiler ........ . 224 Chapter I Introduction "You’re given...notation, a tool that is used throughout the compiler’s implementation. Appendix F lists the source code of the C and Prolog benchmarks. Appendix G lists the...source code of the compilcr. 5 "- standard form Prolog / a-sfomadon / head umrvln Convert to tmeikernel Prol g vrans~fonaon 1symbolic execution

Description and availability of the SMARTS spectral model for photovoltaic applications

NASA Astrophysics Data System (ADS)

Myers, Daryl R.; Gueymard, Christian A.

2004-11-01

Limited spectral response range of photocoltaic (PV) devices requires device performance be characterized with respect to widely varying terrestrial solar spectra. The FORTRAN code "Simple Model for Atmospheric Transmission of Sunshine" (SMARTS) was developed for various clear-sky solar renewable energy applications. The model is partly based on parameterizations of transmittance functions in the MODTRAN/LOWTRAN band model family of radiative transfer codes. SMARTS computes spectra with a resolution of 0.5 nanometers (nm) below 400 nm, 1.0 nm from 400 nm to 1700 nm, and 5 nm from 1700 nm to 4000 nm. Fewer than 20 input parameters are required to compute spectral irradiance distributions including spectral direct beam, total, and diffuse hemispherical radiation, and up to 30 other spectral parameters. A spreadsheet-based graphical user interface can be used to simplify the construction of input files for the model. The model is the basis for new terrestrial reference spectra developed by the American Society for Testing and Materials (ASTM) for photovoltaic and materials degradation applications. We describe the model accuracy, functionality, and the availability of source and executable code. Applications to PV rating and efficiency and the combined effects of spectral selectivity and varying atmospheric conditions are briefly discussed.

ITS version 5.0 : the integrated TIGER series of coupled electron/photon Monte Carlo transport codes.

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

Franke, Brian Claude; Kensek, Ronald Patrick; Laub, Thomas William

ITS is a powerful and user-friendly software package permitting state of the art Monte Carlo solution of linear time-independent couple electron/photon radiation transport problems, with or without the presence of macroscopic electric and magnetic fields of arbitrary spatial dependence. Our goal has been to simultaneously maximize operational simplicity and physical accuracy. Through a set of preprocessor directives, the user selects one of the many ITS codes. The ease with which the makefile system is applied combines with an input scheme based on order-independent descriptive keywords that makes maximum use of defaults and internal error checking to provide experimentalists and theoristsmore » alike with a method for the routine but rigorous solution of sophisticated radiation transport problems. Physical rigor is provided by employing accurate cross sections, sampling distributions, and physical models for describing the production and transport of the electron/photon cascade from 1.0 GeV down to 1.0 keV. The availability of source code permits the more sophisticated user to tailor the codes to specific applications and to extend the capabilities of the codes to more complex applications. Version 5.0, the latest version of ITS, contains (1) improvements to the ITS 3.0 continuous-energy codes, (2)multigroup codes with adjoint transport capabilities, and (3) parallel implementations of all ITS codes. Moreover the general user friendliness of the software has been enhanced through increased internal error checking and improved code portability.« less

User's Guide for RESRAD-OFFSITE

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

Gnanapragasam, E.; Yu, C.

2015-04-01

The RESRAD-OFFSITE code can be used to model the radiological dose or risk to an offsite receptor. This User’s Guide for RESRAD-OFFSITE Version 3.1 is an update of the User’s Guide for RESRAD-OFFSITE Version 2 contained in the Appendix A of the User’s Manual for RESRAD-OFFSITE Version 2 (ANL/EVS/TM/07-1, DOE/HS-0005, NUREG/CR-6937). This user’s guide presents the basic information necessary to use Version 3.1 of the code. It also points to the help file and other documents that provide more detailed information about the inputs, the input forms and features/tools in the code; two of the features (overriding the source termmore » and computing area factors) are discussed in the appendices to this guide. Section 2 describes how to download and install the code and then verify the installation of the code. Section 3 shows ways to navigate through the input screens to simulate various exposure scenarios and to view the results in graphics and text reports. Section 4 has screen shots of each input form in the code and provides basic information about each parameter to increase the user’s understanding of the code. Section 5 outlines the contents of all the text reports and the graphical output. It also describes the commands in the two output viewers. Section 6 deals with the probabilistic and sensitivity analysis tools available in the code. Section 7 details the various ways of obtaining help in the code.« less

Final Report for ALCC Allocation: Predictive Simulation of Complex Flow in Wind Farms

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

Barone, Matthew F.; Ananthan, Shreyas; Churchfield, Matt

This report documents work performed using ALCC computing resources granted under a proposal submitted in February 2016, with the resource allocation period spanning the period July 2016 through June 2017. The award allocation was 10.7 million processor-hours at the National Energy Research Scientific Computing Center. The simulations performed were in support of two projects: the Atmosphere to Electrons (A2e) project, supported by the DOE EERE office; and the Exascale Computing Project (ECP), supported by the DOE Office of Science. The project team for both efforts consists of staff scientists and postdocs from Sandia National Laboratories and the National Renewable Energymore » Laboratory. At the heart of these projects is the open-source computational-fluid-dynamics (CFD) code, Nalu. Nalu solves the low-Mach-number Navier-Stokes equations using an unstructured- grid discretization. Nalu leverages the open-source Trilinos solver library and the Sierra Toolkit (STK) for parallelization and I/O. This report documents baseline computational performance of the Nalu code on problems of direct relevance to the wind plant physics application - namely, Large Eddy Simulation (LES) of an atmospheric boundary layer (ABL) flow and wall-modeled LES of a flow past a static wind turbine rotor blade. Parallel performance of Nalu and its constituent solver routines residing in the Trilinos library has been assessed previously under various campaigns. However, both Nalu and Trilinos have been, and remain, in active development and resources have not been available previously to rigorously track code performance over time. With the initiation of the ECP, it is important to establish and document baseline code performance on the problems of interest. This will allow the project team to identify and target any deficiencies in performance, as well as highlight any performance bottlenecks as we exercise the code on a greater variety of platforms and at larger scales. The current study is rather modest in scale, examining performance on problem sizes of O(100 million) elements and core counts up to 8k cores. This will be expanded as more computational resources become available to the projects.« less

Opening up Architectures of Software-Intensive Systems: A Functional Decomposition to Support System Comprehension

DTIC Science & Technology

2007-10-01

Architecture ................................................................................ 14 Figure 2. Eclipse Java Model...16 Figure 3. Eclipse Java Model at the Source Code Level...24 Figure 9. Java Source Code

Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification.

PubMed

Zhang, Jingpu; Zhang, Zuping; Wang, Zixiang; Liu, Yuting; Deng, Lei

2018-05-15

Long non-coding RNAs (lncRNAs) are an enormous collection of functional non-coding RNAs. Over the past decades, a large number of novel lncRNA genes have been identified. However, most of the lncRNAs remain function uncharacterized at present. Computational approaches provide a new insight to understand the potential functional implications of lncRNAs. Considering that each lncRNA may have multiple functions and a function may be further specialized into sub-functions, here we describe NeuraNetL2GO, a computational ontological function prediction approach for lncRNAs using hierarchical multi-label classification strategy based on multiple neural networks. The neural networks are incrementally trained level by level, each performing the prediction of gene ontology (GO) terms belonging to a given level. In NeuraNetL2GO, we use topological features of the lncRNA similarity network as the input of the neural networks and employ the output results to annotate the lncRNAs. We show that NeuraNetL2GO achieves the best performance and the overall advantage in maximum F-measure and coverage on the manually annotated lncRNA2GO-55 dataset compared to other state-of-the-art methods. The source code and data are available at http://denglab.org/NeuraNetL2GO/. leideng@csu.edu.cn. Supplementary data are available at Bioinformatics online.

Unipro UGENE: a unified bioinformatics toolkit.

PubMed

Okonechnikov, Konstantin; Golosova, Olga; Fursov, Mikhail

2012-04-15

Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http://ugene.unipro.ru/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.

MultiElec: A MATLAB Based Application for MEA Data Analysis.

PubMed

Georgiadis, Vassilis; Stephanou, Anastasis; Townsend, Paul A; Jackson, Thomas R

2015-01-01

We present MultiElec, an open source MATLAB based application for data analysis of microelectrode array (MEA) recordings. MultiElec displays an extremely user-friendly graphic user interface (GUI) that allows the simultaneous display and analysis of voltage traces for 60 electrodes and includes functions for activation-time determination, the production of activation-time heat maps with activation time and isoline display. Furthermore, local conduction velocities are semi-automatically calculated along with their corresponding vector plots. MultiElec allows ad hoc signal suppression, enabling the user to easily and efficiently handle signal artefacts and for incomplete data sets to be analysed. Voltage traces and heat maps can be simply exported for figure production and presentation. In addition, our platform is able to produce 3D videos of signal progression over all 60 electrodes. Functions are controlled entirely by a single GUI with no need for command line input or any understanding of MATLAB code. MultiElec is open source under the terms of the GNU General Public License as published by the Free Software Foundation, version 3. Both the program and source code are available to download from http://www.cancer.manchester.ac.uk/MultiElec/.

Scalable Video Transmission Over Multi-Rate Multiple Access Channels

DTIC Science & Technology

2007-06-01

Rate - compatible punctured convolutional codes (RCPC codes ) and their ap- plications,” IEEE...source encoded using the MPEG-4 video codec. The source encoded bitstream is then channel encoded with Rate Compatible Punctured Convolutional (RCPC...Clark, and J. M. Geist, “ Punctured convolutional codes or rate (n-1)/n and simplified maximum likelihood decoding,” IEEE Transactions on

Comparison of TG‐43 dosimetric parameters of brachytherapy sources obtained by three different versions of MCNP codes

PubMed Central

Zaker, Neda; Sina, Sedigheh; Koontz, Craig; Meigooni1, Ali S.

2016-01-01

Monte Carlo simulations are widely used for calculation of the dosimetric parameters of brachytherapy sources. MCNP4C2, MCNP5, MCNPX, EGS4, EGSnrc, PTRAN, and GEANT4 are among the most commonly used codes in this field. Each of these codes utilizes a cross‐sectional library for the purpose of simulating different elements and materials with complex chemical compositions. The accuracies of the final outcomes of these simulations are very sensitive to the accuracies of the cross‐sectional libraries. Several investigators have shown that inaccuracies of some of the cross section files have led to errors in  125I and  103Pd parameters. The purpose of this study is to compare the dosimetric parameters of sample brachytherapy sources, calculated with three different versions of the MCNP code — MCNP4C, MCNP5, and MCNPX. In these simulations for each source type, the source and phantom geometries, as well as the number of the photons, were kept identical, thus eliminating the possible uncertainties. The results of these investigations indicate that for low‐energy sources such as  125I and  103Pd there are discrepancies in gL(r) values. Discrepancies up to 21.7% and 28% are observed between MCNP4C and other codes at a distance of 6 cm for  103Pd and 10 cm for  125I from the source, respectively. However, for higher energy sources, the discrepancies in gL(r) values are less than 1.1% for  192Ir and less than 1.2% for  137Cs between the three codes. PACS number(s): 87.56.bg PMID:27074460

Coupled Physics Environment (CouPE) library - Design, Implementation, and Release

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

Mahadevan, Vijay S.

Over several years, high fidelity, validated mono-­physics solvers with proven scalability on peta-­scale architectures have been developed independently. Based on a unified component-­based architecture, these existing codes can be coupled with a unified mesh-­data backplane and a flexible coupling-­strategy-­based driver suite to produce a viable tool for analysts. In this report, we present details on the design decisions and developments on CouPE, an acronym that stands for Coupled Physics Environment that orchestrates a coupled physics solver through the interfaces exposed by MOAB array-­based unstructured mesh, both of which are part of SIGMA (Scalable Interfaces for Geometry and Mesh-­Based Applications) toolkit.more » The SIGMA toolkit contains libraries that enable scalable geometry and unstructured mesh creation and handling in a memory and computationally efficient implementation. The CouPE version being prepared for a full open-­source release along with updated documentation will contain several useful examples that will enable users to start developing their applications natively using the native MOAB mesh and couple their models to existing physics applications to analyze and solve real world problems of interest. An integrated multi-­physics simulation capability for the design and analysis of current and future nuclear reactor models is also being investigated as part of the NEAMS RPL, to tightly couple neutron transport, thermal-­hydraulics and structural mechanics physics under the SHARP framework. This report summarizes the efforts that have been invested in CouPE to bring together several existing physics applications namely PROTEUS (neutron transport code), Nek5000 (computational fluid-dynamics code) and Diablo (structural mechanics code). The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The design of CouPE along with motivations that led to implementation choices are also discussed. The first release of the library will be different from the current version of the code that integrates the components in SHARP and explanation on the need for forking the source base will also be provided. Enhancements in the functionality and improved user guides will be available as part of the release. CouPE v0.1 is scheduled for an open-­source release in December 2014 along with SIGMA v1.1 components that provide support for language-agnostic mesh loading, traversal and query interfaces along with scalable solution transfer of fields between different physics codes. The coupling methodology and software interfaces of the library are presented, along with verification studies on two representative fast sodium-­cooled reactor demonstration problems to prove the usability of the CouPE library.« less

General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

The General Mission Analysis Tool (GMAT) is a space trajectory optimization and mission analysis system developed by NASA and private industry in the spirit of the NASA Mission. GMAT contains new technology and is a testbed for future technology development. The goal of the GMAT project is to develop new space trajectory optimization and mission design technology by working inclusively with ordinary people, universities, businesses, and other government organizations, and to share that technology in an open and unhindered way. GMAT is a free and open source software system licensed under the NASA Open Source Agreement: free for anyone to use in development of new mission concepts or to improve current missions, freely available in source code form for enhancement or further technology development.

Coding conventions and principles for a National Land-Change Modeling Framework

USGS Publications Warehouse

Donato, David I.

2017-07-14

This report establishes specific rules for writing computer source code for use with the National Land-Change Modeling Framework (NLCMF). These specific rules consist of conventions and principles for writing code primarily in the C and C++ programming languages. Collectively, these coding conventions and coding principles create an NLCMF programming style. In addition to detailed naming conventions, this report provides general coding conventions and principles intended to facilitate the development of high-performance software implemented with code that is extensible, flexible, and interoperable. Conventions for developing modular code are explained in general terms and also enabled and demonstrated through the appended templates for C++ base source-code and header files. The NLCMF limited-extern approach to module structure, code inclusion, and cross-module access to data is both explained in the text and then illustrated through the module templates. Advice on the use of global variables is provided.

Personalized reminiscence therapy M-health application for patients living with dementia: Innovating using open source code repository.

PubMed

Zhang, Melvyn W B; Ho, Roger C M

2017-01-01

Dementia is known to be an illness which brings forth marked disability amongst the elderly individuals. At times, patients living with dementia do also experience non-cognitive symptoms, and these symptoms include that of hallucinations, delusional beliefs as well as emotional liability, sexualized behaviours and aggression. According to the National Institute of Clinical Excellence (NICE) guidelines, non-pharmacological techniques are typically the first-line option prior to the consideration of adjuvant pharmacological options. Reminiscence and music therapy are thus viable options. Lazar et al. [3] previously performed a systematic review with regards to the utilization of technology to delivery reminiscence based therapy to individuals who are living with dementia and has highlighted that technology does have benefits in the delivery of reminiscence therapy. However, to date, there has been a paucity of M-health innovations in this area. In addition, most of the current innovations are not personalized for each of the person living with Dementia. Prior research has highlighted the utility for open source repository in bioinformatics study. The authors hoped to explain how they managed to tap upon and make use of open source repository in the development of a personalized M-health reminiscence therapy innovation for patients living with dementia. The availability of open source code repository has changed the way healthcare professionals and developers develop smartphone applications today. Conventionally, a long iterative process is needed in the development of native application, mainly because of the need for native programming and coding, especially so if the application needs to have interactive features or features that could be personalized. Such repository enables the rapid and cost effective development of application. Moreover, developers are also able to further innovate, as less time is spend in the iterative process.

ROS Hexapod

NASA Technical Reports Server (NTRS)

Davis, Kirsch; Bankieris, Derek

2016-01-01

As an intern project for NASA Johnson Space Center (JSC), my job was to familiarize myself and operate a Robotics Operating System (ROS). The project outcome converted existing software assets into ROS using nodes, enabling a robotic Hexapod to communicate to be functional and controlled by an existing PlayStation 3 (PS3) controller. Existing control algorithms and current libraries have no ROS capabilities within the Hexapod C++ source code when the internship started, but that has changed throughout my internship. Conversion of C++ codes to ROS enabled existing code to be compatible with ROS, and is now controlled using an existing PS3 controller. Furthermore, my job description was to design ROS messages and script programs that enabled assets to participate in the ROS ecosystem by subscribing and publishing messages. Software programming source code is written in directories using C++. Testing of software assets included compiling code within the Linux environment using a terminal. The terminal ran the code from a directory. Several problems occurred while compiling code and the code would not compile. So modifying code to where C++ can read the source code were made. Once the code was compiled and ran, the code was uploaded to Hexapod and then controlled by a PS3 controller. The project outcome has the Hexapod fully functional and compatible with ROS and operates using the PlayStation 3 controller. In addition, an open source software (IDE) Arduino board will be integrated into the ecosystem with designing circuitry on a breadboard to add additional behavior with push buttons, potentiometers and other simple elements in the electrical circuitry. Other projects with the Arduino will be a GPS module, digital clock that will run off 22 satellites to show accurate real time using a GPS signal and an internal patch antenna to communicate with satellites. In addition, this internship experience has led me to pursue myself to learn coding more efficiently and effectively to write, subscribe and publish my own source code in different programming languages. With some familiarity with software programming, it will enhance my skills in the electrical engineering field. In contrast, my experience here at JSC with the Simulation and Graphics Branch (ER7) has led me to take my coding skill to be more proficient to increase my knowledge in software programming, and also enhancing my skills in ROS. This knowledge will be taken back to my university to implement coding in a school project that will use source coding and ROS to work on the PR2 robot which is controlled by ROS software. My skills learned here will be used to integrate messages to subscribe and publish ROS messages to a PR2 robot. The PR2 robot will be controlled by an existing PS3 controller by changing C++ coding to subscribe and publish messages to ROS. Overall the skills that were obtained here will not be lost, but increased.

Fortran graphics routines for the Macintosh

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

Shore, B.W.

1992-06-01

The Language Systems MPW Fortran is a popular Fortran compiler for the Macintosh. Unfortunately, it does not have any built-in calls to graphics routines (such as are available with Graflib on the NLTSS), so there is no simple way to make x-y plots from calls within Fortran. Instead, a file of data must be created and a commercial plotting routine (such as IGOR or KALEIDAGRAPH) or a spreadsheet with graphics (such as WINGZ) must be applied to post-process the data. The Macintosh does have available many built-in calls (to the Macintosh Toolbox) that allow drawing shapes and lines with quickdraw,more » but these are not designed for plotting functions and are difficult to learn to use. This work outlines some Fortran routines that can be called from LS Fortran to make the necessary calls to the Macintosh toolbox to create simple two-dimensional plots or contour plots. The source code DEMOGRAF.F shows how these routines may be used. DEMOGRAF.F simply demonstrates some Fortran subroutines that can be called with language systems MPW Fortran on the Macintosh to plot arrays of numbers. The subroutines essentially mimic the functionality that has been available at LTSS and NLTSS and UNICOS at LLNL. The graphics primitives are kept in four separate files, each containing several subroutines. The subroutines are compiled and stored in a library file, LIBgraf.o. Makefile is used to link this library to the source code. A discussion is included on requirements for interactive plotting of functions.« less

Development of the FITS tools package for multiple software environments

NASA Technical Reports Server (NTRS)

Pence, W. D.; Blackburn, J. K.

1992-01-01

The HEASARC is developing a package of general purpose software for analyzing data files in FITS format. This paper describes the design philosophy which makes the software both machine-independent (it runs on VAXs, Suns, and DEC-stations) and software environment-independent. Currently the software can be compiled and linked to produce IRAF tasks, or alternatively, the same source code can be used to generate stand-alone tasks using one of two implementations of a user-parameter interface library. The machine independence of the software is achieved by writing the source code in ANSI standard Fortran or C, using the machine-independent FITSIO subroutine interface for all data file I/O, and using a standard user-parameter subroutine interface for all user I/O. The latter interface is based on the Fortran IRAF Parameter File interface developed at STScI. The IRAF tasks are built by linking to the IRAF implementation of this parameter interface library. Two other implementations of this parameter interface library, which have no IRAF dependencies, are now available which can be used to generate stand-alone executable tasks. These stand-alone tasks can simply be executed from the machine operating system prompt either by supplying all the task parameters on the command line or by entering the task name after which the user will be prompted for any required parameters. A first release of this FTOOLS package is now publicly available. The currently available tasks are described, along with instructions on how to obtain a copy of the software.

Runtime Detection of C-Style Errors in UPC Code

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

Pirkelbauer, P; Liao, C; Panas, T

2011-09-29

Unified Parallel C (UPC) extends the C programming language (ISO C 99) with explicit parallel programming support for the partitioned global address space (PGAS), which provides a global memory space with localized partitions to each thread. Like its ancestor C, UPC is a low-level language that emphasizes code efficiency over safety. The absence of dynamic (and static) safety checks allows programmer oversights and software flaws that can be hard to spot. In this paper, we present an extension of a dynamic analysis tool, ROSE-Code Instrumentation and Runtime Monitor (ROSECIRM), for UPC to help programmers find C-style errors involving the globalmore » address space. Built on top of the ROSE source-to-source compiler infrastructure, the tool instruments source files with code that monitors operations and keeps track of changes to the system state. The resulting code is linked to a runtime monitor that observes the program execution and finds software defects. We describe the extensions to ROSE-CIRM that were necessary to support UPC. We discuss complications that arise from parallel code and our solutions. We test ROSE-CIRM against a runtime error detection test suite, and present performance results obtained from running error-free codes. ROSE-CIRM is released as part of the ROSE compiler under a BSD-style open source license.« less

YNOGK: A New Public Code for Calculating Null Geodesics in the Kerr Spacetime

NASA Astrophysics Data System (ADS)

Yang, Xiaolin; Wang, Jiancheng

2013-07-01

Following the work of Dexter & Agol, we present a new public code for the fast calculation of null geodesics in the Kerr spacetime. Using Weierstrass's and Jacobi's elliptic functions, we express all coordinates and affine parameters as analytical and numerical functions of a parameter p, which is an integral value along the geodesic. This is the main difference between our code and previous similar ones. The advantage of this treatment is that the information about the turning points does not need to be specified in advance by the user, and many applications such as imaging, the calculation of line profiles, and the observer-emitter problem, become root-finding problems. All elliptic integrations are computed by Carlson's elliptic integral method as in Dexter & Agol, which guarantees the fast computational speed of our code. The formulae to compute the constants of motion given by Cunningham & Bardeen have been extended, which allow one to readily handle situations in which the emitter or the observer has an arbitrary distance from, and motion state with respect to, the central compact object. The validation of the code has been extensively tested through applications to toy problems from the literature. The source FORTRAN code is freely available for download on our Web site http://www1.ynao.ac.cn/~yangxl/yxl.html.

On transform coding tools under development for VP10

NASA Astrophysics Data System (ADS)

Parker, Sarah; Chen, Yue; Han, Jingning; Liu, Zoe; Mukherjee, Debargha; Su, Hui; Wang, Yongzhe; Bankoski, Jim; Li, Shunyao

2016-09-01

Google started the WebM Project in 2010 to develop open source, royaltyfree video codecs designed specifically for media on the Web. The second generation codec released by the WebM project, VP9, is currently served by YouTube, and enjoys billions of views per day. Realizing the need for even greater compression efficiency to cope with the growing demand for video on the web, the WebM team embarked on an ambitious project to develop a next edition codec, VP10, that achieves at least a generational improvement in coding efficiency over VP9. Starting from VP9, a set of new experimental coding tools have already been added to VP10 to achieve decent coding gains. Subsequently, Google joined a consortium of major tech companies called the Alliance for Open Media to jointly develop a new codec AV1. As a result, the VP10 effort is largely expected to merge with AV1. In this paper, we focus primarily on new tools in VP10 that improve coding of the prediction residue using transform coding techniques. Specifically, we describe tools that increase the flexibility of available transforms, allowing the codec to handle a more diverse range or residue structures. Results are presented on a standard test set.

Task 7: ADPAC User's Manual

NASA Technical Reports Server (NTRS)

Hall, E. J.; Topp, D. A.; Delaney, R. A.

1996-01-01

The overall objective of this study was to develop a 3-D numerical analysis for compressor casing treatment flowfields. The current version of the computer code resulting from this study is referred to as ADPAC (Advanced Ducted Propfan Analysis Codes-Version 7). This report is intended to serve as a computer program user's manual for the ADPAC code developed under Tasks 6 and 7 of the NASA Contract. The ADPAC program is based on a flexible multiple- block grid discretization scheme permitting coupled 2-D/3-D mesh block solutions with application to a wide variety of geometries. Aerodynamic calculations are based on a four-stage Runge-Kutta time-marching finite volume solution technique with added numerical dissipation. Steady flow predictions are accelerated by a multigrid procedure. An iterative implicit algorithm is available for rapid time-dependent flow calculations, and an advanced two equation turbulence model is incorporated to predict complex turbulent flows. The consolidated code generated during this study is capable of executing in either a serial or parallel computing mode from a single source code. Numerous examples are given in the form of test cases to demonstrate the utility of this approach for predicting the aerodynamics of modem turbomachinery configurations.

Multiple-rule bias in the comparison of classification rules

PubMed Central

Yousefi, Mohammadmahdi R.; Hua, Jianping; Dougherty, Edward R.

2011-01-01

Motivation: There is growing discussion in the bioinformatics community concerning overoptimism of reported results. Two approaches contributing to overoptimism in classification are (i) the reporting of results on datasets for which a proposed classification rule performs well and (ii) the comparison of multiple classification rules on a single dataset that purports to show the advantage of a certain rule. Results: This article provides a careful probabilistic analysis of the second issue and the ‘multiple-rule bias’, resulting from choosing a classification rule having minimum estimated error on the dataset. It quantifies this bias corresponding to estimating the expected true error of the classification rule possessing minimum estimated error and it characterizes the bias from estimating the true comparative advantage of the chosen classification rule relative to the others by the estimated comparative advantage on the dataset. The analysis is applied to both synthetic and real data using a number of classification rules and error estimators. Availability: We have implemented in C code the synthetic data distribution model, classification rules, feature selection routines and error estimation methods. The code for multiple-rule analysis is implemented in MATLAB. The source code is available at http://gsp.tamu.edu/Publications/supplementary/yousefi11a/. Supplementary simulation results are also included. Contact: edward@ece.tamu.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21546390

Effect of the diffusion parameters on the observed γ-ray spectrum of sources and their contribution to the local all-electron spectrum: The EDGE code

NASA Astrophysics Data System (ADS)

López-Coto, R.; Hahn, J.; BenZvi, S.; Dingus, B.; Hinton, J.; Nisa, M. U.; Parsons, R. D.; Greus, F. Salesa; Zhang, H.; Zhou, H.

2018-11-01

The positron excess measured by PAMELA and AMS can only be explained if there is one or several sources injecting them. Moreover, at the highest energies, it requires the presence of nearby ( ∼ hundreds of parsecs) and middle age (maximum of ∼ hundreds of kyr) sources. Pulsars, as factories of electrons and positrons, are one of the proposed candidates to explain the origin of this excess. To calculate the contribution of these sources to the electron and positron flux at the Earth, we developed EDGE (Electron Diffusion and Gamma rays to the Earth), a code to treat the propagation of electrons and compute their diffusion from a central source with a flexible injection spectrum. Using this code, we can derive the source's gamma-ray spectrum, spatial extension, the all-electron density in space, the electron and positron flux reaching the Earth and the positron fraction measured at the Earth. We present in this paper the foundations of the code and study how different parameters affect the gamma-ray spectrum of a source and the electron flux measured at the Earth. We also studied the effect of several approximations usually performed in these studies. This code has been used to derive the results of the positron flux measured at the Earth in [1].

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.

PubMed

Pang, Chao; van Enckevort, David; de Haan, Mark; Kelpin, Fleur; Jetten, Jonathan; Hendriksen, Dennis; de Boer, Tommy; Charbon, Bart; Winder, Erwin; van der Velde, K Joeri; Doiron, Dany; Fortier, Isabel; Hillege, Hans; Swertz, Morris A

2016-07-15

While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect : m.a.swertz@rug.nl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

GENPLOT: A formula-based Pascal program for data manipulation and plotting

NASA Astrophysics Data System (ADS)

Kramer, Matthew J.

Geochemical processes involving alteration, differentiation, fractionation, or migration of elements may be elucidated by a number of discrimination or variation diagrams (e.g., AFM, Harker, Pearce, and many others). The construction of these diagrams involves arithmetic combination of selective elements (involving major, minor, or trace elements). GENPLOT utilizes a formula-based algorithm (an expression parser) which enables the program to manipulate multiparameter databases and plot XY, ternary, tetrahedron, and REE type plots without needing to change either the source code or rearranging databases. Formulae may be any quadratic expression whose variables are the column headings of the data matrix. A full-screen editor with limited equations and arithmetic functions (spreadsheet) has been incorporated into the program to aid data entry and editing. Data are stored as ASCII files to facilitate interchange of data between other programs and computers. GENPLOT was developed in Turbo Pascal for the IBM and compatible computers but also is available in Apple Pascal for the Apple Ile and Ill. Because the source code is too extensive to list here (about 5200 lines of Pascal code), the expression parsing routine, which is central to GENPLOT's flexibility is incorporated into a smaller demonstration program named SOLVE. The following paper includes a discussion on how the expression parser works and a detailed description of GENPLOT's capabilities.

A new free and open source tool for space plasma modeling.

NASA Astrophysics Data System (ADS)

Honkonen, I. J.

2014-12-01

I will present a new distributed memory parallel, free and open source computational model for studying space plasma. The model is written in C++ with emphasis on good software development practices and code readability without sacrificing serial or parallel performance. As such the model could be especially useful for education, for learning both (magneto)hydrodynamics (MHD) and computational model development. By using latest features of the C++ standard (2011) it has been possible to develop a very modular program which improves not only the readability of code but also the testability of the model and decreases the effort required to make changes to various parts of the program. Major parts of the model, functionality not directly related to (M)HD, have been outsourced to other freely available libraries which has reduced the development time of the model significantly. I will present an overview of the code architecture as well as details of different parts of the model and will show examples of using the model including preparing input files and plotting results. A multitude of 1-, 2- and 3-dimensional test cases are included in the software distribution and the results of, for example, Kelvin-Helmholtz, bow shock, blast wave and reconnection tests, will be presented.

A System for Information Management in BioMedical Studies—SIMBioMS

PubMed Central

Krestyaninova, Maria; Zarins, Andris; Viksna, Juris; Kurbatova, Natalja; Rucevskis, Peteris; Neogi, Sudeshna Guha; Gostev, Mike; Perheentupa, Teemu; Knuuttila, Juha; Barrett, Amy; Lappalainen, Ilkka; Rung, Johan; Podnieks, Karlis; Sarkans, Ugis; McCarthy, Mark I; Brazma, Alvis

2009-01-01

Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. Availability: The source code, documentation and initialization scripts are available at http://simbioms.org. Contact: support@simbioms.org; mariak@ebi.ac.uk PMID:19633095

Using clinician text notes in electronic medical record data to validate transgender-related diagnosis codes.

PubMed

Blosnich, John R; Cashy, John; Gordon, Adam J; Shipherd, Jillian C; Kauth, Michael R; Brown, George R; Fine, Michael J

2018-04-04

Transgender individuals are vulnerable to negative health risks and outcomes, but research remains limited because data sources, such as electronic medical records (EMRs), lack standardized collection of gender identity information. Most EMR do not include the gold standard of self-identified gender identity, but International Classification of Diseases (ICDs) includes diagnostic codes indicating transgender-related clinical services. However, it is unclear if these codes can indicate transgender status. The objective of this study was to determine the extent to which patients' clinician notes in EMR contained transgender-related terms that could corroborate ICD-coded transgender identity. Data are from the US Department of Veterans Affairs Corporate Data Warehouse. Transgender patients were defined by the presence of ICD9 and ICD10 codes associated with transgender-related clinical services, and a 3:1 comparison group of nontransgender patients was drawn. Patients' clinician text notes were extracted and searched for transgender-related words and phrases. Among 7560 patients defined as transgender based on ICD codes, the search algorithm identified 6753 (89.3%) with transgender-related terms. Among 22 072 patients defined as nontransgender without ICD codes, 246 (1.1%) had transgender-related terms; after review, 11 patients were identified as transgender, suggesting a 0.05% false negative rate. Using ICD-defined transgender status can facilitate health services research when self-identified gender identity data are not available in EMR.

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix.

PubMed

Ambrosini, Giovanna; Groux, Romain; Bucher, Philipp

2018-03-05

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-resident genomes for matches to a user-supplied PWM or TF binding site model from a public database. The web server and source code are available at http://ccg.vital-it.ch/pwmscan and https://sourceforge.net/projects/pwmscan, respectively. giovanna.ambrosini@epfl.ch. SUPPLEMENTARY DATA ARE AVAILABLE AT BIOINFORMATICS ONLINE.

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

PubMed Central

Shankar, Ravi; Parkinson, Helen; Burdett, Tony; Hastings, Emma; Liu, Junmin; Miller, Michael; Srinivasa, Rashmi; White, Joseph; Brazma, Alvis; Sherlock, Gavin; Stoeckert, Christian J.; Ball, Catherine A.

2010-01-01

Summary: Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Availability and Implementation: Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows. Contact: rshankar@stanford.edu PMID:20733062

MetExploreViz: web component for interactive metabolic network visualization.

PubMed

Chazalviel, Maxime; Frainay, Clément; Poupin, Nathalie; Vinson, Florence; Merlet, Benjamin; Gloaguen, Yoann; Cottret, Ludovic; Jourdan, Fabien

2017-09-15

MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyze omics data in a biochemical context. Documentation and link to GIT code repository (GPL 3.0 license)are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc /. Tutorial is available at this URL. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

SCRAM: a pipeline for fast index-free small RNA read alignment and visualization.

PubMed

Fletcher, Stephen J; Boden, Mikael; Mitter, Neena; Carroll, Bernard J

2018-03-15

Small RNAs play key roles in gene regulation, defense against viral pathogens and maintenance of genome stability, though many aspects of their biogenesis and function remain to be elucidated. SCRAM (Small Complementary RNA Mapper) is a novel, simple-to-use short read aligner and visualization suite that enhances exploration of small RNA datasets. The SCRAM pipeline is implemented in Go and Python, and is freely available under MIT license. Source code, multiplatform binaries and a Docker image can be accessed via https://sfletc.github.io/scram/. s.fletcher@uq.edu.au. Supplementary data are available at Bioinformatics online.

Admiralty Inlet Advanced Turbulence Measurements: final data and code archive

DOE Data Explorer

Kilcher, Levi (ORCID:0000000183851131); Thomson, Jim (ORCID:0000000289290088); Harding, Samuel

2011-02-01

Data and code that is not already in a public location that is used in Kilcher, Thomson, Harding, and Nylund (2017) "Turbulence Measurements from Compliant Moorings - Part II: Motion Correction" doi: 10.1175/JTECH-D-16-0213.1. The links point to Python source code used in the publication. All other files are source data used in the publication.

Numerical Electromagnetic Code (NEC)-Basic Scattering Code. Part 2. Code Manual

DTIC Science & Technology

1979-09-01

imaging of source axes for magnetic source. Ax R VSOURC(1,1) + 9 VSOURC(1,2) + T VSOURC(1,3) 4pi = x VIMAG(I,1) + ^ VINAG (1,2)+ VIMAG(l,3) An =unit...VNC A. yt and z components of the end cap unit normal OUTPUT VARIABLE VINAG X.. Y, and z components defining thesource image coordinate system axesin

TOMO3D: 3-D joint refraction and reflection traveltime tomography parallel code for active-source seismic data—synthetic test

NASA Astrophysics Data System (ADS)

Meléndez, A.; Korenaga, J.; Sallarès, V.; Miniussi, A.; Ranero, C. R.

2015-10-01

We present a new 3-D traveltime tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the velocity distribution and the geometry of reflecting boundaries in the subsurface. This code is based on its popular 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The traveltime calculations are done using a hybrid ray-tracing technique combining the graph and bending methods. The LSQR algorithm is used to perform the iterative regularized inversion to improve the initial velocity and depth models. In order to cope with an increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes most of the run time (˜90 per cent in the test presented here), has been parallelized with a combination of multi-processing and message passing interface standards. This parallelization distributes the ray-tracing and traveltime calculations among available computational resources. The code's performance is illustrated with a realistic synthetic example, including a checkerboard anomaly and two reflectors, which simulates the geometry of a subduction zone. The code is designed to invert for a single reflector at a time. A data-driven layer-stripping strategy is proposed for cases involving multiple reflectors, and it is tested for the successive inversion of the two reflectors. Layers are bound by consecutive reflectors, and an initial velocity model for each inversion step incorporates the results from previous steps. This strategy poses simpler inversion problems at each step, allowing the recovery of strong velocity discontinuities that would otherwise be smoothened.

MCNP (Monte Carlo Neutron Photon) capabilities for nuclear well logging calculations

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

Forster, R.A.; Little, R.C.; Briesmeister, J.F.

The Los Alamos Radiation Transport Code System (LARTCS) consists of state-of-the-art Monte Carlo and discrete ordinates transport codes and data libraries. The general-purpose continuous-energy Monte Carlo code MCNP (Monte Carlo Neutron Photon), part of the LARTCS, provides a computational predictive capability for many applications of interest to the nuclear well logging community. The generalized three-dimensional geometry of MCNP is well suited for borehole-tool models. SABRINA, another component of the LARTCS, is a graphics code that can be used to interactively create a complex MCNP geometry. Users can define many source and tally characteristics with standard MCNP features. The time-dependent capabilitymore » of the code is essential when modeling pulsed sources. Problems with neutrons, photons, and electrons as either single particle or coupled particles can be calculated with MCNP. The physics of neutron and photon transport and interactions is modeled in detail using the latest available cross-section data. A rich collections of variance reduction features can greatly increase the efficiency of a calculation. MCNP is written in FORTRAN 77 and has been run on variety of computer systems from scientific workstations to supercomputers. The next production version of MCNP will include features such as continuous-energy electron transport and a multitasking option. Areas of ongoing research of interest to the well logging community include angle biasing, adaptive Monte Carlo, improved discrete ordinates capabilities, and discrete ordinates/Monte Carlo hybrid development. Los Alamos has requested approval by the Department of Energy to create a Radiation Transport Computational Facility under their User Facility Program to increase external interactions with industry, universities, and other government organizations. 21 refs.« less

Cloudy - simulating the non-equilibrium microphysics of gas and dust, and its observed spectrum

NASA Astrophysics Data System (ADS)

Ferland, Gary J.

2014-01-01

Cloudy is an open-source plasma/spectral simulation code, last described in the open-access journal Revista Mexicana (Ferland et al. 2013, 2013RMxAA..49..137F). The project goal is a complete simulation of the microphysics of gas and dust over the full range of density, temperature, and ionization that we encounter in astrophysics, together with a prediction of the observed spectrum. Cloudy is one of the more widely used theory codes in astrophysics with roughly 200 papers citing its documentation each year. It is developed by graduate students, postdocs, and an international network of collaborators. Cloudy is freely available on the web at trac.nublado.org, the user community can post questions on http://groups.yahoo.com/neo/groups/cloudy_simulations/info, and summer schools are organized to learn more about Cloudy and its use (http://cloud9.pa.uky.edu gary/cloudy/CloudySummerSchool/). The code’s widespread use is possible because of extensive automatic testing. It is exercised over its full range of applicability whenever the source is changed. Changes in predicted quantities are automatically detected along with any newly introduced problems. The code is designed to be autonomous and self-aware. It generates a report at the end of a calculation that summarizes any problems encountered along with suggestions of potentially incorrect boundary conditions. This self-monitoring is a core feature since the code is now often used to generate large MPI grids of simulations, making it impossible for a user to verify each calculation by hand. I will describe some challenges in developing a large physics code, with its many interconnected physical processes, many at the frontier of research in atomic or molecular physics, all in an open environment.

Biases in GNSS-Data Processing

NASA Astrophysics Data System (ADS)

Schaer, S. C.; Dach, R.; Lutz, S.; Meindl, M.; Beutler, G.

2010-12-01

Within the Global Positioning System (GPS) traditionally different types of pseudo-range measurements (P-code, C/A-code) are available on the first frequency that are tracked by the receivers with different technologies. For that reason, P1-C1 and P1-P2 Differential Code Biases (DCB) need to be considered in a GPS data processing with a mix of different receiver types. Since the Block IIR-M series of GPS satellites also provide C/A-code on the second frequency, P2-C2 DCB need to be added to the list of biases for maintenance. Potential quarter-cycle biases between different phase observables (specifically L2P and L2C) are another issue. When combining GNSS (currently GPS and GLONASS), careful consideration of inter-system biases (ISB) is indispensable, in particular when an adequate combination of individual GLONASS clock correction results from different sources (using, e.g., different software packages) is intended. Facing the GPS and GLONASS modernization programs and the upcoming GNSS, like the European Galileo and the Chinese Compass, an increasing number of types of biases is expected. The Center for Orbit Determination in Europe (CODE) is monitoring these GPS and GLONASS related biases for a long time based on RINEX files of the tracking network of the International GNSS Service (IGS) and in the frame of the data processing as one of the global analysis centers of the IGS. Within the presentation we give an overview on the stability of the biases based on the monitoring. Biases derived from different sources are compared. Finally, we give an outlook on the potential handling of such biases with the big variety of signals and systems expected in the future.

Benchmarking Heavy Ion Transport Codes FLUKA, HETC-HEDS MARS15, MCNPX, and PHITS

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

Ronningen, Reginald Martin; Remec, Igor; Heilbronn, Lawrence H.

Powerful accelerators such as spallation neutron sources, muon-collider/neutrino facilities, and rare isotope beam facilities must be designed with the consideration that they handle the beam power reliably and safely, and they must be optimized to yield maximum performance relative to their design requirements. The simulation codes used for design purposes must produce reliable results. If not, component and facility designs can become costly, have limited lifetime and usefulness, and could even be unsafe. The objective of this proposal is to assess the performance of the currently available codes PHITS, FLUKA, MARS15, MCNPX, and HETC-HEDS that could be used for designmore » simulations involving heavy ion transport. We plan to access their performance by performing simulations and comparing results against experimental data of benchmark quality. Quantitative knowledge of the biases and the uncertainties of the simulations is essential as this potentially impacts the safe, reliable and cost effective design of any future radioactive ion beam facility. Further benchmarking of heavy-ion transport codes was one of the actions recommended in the Report of the 2003 RIA R&D Workshop".« less

Sequence-based heuristics for faster annotation of non-coding RNA families.

PubMed

Weinberg, Zasha; Ruzzo, Walter L

2006-01-01

Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. The source code is available under GNU Public License at the supplementary web site.

PlotXY: A High Quality Plotting System for the Herschel Interactive Processing Environment (HIPE) and the Astronomical Community

NASA Astrophysics Data System (ADS)

Panuzzo, P.; Li, J.; Caux, E.

2012-09-01

The Herschel Interactive Processing Environment (HIPE) was developed by the European Space Agency (ESA) in collaboration with NASA and the Herschel Instrument Control Centres, to provide the astronomical community a complete environment to process and analyze the data gathered by the Herschel Space Observatory. One of the most important components of HIPE is the plotting system (named PlotXY) that we present here. With PlotXY it is possible to produce easily high quality publication-ready 2D plots. It provides a long list of features, with fully configurable components, and interactive zooming. The entire code of HIPE is written in Java and is open source released under the GNU Lesser General Public License version 3. A new version of PlotXY is being developed to be independent from the HIPE code base; it is available to the software development community for the inclusion in other projects at the URL http://code.google.com/p/jplot2d/.

The Sensitivity of Coded Mask Telescopes

NASA Technical Reports Server (NTRS)

Skinner, Gerald K.

2008-01-01

Simple formulae are often used to estimate the sensitivity of coded mask X-ray or gamma-ray telescopes, but t,hese are strictly only applicable if a number of basic assumptions are met. Complications arise, for example, if a grid structure is used to support the mask elements, if the detector spatial resolution is not good enough to completely resolve all the detail in the shadow of the mask or if any of a number of other simplifying conditions are not fulfilled. We derive more general expressions for the Poisson-noise-limited sensitivity of astronomical telescopes using the coded mask technique, noting explicitly in what circumstances they are applicable. The emphasis is on using nomenclature and techniques that result in simple and revealing results. Where no convenient expression is available a procedure is given which allows the calculation of the sensitivity. We consider certain aspects of the optimisation of the design of a coded mask telescope and show that when the detector spatial resolution and the mask to detector separation are fixed, the best source location accuracy is obtained when the mask elements are equal in size to the detector pixels.

Using Modern C++ Idiom for the Discretisation of Sets of Coupled Transport Equations in Numerical Plasma Physics

NASA Astrophysics Data System (ADS)

van Dijk, Jan; Hartgers, Bart; van der Mullen, Joost

2006-10-01

Self-consistent modelling of plasma sources requires a simultaneous treatment of multiple physical phenomena. As a result plasma codes have a high degree of complexity. And with the growing interest in time-dependent modelling of non-equilibrium plasma in three dimensions, codes tend to become increasingly hard to explain-and-maintain. As a result of these trends there has been an increased interest in the software-engineering and implementation aspects of plasma modelling in our group at Eindhoven University of Technology. In this contribution we will present modern object-oriented techniques in C++ to solve an old problem: that of the discretisation of coupled linear(ized) equations involving multiple field variables on ortho-curvilinear meshes. The `LinSys' code has been tailored to the transport equations that occur in transport physics. The implementation has been made both efficient and user-friendly by using modern idiom like expression templates and template meta-programming. Live demonstrations will be given. The code is available to interested parties; please visit www.dischargemodelling.org.

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

SBEToolbox: A Matlab Toolbox for Biological Network Analysis

PubMed Central

Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J.

2013-01-01

We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases. PMID:24027418

SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

PubMed

Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J

2013-01-01

We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases.

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

Making your code citable with the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; DuPrie, Kimberly; Schmidt, Judy; Berriman, G. Bruce; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

2016-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. With nearly 1,200 codes, it is the largest indexed resource for astronomy codes in existence. Established in 1999, it offers software authors a path to citation of their research codes even without publication of a paper describing the software, and offers scientists a way to find codes used in refereed publications, thus improving the transparency of the research. It also provides a method to quantify the impact of source codes in a fashion similar to the science metrics of journal articles. Citations using ASCL IDs are accepted by major astronomy journals and if formatted properly are tracked by ADS and other indexing services. The number of citations to ASCL entries increased sharply from 110 citations in January 2014 to 456 citations in September 2015. The percentage of code entries in ASCL that were cited at least once rose from 7.5% in January 2014 to 17.4% in September 2015. The ASCL's mid-2014 infrastructure upgrade added an easy entry submission form, more flexible browsing, search capabilities, and an RSS feeder for updates. A Changes/Additions form added this past fall lets authors submit links for papers that use their codes for addition to the ASCL entry even if those papers don't formally cite the codes, thus increasing the transparency of that research and capturing the value of their software to the community.

JACOB: an enterprise framework for computational chemistry.

PubMed

Waller, Mark P; Dresselhaus, Thomas; Yang, Jack

2013-06-15

Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob. Copyright © 2013 Wiley Periodicals, Inc.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Nguyen, D. T.; Baddourah, M. A.; Qin, J.

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigen-solution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization algorithm and domain decomposition. The source code for many of these algorithms is available from NASA Langley.

Generation of Mid-Wave Infrared Signature Using Microradiating Devices for Vehicle Mounted Identification Friend or Foe Applications

DTIC Science & Technology

2009-06-01

M. Harkins Approved for public release; distribution is unlimited THIS PAGE INTENTIONALLY LEFT BLANK i REPORT DOCUMENTATION PAGE Form Approved...12a. DISTRIBUTION / AVAILABILITY STATEMENT Approved for public release; distribution is unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200...The integration of a MWIR signature into VMIFF will add a daytime capability. A new generation of compact MWIR sources is emerging to meet demands

STARL -- a Program to Correct CCD Image Defects

NASA Astrophysics Data System (ADS)

Narbutis, D.; Vanagas, R.; Vansevičius, V.

We present a program tool, STARL, designed for automatic detection and correction of various defects in CCD images. It uses genetic algorithm for deblending and restoring of overlapping saturated stars in crowded stellar fields. Using Subaru Telescope Suprime-Cam images we demonstrate that the program can be implemented in the wide-field survey data processing pipelines for production of high quality color mosaics. The source code and examples are available at the STARL website.

A Synopsis of Marine Animal Underwater Sounds in Eight Geographic Areas

DTIC Science & Technology

1971-05-28

MAMMALS (1) HIGHEST PROBABILITY Delphinapterus leucas - In Apr.-June they move up Kola River. Present all months except July) Aug, Sept...its vocali- zations are available from Dr. W. C. Cummings, NUC Code 5054. : ii V, , 71 Delphinapterus leucas --(white-whale or beluga) The beluga is...about 5 msoc. ~7 * Delphinapterus leucas --(white whale or beluga-continued Our own estimates of source level for sounds from an individual whale 2 are

AERO2S - SUBSONIC AERODYNAMIC ANALYSIS OF WINGS WITH LEADING- AND TRAILING-EDGE FLAPS IN COMBINATION WITH CANARD OR HORIZONTAL TAIL SURFACES (IBM PC VERSION)

NASA Technical Reports Server (NTRS)

Carlson, H. W.

1994-01-01

This code was developed to aid design engineers in the selection and evaluation of aerodynamically efficient wing-canard and wing-horizontal-tail configurations that may employ simple hinged-flap systems. Rapid estimates of the longitudinal aerodynamic characteristics of conceptual airplane lifting surface arrangements are provided. The method is particularly well suited to configurations which, because of high speed flight requirements, must employ thin wings with highly swept leading edges. The code is applicable to wings with either sharp or rounded leading edges. The code provides theoretical pressure distributions over the wing, the canard or horizontal tail, and the deflected flap surfaces as well as estimates of the wing lift, drag, and pitching moments which account for attainable leading edge thrust and leading edge separation vortex forces. The wing planform information is specified by a series of leading edge and trailing edge breakpoints for a right hand wing panel. Up to 21 pairs of coordinates may be used to describe both the leading edge and the trailing edge. The code has been written to accommodate 2000 right hand panel elements, but can easily be modified to accommodate a larger or smaller number of elements depending on the capacity of the target computer platform. The code provides solutions for wing surfaces composed of all possible combinations of leading edge and trailing edge flap settings provided by the original deflection multipliers and by the flap deflection multipliers. Up to 25 pairs of leading edge and trailing edge flap deflection schedules may thus be treated simultaneously. The code also provides for an improved accounting of hinge-line singularities in determination of wing forces and moments. To determine lifting surface perturbation velocity distributions, the code provides for a maximum of 70 iterations. The program is constructed so that successive runs may be made with a given code entry. To make additional runs, it is necessary only to add an identification record and the namelist data that are to be changed from the previous run. This code was originally developed in 1989 in FORTRAN V on a CDC 6000 computer system, and was later ported to an MS-DOS environment. Both versions are available from COSMIC. There are only a few differences between the PC version (LAR-14458) and CDC version (LAR-14178) of AERO2S distributed by COSMIC. The CDC version has one main source code file while the PC version has two files which are easier to edit and compile on a PC. The PC version does not require a FORTRAN compiler which supports NAMELIST because a special INPUT subroutine has been added. The CDC version includes two MODIFY decks which can be used to improve the code and prevent the possibility of some infrequently occurring errors while PC-version users will have to make these code changes manually. The PC version includes an executable which was generated with the Ryan McFarland/FORTRAN compiler and requires 253K RAM and an 80x87 math co-processor. Using this executable, the sample case requires about four hours to execute on an 8MHz AT-class microcomputer with a co-processor. The source code conforms to the FORTRAN 77 standard except that it uses variables longer than six characters. With two minor modifications, the PC version should be portable to any computer with a FORTRAN compiler and sufficient memory. The CDC version of AERO2S is available in CDC NOS Internal format on a 9-track 1600 BPI magnetic tape. The PC version is available on a set of two 5.25 inch 360K MS-DOS format diskettes. IBM AT is a registered trademark of International Business Machines. MS-DOS is a registered trademark of Microsoft Corporation. CDC is a registered trademark of Control Data Corporation. NOS is a trademark of Control Data Corporation.

AERO2S - SUBSONIC AERODYNAMIC ANALYSIS OF WINGS WITH LEADING- AND TRAILING-EDGE FLAPS IN COMBINATION WITH CANARD OR HORIZONTAL TAIL SURFACES (CDC VERSION)

NASA Technical Reports Server (NTRS)

Darden, C. M.

1994-01-01

This code was developed to aid design engineers in the selection and evaluation of aerodynamically efficient wing-canard and wing-horizontal-tail configurations that may employ simple hinged-flap systems. Rapid estimates of the longitudinal aerodynamic characteristics of conceptual airplane lifting surface arrangements are provided. The method is particularly well suited to configurations which, because of high speed flight requirements, must employ thin wings with highly swept leading edges. The code is applicable to wings with either sharp or rounded leading edges. The code provides theoretical pressure distributions over the wing, the canard or horizontal tail, and the deflected flap surfaces as well as estimates of the wing lift, drag, and pitching moments which account for attainable leading edge thrust and leading edge separation vortex forces. The wing planform information is specified by a series of leading edge and trailing edge breakpoints for a right hand wing panel. Up to 21 pairs of coordinates may be used to describe both the leading edge and the trailing edge. The code has been written to accommodate 2000 right hand panel elements, but can easily be modified to accommodate a larger or smaller number of elements depending on the capacity of the target computer platform. The code provides solutions for wing surfaces composed of all possible combinations of leading edge and trailing edge flap settings provided by the original deflection multipliers and by the flap deflection multipliers. Up to 25 pairs of leading edge and trailing edge flap deflection schedules may thus be treated simultaneously. The code also provides for an improved accounting of hinge-line singularities in determination of wing forces and moments. To determine lifting surface perturbation velocity distributions, the code provides for a maximum of 70 iterations. The program is constructed so that successive runs may be made with a given code entry. To make additional runs, it is necessary only to add an identification record and the namelist data that are to be changed from the previous run. This code was originally developed in 1989 in FORTRAN V on a CDC 6000 computer system, and was later ported to an MS-DOS environment. Both versions are available from COSMIC. There are only a few differences between the PC version (LAR-14458) and CDC version (LAR-14178) of AERO2S distributed by COSMIC. The CDC version has one main source code file while the PC version has two files which are easier to edit and compile on a PC. The PC version does not require a FORTRAN compiler which supports NAMELIST because a special INPUT subroutine has been added. The CDC version includes two MODIFY decks which can be used to improve the code and prevent the possibility of some infrequently occurring errors while PC-version users will have to make these code changes manually. The PC version includes an executable which was generated with the Ryan McFarland/FORTRAN compiler and requires 253K RAM and an 80x87 math co-processor. Using this executable, the sample case requires about four hours to execute on an 8MHz AT-class microcomputer with a co-processor. The source code conforms to the FORTRAN 77 standard except that it uses variables longer than six characters. With two minor modifications, the PC version should be portable to any computer with a FORTRAN compiler and sufficient memory. The CDC version of AERO2S is available in CDC NOS Internal format on a 9-track 1600 BPI magnetic tape. The PC version is available on a set of two 5.25 inch 360K MS-DOS format diskettes. IBM AT is a registered trademark of International Business Machines. MS-DOS is a registered trademark of Microsoft Corporation. CDC is a registered trademark of Control Data Corporation. NOS is a trademark of Control Data Corporation.

MARE2DEM: a 2-D inversion code for controlled-source electromagnetic and magnetotelluric data

NASA Astrophysics Data System (ADS)

Key, Kerry

2016-10-01

This work presents MARE2DEM, a freely available code for 2-D anisotropic inversion of magnetotelluric (MT) data and frequency-domain controlled-source electromagnetic (CSEM) data from onshore and offshore surveys. MARE2DEM parametrizes the inverse model using a grid of arbitrarily shaped polygons, where unstructured triangular or quadrilateral grids are typically used due to their ease of construction. Unstructured grids provide significantly more geometric flexibility and parameter efficiency than the structured rectangular grids commonly used by most other inversion codes. Transmitter and receiver components located on topographic slopes can be tilted parallel to the boundary so that the simulated electromagnetic fields accurately reproduce the real survey geometry. The forward solution is implemented with a goal-oriented adaptive finite-element method that automatically generates and refines unstructured triangular element grids that conform to the inversion parameter grid, ensuring accurate responses as the model conductivity changes. This dual-grid approach is significantly more efficient than the conventional use of a single grid for both the forward and inverse meshes since the more detailed finite-element meshes required for accurate responses do not increase the memory requirements of the inverse problem. Forward solutions are computed in parallel with a highly efficient scaling by partitioning the data into smaller independent modeling tasks consisting of subsets of the input frequencies, transmitters and receivers. Non-linear inversion is carried out with a new Occam inversion approach that requires fewer forward calls. Dense matrix operations are optimized for memory and parallel scalability using the ScaLAPACK parallel library. Free parameters can be bounded using a new non-linear transformation that leaves the transformed parameters nearly the same as the original parameters within the bounds, thereby reducing non-linear smoothing effects. Data balancing normalization weights for the joint inversion of two or more data sets encourages the inversion to fit each data type equally well. A synthetic joint inversion of marine CSEM and MT data illustrates the algorithm's performance and parallel scaling on up to 480 processing cores. CSEM inversion of data from the Middle America Trench offshore Nicaragua demonstrates a real world application. The source code and MATLAB interface tools are freely available at http://mare2dem.ucsd.edu.

GlycoRDF: an ontology to standardize glycomics data in RDF

PubMed Central

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F.; Campbell, Matthew P.; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-01-01

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). Contact: rene@ccrc.uga.edu or kkiyoko@soka.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388145

BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines.

PubMed

Hernández, Yözen; Bernstein, Rocky; Pagan, Pedro; Vargas, Levy; McCaig, William; Ramrattan, Girish; Akther, Saymon; Larracuente, Amanda; Di, Lia; Vieira, Filipe G; Qiu, Wei-Gang

2018-03-02

Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl ( http://bioperl.org ) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users. Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of some of the most popular BioPerl modules readily accessible on the command line to novice as well as to experienced bioinformatics practitioners. The initial release of BpWrapper includes four utilities with concise command-line user interfaces, bioseq, bioaln, biotree, and biopop, specialized for manipulation of molecular sequences, sequence alignments, phylogenetic trees, and DNA polymorphisms, respectively. Over a hundred methods are currently available as command-line options and new methods are easily incorporated. Performance of BpWrapper utilities lags that of precompiled utilities while equivalent to that of other utilities based on BioPerl. BpWrapper has been tested on BioPerl Release 1.6, Perl versions 5.10.1 to 5.25.10, and operating systems including Apple macOS, Microsoft Windows, and GNU/Linux. Release code is available from the Comprehensive Perl Archive Network (CPAN) at https://metacpan.org/pod/Bio::BPWrapper . Source code is available on GitHub at https://github.com/bioperl/p5-bpwrapper . BpWrapper improves on existing sequence utilities by following the design principles of Unix text utilities such including a concise user interface, extensive command-line options, and standard input/output for serialized operations. Further, dozens of novel methods for manipulation of sequences, alignments, and phylogenetic trees, unavailable in existing utilities (e.g., EMBOSS, Newick Utilities, and FAST), are provided. Bioinformaticians should find BpWrapper useful for rapid prototyping of workflows on the command-line without creating custom scripts for comparative genomics and other bioinformatics applications.

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

PubMed Central

Fong, Christine; Rohmer, Laurence; Radey, Matthew; Wasnick, Michael; Brittnacher, Mitchell J

2008-01-01

Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client side software setup or installation required. Source code is freely available to researchers interested in setting up a local version of PSAT for analysis of genomes not available through the public server. Access to the public web server and instructions for obtaining source code can be found at . PMID:18366802

Differences in the causes of death of HIV-positive patients in a cohort study by data sources and coding algorithms.

PubMed

Hernando, Victoria; Sobrino-Vegas, Paz; Burriel, M Carmen; Berenguer, Juan; Navarro, Gemma; Santos, Ignacio; Reparaz, Jesús; Martínez, M Angeles; Antela, Antonio; Gutiérrez, Félix; del Amo, Julia

2012-09-10

To compare causes of death (CoDs) from two independent sources: National Basic Death File (NBDF) and deaths reported to the Spanish HIV Research cohort [Cohort de adultos con infección por VIH de la Red de Investigación en SIDA CoRIS)] and compare the two coding algorithms: International Classification of Diseases, 10th revision (ICD-10) and revised version of Coding Causes of Death in HIV (revised CoDe). Between 2004 and 2008, CoDs were obtained from the cohort records (free text, multiple causes) and also from NBDF (ICD-10). CoDs from CoRIS were coded according to ICD-10 and revised CoDe by a panel. Deaths were compared by 13 disease groups: HIV/AIDS, liver diseases, malignancies, infections, cardiovascular, blood disorders, pulmonary, central nervous system, drug use, external, suicide, other causes and ill defined. There were 160 deaths. Concordance for the 13 groups was observed in 111 (69%) cases for the two sources and in 115 (72%) cases for the two coding algorithms. According to revised CoDe, the commonest CoDs were HIV/AIDS (53%), non-AIDS malignancies (11%) and liver related (9%), these percentages were similar, 57, 10 and 8%, respectively, for NBDF (coded as ICD-10). When using ICD-10 to code deaths in CoRIS, wherein HIV infection was known in everyone, the proportion of non-AIDS malignancies was 13%, liver-related accounted for 3%, while HIV/AIDS reached 70% due to liver-related, infections and ill-defined causes being coded as HIV/AIDS. There is substantial variation in CoDs in HIV-infected persons according to sources and algorithms. ICD-10 in patients known to be HIV-positive overestimates HIV/AIDS-related deaths at the expense of underestimating liver-related diseases, infections and ill defined causes. CoDe seems as the best option for cohort studies.

Source Methodology for Turbofan Noise Prediction (SOURCE3D Technical Documentation)

NASA Technical Reports Server (NTRS)

Meyer, Harold D.

1999-01-01

This report provides the analytical documentation for the SOURCE3D Rotor Wake/Stator Interaction Code. It derives the equations for the rotor scattering coefficients and stator source vector and scattering coefficients that are needed for use in the TFANS (Theoretical Fan Noise Design/Prediction System). SOURCE3D treats the rotor and stator as isolated source elements. TFANS uses this information, along with scattering coefficients for inlet and exit elements, and provides complete noise solutions for turbofan engines. SOURCE3D is composed of a collection of FORTRAN programs that have been obtained by extending the approach of the earlier V072 Rotor Wake/Stator Interaction Code. Similar to V072, it treats the rotor and stator as a collection of blades and vanes having zero thickness and camber contained in an infinite, hardwall annular duct. SOURCE3D adds important features to the V072 capability-a rotor element, swirl flow and vorticity waves, actuator disks for flow turning, and combined rotor/actuator disk and stator/actuator disk elements. These items allow reflections from the rotor, frequency scattering, and mode trapping, thus providing more complete noise predictions than previously. The code has been thoroughly verified through comparison with D.B. Hanson's CUP2D two- dimensional code using a narrow annulus test case.

Radiolytic Model for Chemical Composition of Europa's Atmosphere and Surface

NASA Technical Reports Server (NTRS)

Cooper, John F.

2004-01-01

The overall objective of the present effort is to produce models for major and selected minor components of Europa s neutral atmosphere in 1-D versus altitude and in 2-D versus altitude and longitude or latitude. A 3-D model versus all three coordinates (alt, long, lat) will be studied but development on this is at present limited by computing facilities available to the investigation team. In this first year we have focused on 1-D modeling with Co-I Valery Shematovich s Direct Simulation Monte Carlo (DSMC) code for water group species (H2O, O2, O, OH) and on 2-D with Co-I Mau Wong's version of a similar code for O2, O, CO, CO2, and Na. Surface source rates of H2O and O2 from sputtering and radiolysis are used in the 1-D model, while observations for CO2 at the Europa surface and Na detected in a neutral cloud ejected from Europa are used, along with the O2 sputtering rate, to constrain source rates in the 2-D version. With these separate approaches we are investigating a range of processes important to eventual implementation of a comprehensive 3-D atmospheric model which could be used to understand present observations and develop science requirements for future observations, e.g. from Earth and in Europa orbit. Within the second year we expect to merge the full water group calculations into the 2-D version of the DSMC code which can then be extended to 3-D, pending availability of computing resources. Another important goal in the second year would be the inclusion of sulk and its more volatile oxides (SO, SO2).

PROFIT: Bayesian profile fitting of galaxy images

NASA Astrophysics Data System (ADS)

Robotham, A. S. G.; Taranu, D. S.; Tobar, R.; Moffett, A.; Driver, S. P.

2017-04-01

We present PROFIT, a new code for Bayesian two-dimensional photometric galaxy profile modelling. PROFIT consists of a low-level C++ library (libprofit), accessible via a command-line interface and documented API, along with high-level R (PROFIT) and PYTHON (PyProFit) interfaces (available at github.com/ICRAR/libprofit, github.com/ICRAR/ProFit, and github.com/ICRAR/pyprofit, respectively). R PROFIT is also available pre-built from CRAN; however, this version will be slightly behind the latest GitHub version. libprofit offers fast and accurate two-dimensional integration for a useful number of profiles, including Sérsic, Core-Sérsic, broken-exponential, Ferrer, Moffat, empirical King, point-source, and sky, with a simple mechanism for adding new profiles. We show detailed comparisons between libprofit and GALFIT. libprofit is both faster and more accurate than GALFIT at integrating the ubiquitous Sérsic profile for the most common values of the Sérsic index n (0.5 < n < 8). The high-level fitting code PROFIT is tested on a sample of galaxies with both SDSS and deeper KiDS imaging. We find good agreement in the fit parameters, with larger scatter in best-fitting parameters from fitting images from different sources (SDSS versus KiDS) than from using different codes (PROFIT versus GALFIT). A large suite of Monte Carlo-simulated images are used to assess prospects for automated bulge-disc decomposition with PROFIT on SDSS, KiDS, and future LSST imaging. We find that the biggest increases in fit quality come from moving from SDSS- to KiDS-quality data, with less significant gains moving from KiDS to LSST.

The Cortical Organization of Speech Processing: Feedback Control and Predictive Coding the Context of a Dual-Stream Model

ERIC Educational Resources Information Center

Hickok, Gregory

2012-01-01

Speech recognition is an active process that involves some form of predictive coding. This statement is relatively uncontroversial. What is less clear is the source of the prediction. The dual-stream model of speech processing suggests that there are two possible sources of predictive coding in speech perception: the motor speech system and the…

Open-source chemogenomic data-driven algorithms for predicting drug-target interactions.

PubMed

Hao, Ming; Bryant, Stephen H; Wang, Yanli

2018-02-06

While novel technologies such as high-throughput screening have advanced together with significant investment by pharmaceutical companies during the past decades, the success rate for drug development has not yet been improved prompting researchers looking for new strategies of drug discovery. Drug repositioning is a potential approach to solve this dilemma. However, experimental identification and validation of potential drug targets encoded by the human genome is both costly and time-consuming. Therefore, effective computational approaches have been proposed to facilitate drug repositioning, which have proved to be successful in drug discovery. Doubtlessly, the availability of open-accessible data from basic chemical biology research and the success of human genome sequencing are crucial to develop effective in silico drug repositioning methods allowing the identification of potential targets for existing drugs. In this work, we review several chemogenomic data-driven computational algorithms with source codes publicly accessible for predicting drug-target interactions (DTIs). We organize these algorithms by model properties and model evolutionary relationships. We re-implemented five representative algorithms in R programming language, and compared these algorithms by means of mean percentile ranking, a new recall-based evaluation metric in the DTI prediction research field. We anticipate that this review will be objective and helpful to researchers who would like to further improve existing algorithms or need to choose appropriate algorithms to infer potential DTIs in the projects. The source codes for DTI predictions are available at: https://github.com/minghao2016/chemogenomicAlg4DTIpred. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.

Monte Carlo Determination of Dosimetric Parameters of a New (125)I Brachytherapy Source According to AAPM TG-43 (U1) Protocol.

PubMed

Baghani, Hamid Reza; Lohrabian, Vahid; Aghamiri, Mahmoud Reza; Robatjazi, Mostafa

2016-03-01

(125)I is one of the important sources frequently used in brachytherapy. Up to now, several different commercial models of this source type have been introduced to the clinical radiation oncology applications. Recently, a new source model, IrSeed-125, has been added to this list. The aim of the present study is to determine the dosimetric parameters of this new source model based on the recommendations of TG-43 (U1) protocol using Monte Carlo simulation. The dosimetric characteristics of Ir-125 including dose rate constant, radial dose function, 2D anisotropy function and 1D anisotropy function were determined inside liquid water using MCNPX code and compared to those of other commercially available iodine sources. The dose rate constant of this new source was found to be 0.983+0.015 cGyh-1U-1 that was in good agreement with the TLD measured data (0.965 cGyh-1U-1). The 1D anisotropy function at 3, 5, and 7 cm radial distances were obtained as 0.954, 0.953 and 0.959, respectively. The results of this study showed that the dosimetric characteristics of this new brachytherapy source are comparable with those of other commercially available sources. Furthermore, the simulated parameters were in accordance with the previously measured ones. Therefore, the Monte Carlo calculated dosimetric parameters could be employed to obtain the dose distribution around this new brachytherapy source based on TG-43 (U1) protocol.

Hypersonic simulations using open-source CFD and DSMC solvers

NASA Astrophysics Data System (ADS)

Casseau, V.; Scanlon, T. J.; John, B.; Emerson, D. R.; Brown, R. E.

2016-11-01

Hypersonic hybrid hydrodynamic-molecular gas flow solvers are required to satisfy the two essential requirements of any high-speed reacting code, these being physical accuracy and computational efficiency. The James Weir Fluids Laboratory at the University of Strathclyde is currently developing an open-source hybrid code which will eventually reconcile the direct simulation Monte-Carlo method, making use of the OpenFOAM application called dsmcFoam, and the newly coded open-source two-temperature computational fluid dynamics solver named hy2Foam. In conjunction with employing the CVDV chemistry-vibration model in hy2Foam, novel use is made of the QK rates in a CFD solver. In this paper, further testing is performed, in particular with the CFD solver, to ensure its efficacy before considering more advanced test cases. The hy2Foam and dsmcFoam codes have shown to compare reasonably well, thus providing a useful basis for other codes to compare against.

Advanced complex trait analysis.

PubMed

Gray, A; Stewart, I; Tenesa, A

2012-12-01

The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance. We restructure the genetic relationship matrix (GRM) estimation phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum likelihood (REML) analysis stage. For a test case with 8999 individuals and 279,435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from ∼17 h to ∼11 min. The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta. a.gray@ed.ac.uk Supplementary data are available at Bioinformatics online.

SKIRT: The design of a suite of input models for Monte Carlo radiative transfer simulations

NASA Astrophysics Data System (ADS)

Baes, M.; Camps, P.

2015-09-01

The Monte Carlo method is the most popular technique to perform radiative transfer simulations in a general 3D geometry. The algorithms behind and acceleration techniques for Monte Carlo radiative transfer are discussed extensively in the literature, and many different Monte Carlo codes are publicly available. On the contrary, the design of a suite of components that can be used for the distribution of sources and sinks in radiative transfer codes has received very little attention. The availability of such models, with different degrees of complexity, has many benefits. For example, they can serve as toy models to test new physical ingredients, or as parameterised models for inverse radiative transfer fitting. For 3D Monte Carlo codes, this requires algorithms to efficiently generate random positions from 3D density distributions. We describe the design of a flexible suite of components for the Monte Carlo radiative transfer code SKIRT. The design is based on a combination of basic building blocks (which can be either analytical toy models or numerical models defined on grids or a set of particles) and the extensive use of decorators that combine and alter these building blocks to more complex structures. For a number of decorators, e.g. those that add spiral structure or clumpiness, we provide a detailed description of the algorithms that can be used to generate random positions. Advantages of this decorator-based design include code transparency, the avoidance of code duplication, and an increase in code maintainability. Moreover, since decorators can be chained without problems, very complex models can easily be constructed out of simple building blocks. Finally, based on a number of test simulations, we demonstrate that our design using customised random position generators is superior to a simpler design based on a generic black-box random position generator.

Fan Noise Prediction System Development: Source/Radiation Field Coupling and Workstation Conversion for the Acoustic Radiation Code

NASA Technical Reports Server (NTRS)

Meyer, H. D.

1993-01-01

The Acoustic Radiation Code (ARC) is a finite element program used on the IBM mainframe to predict far-field acoustic radiation from a turbofan engine inlet. In this report, requirements for developers of internal aerodynamic codes regarding use of their program output an input for the ARC are discussed. More specifically, the particular input needed from the Bolt, Beranek and Newman/Pratt and Whitney (turbofan source noise generation) Code (BBN/PWC) is described. In a separate analysis, a method of coupling the source and radiation models, that recognizes waves crossing the interface in both directions, has been derived. A preliminary version of the coupled code has been developed and used for initial evaluation of coupling issues. Results thus far have shown that reflection from the inlet is sufficient to indicate that full coupling of the source and radiation fields is needed for accurate noise predictions ' Also, for this contract, the ARC has been modified for use on the Sun and Silicon Graphics Iris UNIX workstations. Changes and additions involved in this effort are described in an appendix.

NucliTrack: an integrated nuclei tracking application.

PubMed

Cooper, Sam; Barr, Alexis R; Glen, Robert; Bakal, Chris

2017-10-15

Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly. NucliTrack is available as a free, cross platform application and open source Python package. Installation details and documentation are at: http://nuclitrack.readthedocs.io/en/latest/ A video guide can be viewed online: https://www.youtube.com/watch?v=J6e0D9F-qSU Source code is available through Github: https://github.com/samocooper/nuclitrack. A Matlab toolbox is also available at: https://uk.mathworks.com/matlabcentral/fileexchange/61479-samocooper-nuclitrack-matlab. sam@socooper.com. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

PubMed Central

Safonova, Yana; Bonissone, Stefano; Kurpilyansky, Eugene; Starostina, Ekaterina; Lapidus, Alla; Stinson, Jeremy; DePalatis, Laura; Sandoval, Wendy; Lill, Jennie; Pevzner, Pavel A.

2015-01-01

The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. Availability and implementation: IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools. Contact: ppevzner@ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072509

Methods for Coding Tobacco-Related Twitter Data: A Systematic Review.

PubMed

Lienemann, Brianna A; Unger, Jennifer B; Cruz, Tess Boley; Chu, Kar-Hai

2017-03-31

As Twitter has grown in popularity to 313 million monthly active users, researchers have increasingly been using it as a data source for tobacco-related research. The objective of this systematic review was to assess the methodological approaches of categorically coded tobacco Twitter data and make recommendations for future studies. Data sources included PsycINFO, Web of Science, PubMed, ABI/INFORM, Communication Source, and Tobacco Regulatory Science. Searches were limited to peer-reviewed journals and conference proceedings in English from January 2006 to July 2016. The initial search identified 274 articles using a Twitter keyword and a tobacco keyword. One coder reviewed all abstracts and identified 27 articles that met the following inclusion criteria: (1) original research, (2) focused on tobacco or a tobacco product, (3) analyzed Twitter data, and (4) coded Twitter data categorically. One coder extracted data collection and coding methods. E-cigarettes were the most common type of Twitter data analyzed, followed by specific tobacco campaigns. The most prevalent data sources were Gnip and Twitter's Streaming application programming interface (API). The primary methods of coding were hand-coding and machine learning. The studies predominantly coded for relevance, sentiment, theme, user or account, and location of user. Standards for data collection and coding should be developed to be able to more easily compare and replicate tobacco-related Twitter results. Additional recommendations include the following: sample Twitter's databases multiple times, make a distinction between message attitude and emotional tone for sentiment, code images and URLs, and analyze user profiles. Being relatively novel and widely used among adolescents and black and Hispanic individuals, Twitter could provide a rich source of tobacco surveillance data among vulnerable populations. ©Brianna A Lienemann, Jennifer B Unger, Tess Boley Cruz, Kar-Hai Chu. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 31.03.2017.

Aeroacoustic Prediction Codes

NASA Technical Reports Server (NTRS)

Gliebe, P; Mani, R.; Shin, H.; Mitchell, B.; Ashford, G.; Salamah, S.; Connell, S.; Huff, Dennis (Technical Monitor)

2000-01-01

This report describes work performed on Contract NAS3-27720AoI 13 as part of the NASA Advanced Subsonic Transport (AST) Noise Reduction Technology effort. Computer codes were developed to provide quantitative prediction, design, and analysis capability for several aircraft engine noise sources. The objective was to provide improved, physics-based tools for exploration of noise-reduction concepts and understanding of experimental results. Methods and codes focused on fan broadband and 'buzz saw' noise and on low-emissions combustor noise and compliment work done by other contractors under the NASA AST program to develop methods and codes for fan harmonic tone noise and jet noise. The methods and codes developed and reported herein employ a wide range of approaches, from the strictly empirical to the completely computational, with some being semiempirical analytical, and/or analytical/computational. Emphasis was on capturing the essential physics while still considering method or code utility as a practical design and analysis tool for everyday engineering use. Codes and prediction models were developed for: (1) an improved empirical correlation model for fan rotor exit flow mean and turbulence properties, for use in predicting broadband noise generated by rotor exit flow turbulence interaction with downstream stator vanes: (2) fan broadband noise models for rotor and stator/turbulence interaction sources including 3D effects, noncompact-source effects. directivity modeling, and extensions to the rotor supersonic tip-speed regime; (3) fan multiple-pure-tone in-duct sound pressure prediction methodology based on computational fluid dynamics (CFD) analysis; and (4) low-emissions combustor prediction methodology and computer code based on CFD and actuator disk theory. In addition. the relative importance of dipole and quadrupole source mechanisms was studied using direct CFD source computation for a simple cascadeigust interaction problem, and an empirical combustor-noise correlation model was developed from engine acoustic test results. This work provided several insights on potential approaches to reducing aircraft engine noise. Code development is described in this report, and those insights are discussed.

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.

phylo-node: A molecular phylogenetic toolkit using Node.js.

PubMed

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

A rapid response air quality analysis system for use in projects having stringent quality assurance requirements

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

Bowman, A.W.

1990-04-01

This paper describes an approach to solve air quality problems which frequently occur during iterations of the baseline change process. From a schedule standpoint, it is desirable to perform this evaluation in as short a time as possible while budgetary pressures limit the size of the staff available to do the work. Without a method in place to deal with baseline change proposal requests the environment analysts may not be able to produce the analysis results in the time frame expected. Using a concept called the Rapid Response Air Quality Analysis System (RAAS), the problems of timing and cost becomemore » tractable. The system could be adapted to assess other atmospheric pathway impacts, e.g., acoustics or visibility. The air quality analysis system used to perform the EA analysis (EA) for the Salt Repository Project (part of the Civilian Radioactive Waste Management Program), and later to evaluate the consequences of proposed baseline changes, consists of three components: Emission source data files; Emission rates contained in spreadsheets; Impact assessment model codes. The spreadsheets contain user-written codes (macros) that calculate emission rates from (1) emission source data (e.g., numbers and locations of sources, detailed operating schedules, and source specifications including horsepower, load factor, and duty cycle); (2) emission factors such as those published by the U.S. Environmental Protection Agency, and (3) control efficiencies.« less

Astrophysics Source Code Library Enhancements

NASA Astrophysics Data System (ADS)

Hanisch, R. J.; Allen, A.; Berriman, G. B.; DuPrie, K.; Mink, J.; Nemiroff, R. J.; Schmidt, J.; Shamir, L.; Shortridge, K.; Taylor, M.; Teuben, P. J.; Wallin, J.

2015-09-01

The Astrophysics Source Code Library (ASCL)1 is a free online registry of codes used in astronomy research; it currently contains over 900 codes and is indexed by ADS. The ASCL has recently moved a new infrastructure into production. The new site provides a true database for the code entries and integrates the WordPress news and information pages and the discussion forum into one site. Previous capabilities are retained and permalinks to ascl.net continue to work. This improvement offers more functionality and flexibility than the previous site, is easier to maintain, and offers new possibilities for collaboration. This paper covers these recent changes to the ASCL.

Modeling the Volcanic Source at Long Valley, CA, Using a Genetic Algorithm Technique

NASA Technical Reports Server (NTRS)

Tiampo, Kristy F.

1999-01-01

In this project, we attempted to model the deformation pattern due to the magmatic source at Long Valley caldera using a real-value coded genetic algorithm (GA) inversion similar to that found in Michalewicz, 1992. The project has been both successful and rewarding. The genetic algorithm, coded in the C programming language, performs stable inversions over repeated trials, with varying initial and boundary conditions. The original model used a GA in which the geophysical information was coded into the fitness function through the computation of surface displacements for a Mogi point source in an elastic half-space. The program was designed to invert for a spherical magmatic source - its depth, horizontal location and volume - using the known surface deformations. It also included the capability of inverting for multiple sources.

Bottled SAFT: A Web App Providing SAFT-γ Mie Force Field Parameters for Thousands of Molecular Fluids.

PubMed

Ervik, Åsmund; Mejía, Andrés; Müller, Erich A

2016-09-26

Coarse-grained molecular simulation has become a popular tool for modeling simple and complex fluids alike. The defining aspects of a coarse grained model are the force field parameters, which must be determined for each particular fluid. Because the number of molecular fluids of interest in nature and in engineering processes is immense, constructing force field parameter tables by individually fitting to experimental data is a futile task. A step toward solving this challenge was taken recently by Mejía et al., who proposed a correlation that provides SAFT-γ Mie force field parameters for a fluid provided one knows the critical temperature, the acentric factor and a liquid density, all relatively accessible properties. Building on this, we have applied the correlation to more than 6000 fluids, and constructed a web application, called "Bottled SAFT", which makes this data set easily searchable by CAS number, name or chemical formula. Alternatively, the application allows the user to calculate parameters for components not present in the database. Once the intermolecular potential has been found through Bottled SAFT, code snippets are provided for simulating the desired substance using the "raaSAFT" framework, which leverages established molecular dynamics codes to run the simulations. The code underlying the web application is written in Python using the Flask microframework; this allows us to provide a modern high-performance web app while also making use of the scientific libraries available in Python. Bottled SAFT aims at taking the complexity out of obtaining force field parameters for a wide range of molecular fluids, and facilitates setting up and running coarse-grained molecular simulations. The web application is freely available at http://www.bottledsaft.org . The underlying source code is available on Bitbucket under a permissive license.

Methodology of decreasing software complexity using ontology

NASA Astrophysics Data System (ADS)

DÄ browska-Kubik, Katarzyna

2015-09-01

In this paper a model of web application`s source code, based on the OSD ontology (Ontology for Software Development), is proposed. This model is applied to implementation and maintenance phase of software development process through the DevOntoCreator tool [5]. The aim of this solution is decreasing software complexity of that source code, using many different maintenance techniques, like creation of documentation, elimination dead code, cloned code or bugs, which were known before [1][2]. Due to this approach saving on software maintenance costs of web applications will be possible.

Bit-wise arithmetic coding for data compression

NASA Technical Reports Server (NTRS)

Kiely, A. B.

1994-01-01

This article examines the problem of compressing a uniformly quantized independent and identically distributed (IID) source. We present a new compression technique, bit-wise arithmetic coding, that assigns fixed-length codewords to the quantizer output and uses arithmetic coding to compress the codewords, treating the codeword bits as independent. We examine the performance of this method and evaluate the overhead required when used block-adaptively. Simulation results are presented for Gaussian and Laplacian sources. This new technique could be used as the entropy coder in a transform or subband coding system.